Sometimes I get interesting questions that don’t quite fit into any of the existing topics already discussed within the blog and my obsessive/compulsive nature tells me that getting this questions in a random part/page/post of the blog doesn’t look quite neat either. Therefore I open this new page for all those questions you have! I don’t intend to have a repository like the one on the CCL, of course, but at least we could organize the info and make it readily available for those who might need it; in the end, that is what we do as scientists, right?
Please use tags at the begining of your comment, e.g.: #convergencefailure #visualization #gaussianerror or whatever you might think could help me, and others, to quickly find an answer to your queries. Feel free to reply to any comment you think you might have an answer to because the thing is, I don’t have all the answers (I wish I did, trust me). One other thing, try to summarize your questions in a coherent way and please do not post entire output files! I don’t have the time to check them in their entirety.
Well then, leave a question!
Dr. Joaquin Barroso's Blog 
Hello,
I would be grateful if you could explain me the difference between the normal analysis done using HPmodes and without that. I want to compute the vibronic spectra of some dyes. I have used G09 to do that. However, the code is error prone! I got alot of error message without any documentation. Then, I shifted to source code, FCClasses to follow up. Now, I understood that I need normal mode analysis using HPmodes syntax to feed the code. I compared the outputs there is two series of normal analysis. I don’t clearly know how are the anlysi are done and what are the differences. For the first analysis after printing frequencies is like this:
1 2 3 4 5
A A A A A
Frequencies — 50.1139 53.0576 78.4365 108.7226 132.2478
Reduced masses — 5.1998 3.9481 5.5278 3.3061 1.5043
Force constants — 0.0077 0.0065 0.0200 0.0230 0.0155
IR Intensities — 0.3409 0.4114 0.5722 4.3762 1.4973
Coord Atom Element:
1 1 6 0.00006 0.00025 0.26758 0.00003 0.00017
and the second analysis is like this :
1 2 3
A A A
Frequencies — 50.1139 53.0576 78.4365
Red. masses — 5.1998 3.9481 5.5278
Frc consts — 0.0077 0.0065 0.0200
IR Inten — 0.3409 0.4114 0.5722
Atom AN X Y Z X Y Z X Y Z
1 6 0.00 0.00 0.00 0.00 0.00 0.17 0.27 -0.05 0.00
as far as I got, the G09 uses the second analysis while the FCClasses needs the first to perform the analysis. Any help would be appreciated.
Saman
Hi Saman
The HPmodes option only uses the high precision format (to five figures) vibrational frequency eigenvectors in the frequency output in addition to the normal three-figure output. So basically there is no difference, since it is using the whole set of numbers to do the math it only varies in the number of decimals used in the output.
I hope this helps but if it doesn’t let me know, ok? Have a nice day!
Hi,
I would like to calculate the frequencies of the excited states using G09. Is that possible? Any help would be appreciated.
Thank you so much in advance.
Srijana
Hello Srijana
It is indeed possible, just specify the freq option in the same route section where you asked for an excited state calculation.
I hope this helps
Hello,
I would be grateful if you could explain me that how can I calculate Fukui functions on different atoms of a molecule using B3LYP 311-G ++ dp basis set G03 program. I have been successfully run the DFT of the organic molecule 2,2’-(1Z.1’Z)-(4,4’-methylenebis(4,1-phenylene)bis(azan-1-yl-1-ylidene))bis(methan-1-yl-1-ylidene)diphenol and now i want to calculate Fukui function on each atoms of this organic molecule. Please advise me how can I calculate fukui function.
Thanking You
Vinay Jaiswal
Hello, i am facing one problem related to my calculation. When i upload my input file having B3LYP/6-31G (d) set to gaussian then it gives an error :small molecule interaction” atoms too close. so, how i can remove it ???
Hello Adnan,
You have to open your molecule with a visualizer that will allow you to modify the structure like GaussView.
The error above means that two atoms are very close or even overlapping which makes no physical/chemical sense. G09 wont waste time in optimizing or calculating a structure in which two atoms are closer than the sum of their covalent radii. Imagine two H atoms at a 0.1 A, that is 20% of the Bohr radius! which implies that both protons are now touching each other.
Visualize your molecule, find the atoms overlapping and modify the structure to avoid the error.
Have a nice day
Hi Sir,
How can I make Gaussian print the first derivative of energy (dV/dx) for a given molecule in cartesian coordinates?
Hi!
there must be an overlay (IOp) for that but unfortunately I don’t know it. Please contact Gaussian Tech support at their website. Do not worry about not having a license if that is the case, they will provide support for you even if you use a non-academic address.
Sorry for not being too helpful this time. Thanks for reading!
i am Harish jangra from the National Institute of Pharmaceutical Education and Reserach studing pharmacoinformatics. Sir, it will be my great pleasure to get your guidance, i am highly obliged and thankful if you suggest me about the basic algorithm behind Gaussian calculation (optimization)
Hi Harish!
Wow, your question is not a short one! Basically Gaussian uses the Berny Optimization algorithm which calculates all forces on every atom (i.e. which way and how strongly is each atom being pushed or pulled by the rest of the atoms) then it also calculates the gradient of such forces and allows them to be pushed -or pulled- just a little bit and repeats the operation until the change in energy, forces and gradient, respect to the previous step is below a certain threshold.
There are tons of papers about the original algorithm that you can find online.
I hope this helps! Thanks for reading
THANK YOU SO MUCH SIR FOR YOUR GENEROUS HELP.
Hi,
I’m currently a graduate student in an American University. I was wondering if you could comment on the opportunities in Mexico for computational chemists presently and how you see them developing in the future.
Thanks,
Hector
Hola Héctor,
There are some oportunities for theoretical chemists in academia in Mexico but unfortunately not in the big universities, you’d have to look for a job in a smaller university or maybe at a private one which are right now trying to turn to research and not only teaching. The private industry could be another way to go although not many companies in Mexico do any research.
I can’t speak as an authority on how the job market is moving for us comp chems, all I can do is give you this insight of mine and advice you to search search search within conacyt, universities all over the place, transnational companies, etc. Something good comes always up for people who is prepared for it.
I hope you find something worth your while, in the meantime thanks for reading!
Dear sir,
I am having a error while optimizing an structre in Gaussian 09. the error is as follows
Berny optimization.
Error in internal coordinate system.
Error termination via Lnk1e in /home/software/g09-i7/g09/l103.
Your suggestion is needed.
Thank you
Hi Vijay,
I think this means your structure is not well defined in terms of the internal coordinates. Check it with a visualizer and if possible use it to change the coordinate system from internal to cartesian. Also check if some atoms are too close to one another or if bonds are crossing paths.
I hope this helps. Thanks for reading!
hi sir
i am facing same problem i.e., error in internal coordinate system.but i very new to this computational chemistry i don’t know how to change the coordinate system from internal to Cartesian,and what do meant by bonds crossing paths..really i am running out of time.since one month kept on getting this problem when i try to optimize transition state to molecule on Gaussian 09. i am thankful if you suggest me any solution for this error .
thank you
hi vijay
if you could have solved this problem based on sir suggestion,please why cant you help me to solve my problem.
thank you
Hello again Vijay
Can you use gaussview? you have to click on “save cartesians” when you save the structure. Generate it with gaussview and then save it. That should fix it. Move all the atoms around until you eliminate all the bonds crossing each other.
I hope this helps!
hey do u know any free software available for chromatography ????then plz suggest me it s urgent plzzzzzz…………
Sorry but I’m not aware of any. Try the ACDLabs website.
Hi sir,
Can you give me some ideas on spin-orbit coupling leading to the mixing of single and triplet states. Also can you mention the best program to calculate SOC. If you have already written about this please share me the link.
Thanking
Jo
Hi…would you please help me how to calculate the reduction potential using Gaussian?
Dear Sir,
I am using G09 for metal ion studies and have tried giving different basis sets for the ligands and the metal ions.Both the moment I’ve used Gen or Pseudo keywords like shown below, the following errors are obtained.
#RHF/GEN Pseudo=read
comments…
charge multiplicity
molecular specifications
C N 0
6-31+G(d’)
****
Hg 0
LANL2DZ
****
Hg 0
LANL2DZ
error : Wanted an integer as input
Found a floating point number as input
#B3LYP/GEN Opt Pseudo(SDD)
#B3LYP/GEN Opt Pseudo(Read)
Here I’ve specified the ECP basis set in the script but it still does not read the basis set.
#B3LYP/6-31G Opt Pseudo(SDD)
error : the heavy metal ion is not read by 6-31G basis set.
Also the keyword pseudo=Read and pseudo=LanL2 with LanL2DZ with the heavy metal study the same?
Dear Jyotsna,
Did you get any solution of your first error??
Please share with me, I am having the same problem.
Many thanks
Bijan
Dear Bijan,
The problem is that when you are using different basis sets for different atoms esp. an ECP basis set then you have to specify the ECP basis set in the input file as
C N 0
6-31+G(d’)
****
Hg 0
LANL2DZ
****
Hg 0
(put the ECP basis set of the desired metal here)
Hope this helps
Regards
Jyotsna
Dear Sir,
I’m interested to know if there is a software (better if it is free) that can create and plot Fukui functions from gaussian output.
Thank you!
Nick
I would suggest to use Molekel or Molden. As far as I know there isn’t a “button” to click on and get the plots so what you have to do is to substract the electronic density of the altered wavefunction (the one with a different Ne) from the one of your reference state (the one with the reference Ne). So, you have to generate both densities first and then you have to substract one from the other according to the equations found here
I hope this helps. Thanks for reading!
Dear Sir,
Now I use gaussian to calculate a cluster which made by 85 atoms, I make it two layers the higher layer is QM and lower layer is MM. Here is a problem comes, I cannot view the MO in the gaussview. As I see, the reason is the gaussian don’t calculate orbital for MM layer. Do you know any other ways to let it show MO for only QM layer?
Here is my input file,
#p opt=tight freq oniom(b3lyp/lanl2dz:uff) nosymm geom=connectivity scf=maxcycles=300 int=ultrafine
pt4
0 2 0 3 0 3
Au- 0 3.558584 2.275638 -3.710549 L
Au- 0 1.820176 2.360213 -1.802881 L
Au- 0 0.153637 2.484202 0.005572 L
Au- 0 -1.572773 2.561742 1.759631 L
Au- 0 -3.392271 2.688492 3.587681 L
Au- 0 -3.411779 0.208170 3.726424 L
.
.
.
Many Thanks!
Minmin
Hi Minmin!
I’m not sure this is possible with Gaussview and I’m not aware of any other software that could do it.
Try to visualize them directly from a formatted chk file. It might work
Hope this helps
Dear Sir,
I try to calculate sodium cation affinities with MP2=Full. Geometry optimization for neutral and sodiated species using e.g.
%chk=/home/j/neutral.chk
%nproc=12
%Mem=46GB
#MaxDisk=1000GB
#MP2=Full/6-311+G(2d,2p) Opt Test
works fine with the Linux 64 Bit G09 (Revision A.02) version. However, all subsequent frequency calculations using optimized geometries crash. The Input-File is e.g.
%RWF=/scratch/tmp/j/1,200GB,/scratch/tmp/j/2,200GB,/scratch/tmp/j/3,200GB,/scratch/tmp/j/4,200GB
%chk=/home/j/sodiated.chk
%nproc=12
%Mem=46GB
#MaxDisk=4000GB
# freq rmp2=full/6-311+g(2d,2p) geom=connectivity test
[No Title]
1 1
C -3.46469800 -0.12993500 -0.00003900
C -3.12196400 1.22077200 0.00005500
C -1.78463000 1.58038600 0.00014400
C -0.77093400 0.60304900 0.00012400
C -1.13980000 -0.75590900 0.00002700
C -2.47539400 -1.11671900 -0.00005200
Cl -5.12660400 -0.59284000 -0.00014700
C 0.58398800 1.07838200 0.00019300
C 1.75328900 0.38429100 0.00026000
C 3.07273300 1.04229600 0.00048100
C 1.89914400 -1.03108600 0.00019200
O 4.12878100 0.41326000 -0.00007800
N 2.22857600 -2.15703400 0.00018700
O 3.02120100 2.36840300 -0.00043000
H -3.89510400 1.97234700 0.00006100
H -1.51424800 2.62675400 0.00021800
H -0.39860800 -1.53873900 0.00000300
H -2.76030400 -2.15684400 -0.00013200
H 0.70057800 2.15472200 0.00027200
H 3.92868400 2.70551800 -0.00095500
Na 4.63463400 -1.82660900 -0.00023000
1 2 1.5 6 1.5 7 1.0
2 3 2.0 15 1.0
3 4 1.5 16 1.0
4 5 1.5 8 1.5
5 6 2.0 17 1.0
6 18 1.0
7
8 9 2.0 19 1.0
9 10 1.0 11 1.5
10 12 2.0 14 1.5
11 13 3.0
12
13
14 20 1.0
15
16
17
18
19
20
21
The calculation works for about 2 days and generates a combined scratch-file size of about 258 GB (splitted files). Without an error the calculations ends at the same point (just before the population analysis would start):
Gaussian Output File:
Entering Gaussian System, Link 0=/Applic.PALMA/gruppen/q0grimme/g09/g09
Initial command:
/Applic.PALMA/gruppen/q0grimme/g09/l1.exe /scratch/tmp/j.9544/Gau-9549.inp -scrdir=/scratch/tmp/j.9544/
Entering Link 1 = /Applic.PALMA/gruppen/q0grimme/g09/l1.exe PID= 9550.
******************************************
Gaussian 09: EM64L-G09RevA.02 11-Jun-2009
19-Sep-2011
******************************************
%RWF=/scratch/tmp/j/1,200GB,/scratch/tmp/j/2,200GB,/scratch/tmp/j/3,200GB,/scratch/tmp/j/4,200GB
%chk=/home/j/sodiated.chk
%nproc=12
Will use up to 12 processors via shared memory.
%Mem=46GB
———————————————————————-
#MaxDisk=4000GB # freq rmp2=full/6-311+g(2d,2p) geom=connectivity test
———————————————————————-
1/10=4,30=1,38=1,57=2/1,3;
.
.
.
.
Inverted reduced A of dimension 497 with in-core refinement.
End of Minotr Frequency-dependent properties file 721 does not exist.
End of Minotr Frequency-dependent properties file 722 does not exist.
MDV= 6174015488.
Form MO integral derivatives with frozen-active canonical formalism.
Discarding MO integrals.
Reordered first order wavefunction length = 1153152288
WUsed= 838072415 WInt= 6228120 WEnd= 13283563520
Dk804= 4115560752. Dk1111= 0. Dk1112= 12923258400.
MaxDsk=536870912000 LAFull= 1153152288 DskLim=536870912000.
NUsed=29632743563.20077466863.14050795516.12680526328.10543911627. 9119501826.
In DefCFB: NBatch= 1 ICI= 58 ICA=414 LFMax= 60
Large arrays: LIAPS= 22894001280 LIARS= 3140649540 words.
Semi-Direct transformation.
ModeAB= 4 MOrb= 58 LenV= 6168992221
LASXX= 2811761526 LTotXX= 2811761526 LenRXX= 5642084038
LTotAB= 2830322512 MaxLAS= 2944453056 LenRXY= 0
NonZer= 8453845564 LenScr= 16973996032 LnRSAI= 2944453056
LnScr1= 5912000000 LExtra= 866684027 Total= 32339217153
MaxDsk=536870912000 SrtSym= T ITran= 4
JobTyp=0 Pass 1: I= 1 to 58.
(rs|ai) integrals will be sorted in core.
SymMOI: orbitals are not symmetric.
Spin components of T(2) and E(2):
alpha-alpha T2 = 0.1101843022D+00 E2= -0.3379652408D+00
alpha-beta T2 = 0.5524282940D+00 E2= -0.1962767113D+01
beta-beta T2 = 0.1101843022D+00 E2= -0.3379652408D+00
ANorm= 0.1882974720D+01
E2 = -0.2638697594D+01 EUMP2 = -0.12103953608513D+04
IDoAtm=111111111111111111111
Differentiating once with respect to electric field.
with respect to dipole field.
Differentiating once with respect to nuclear coordinates.
There are 1 degrees of freedom in the 1st order CPHF. IDoFFX=0.
LinEq1: Iter= 0 NonCon= 1 RMS=2.81D-03 Max=1.47D-01
LinEq1: Iter= 1 NonCon= 1 RMS=7.99D-04 Max=1.87D-02
LinEq1: Iter= 2 NonCon= 1 RMS=3.70D-04 Max=1.80D-02
LinEq1: Iter= 3 NonCon= 1 RMS=2.02D-04 Max=9.45D-03
LinEq1: Iter= 4 NonCon= 1 RMS=8.56D-05 Max=4.10D-03
LinEq1: Iter= 5 NonCon= 1 RMS=4.33D-05 Max=3.30D-03
LinEq1: Iter= 6 NonCon= 1 RMS=1.53D-05 Max=5.51D-04
LinEq1: Iter= 7 NonCon= 1 RMS=6.04D-06 Max=2.60D-04
LinEq1: Iter= 8 NonCon= 1 RMS=2.19D-06 Max=5.37D-05
LinEq1: Iter= 9 NonCon= 1 RMS=7.24D-07 Max=2.39D-05
LinEq1: Iter= 10 NonCon= 1 RMS=2.61D-07 Max=9.41D-06
LinEq1: Iter= 11 NonCon= 1 RMS=1.05D-07 Max=4.89D-06
LinEq1: Iter= 12 NonCon= 1 RMS=5.11D-08 Max=2.64D-06
LinEq1: Iter= 13 NonCon= 1 RMS=1.81D-08 Max=7.44D-07
LinEq1: Iter= 14 NonCon= 1 RMS=5.33D-09 Max=1.51D-07
LinEq1: Iter= 15 NonCon= 1 RMS=1.97D-09 Max=6.96D-08
LinEq1: Iter= 16 NonCon= 1 RMS=7.09D-10 Max=2.36D-08
LinEq1: Iter= 17 NonCon= 1 RMS=2.14D-10 Max=5.42D-09
LinEq1: Iter= 18 NonCon= 1 RMS=6.35D-11 Max=2.21D-09
LinEq1: Iter= 19 NonCon= 1 RMS=2.25D-11 Max=1.02D-09
LinEq1: Iter= 20 NonCon= 0 RMS=8.24D-12 Max=4.12D-10
Linear equations converged to 1.000D-10 1.000D-09 after 20 iterations.
End of Minotr Frequency-dependent properties file 721 does not exist.
End of Minotr Frequency-dependent properties file 722 does not exist.
Symmetrizing basis deriv contribution to polar:
IMax=3 JMax=2 DiffMx= 0.00D+00
G2DrvN: will do 22 centers at a time, making 1 passes doing MaxLOS=2.
Calling FoFCou, ICntrl= 3107 FMM=F I1Cent= 0 AccDes= 0.00D+00.
FoFDir/FoFCou used for L=0 through L=2.
End of G2Drv Frequency-dependent properties file 721 does not exist.
End of G2Drv Frequency-dependent properties file 722 does not exist.
Do you have any explanation for this error?
Sincerely,
T. Jaskolla
Hello T.
I haven’t seen this error before. Are you performing the second set of calculations on the same machine?
Try using density=current
Hope this helps!
Dear Thorsten,
Did you get any solution of your error?
Please share with me, I am having the same problem when I use gaussian to calculate the frequency of a cluster which made by 480 atoms.
Many thanks
Xiaohong Yuan
Dear sir,
My molecule name is 2-Chloro alpha alpha alpha trifluoro 3,5-dinitrotoluene. While submitting this molecule for frequency calculation, it is saying that there is ” Input conversion error in IntKMC” . I don’t know how to eliminate that error .and seeking your assistance to continue my work.
Hello Meenakshi
Haven’t seen this error before but there seems to be something wrong with the input. Try redefining the molecule specification section. Did you pre-optimized the structure? Are you reading it from another program?
I think I need more information to help you, ok?
I hope I can help you in the near future.
Hi, i solved it deleting the comma in the name of input file. If you use GaussView 5.0.8, the option in Gaussian Calculation Setup for Link 0/Chkpoint File is Default name, at start it will create a Chekpoint file (.chk) with the same name of the input file, and if this file contained a comma in the name, the software will be confused and won’t can make the .chk file. Only is a comma in the input file name.
Dr. Barroso,
In a reponse to someone trying to visualize a hypersurface of a scan you suggest using “Origin, GNUplot or in the worst case scenario with MS Excel”. What other programs would you suggest a S.T.E.M. student should be familiar with before entering grad school? Excluding, the basic Microsoft suite of programs like word, ppt, and excel.
Thank you,
Agapito
Hello Agapito, my friend who I still haven’t met!
I would suggest learning how to work with software for statistical analysis such as Origin or other commercial packages with the same purpose.
Learning your way around Unix/Linux/etc. is important since you will have the need for more powerful computing capabilities which are best provided by these systems.
Coding is a very valuable skill these days, although you don’t have to be exactly an expert on programming, just knowing your way around a certain language will help you understand and modify existing codes (almost nobody codes from scratch anymore, the closest thing still involves taking published subroutines for tasks such as integrating). Suggested languages to learn: C and its variants, Python and Fortran if available (in that order of priority).
MATLAB can also be a great asset to your skills.
From the top of my head I think this is the most important I can think of right now for any generic STEM grad student but if I think of something else I’ll get back to this comment.
How about those Rangers? Texans are pretty excited, I guess. I’m betting on them to win the World Series, despite the fact I was secretly rooting for the Tigers.
Have a nice day!
Dr. Barroso,
Wow this is a great Gaussian site, and you are so helpful and prompt with all levels of questions. if you don’t mind, I have two totally basic ones, and would really appreciate your help. I’m using 09, and have Gauss-View. : )
1st involves the Gen keyword and a .gbs file. When “downloading” a basis set from the EMSL, is it just copy-paste the desired atoms from the pop-up window (from the desired set) and save as a .gbs in your directory? Basically how does downloading basis sets from the EMSL work if Gaussian needs a .gbs file?
2nd involves Using NBO analysis in a TD excited states calculation. I know where the bond population and energy are for “natural” orbitals in the analysis. How/where do I assign calculated UV-vis peaks to their natural orbital excited transitions? Thanks so much!
Dr. Joaquin,
Scratch the NBO TD analysis. I’ve been able to parse the .log files to assign population density types to transitions by coefficients etc. As I believe you’ve commented on, NBO & DFT do not really mix in GaussView (using 5). So I’ll only be using NBO for bond energy (kcal) for certain donor interactions in the .log.
However, If you have any advise on the Gen keyword related to installing basis sets from the EMSL, your help would be truly appreciated.
-b
Hi Brady
First of all please forgive the lateness of my response (sheesh! this has become a usual opening line in my replies; I either reply sooner or create a shortcut so I don’t have to type it all every time!)
About the GEN keyword, please defer to my latest post which can be seen here
It is sometimes confusing what to do with the EMSL basis sets but I hope this post helps you.
Best wishes and thanks for reading!
Dear Brady,
Please share how you solve your problems regarding gen keyword and EMSL basis set, and how you assigned uv-vis peaks to their natural orbital exited transition in a TD calculation?
Many thanks
With best regards,
Bijan Mondal
In this blog there is a post about the use of the GEN keyword. Try searching it with the search field at the left side of the page
Hello Sir,
Let me know about PBC calculations in Gauassian. Is it calculations in solid phase? Is it possible to do calculations in solid state with Gaussian?
Thank-you
Hello Alam!
PBC would be a great post for the near future! Thanks for the idea 🙂
Now, to answer your question. PBC generates a periodic model from a small set of atomic coordinates based on symmetry considerations you impose. Therefore you can run calculations on a polymer based on the calculations of the corresponding monomer (1D replication). The same holds true for a surface (2D replication) or a crystalline solid (3D). The problem is getting the band structure of the solid which could be obtained as a result of a (very demanding) DFT calculation in which the MOs would get so packed they would constitute a band.
I would suggest to get another software such as CRYSTAL but PBC in G09 could be a great first step in calculating the electronic structure of a solid.
Hope this helps
Thanks for reading!
Dear Alam,
i am trying to do DFT calculation of TiO2 crystal for interaction qith simple molecules like water
when I’m taking / cleaving the crystal from a particular surface like 0 0 1 surface and interacting the water molecule
But in doing so using G09
the error is
“Symmetry turned off by external request
Symmetry turned off
Cannot cope with the ghost atoms or with translational vectors”
Do I have to give a PBC calculation for the crystal
Also how do I see the interacting atoms as it is a symmetrical structure and on cleaving the infinte structure still remains
Do I have to saturate the O ends of TiO2 with hydrogen/ make it a double bond?
Regards
Jyotsna
Hello sir,
Please let me know ho to calculate EPR parameters (hyperfine splitting constants, g-tensor) using gaussian 03..
thanking
you
Jo
Hello sir,
i hope to know how can an intramolecular H-bond in guest molecule effect i the inclusion complex
Try calculating the wiberg bond index between those atoms involved. Find the procedure in the post with the NBO calculations in this blog.
I hope this helps
Hello sir,
I hope to know the relationships with the inclusion and the intramolecular h bond in guest molecule
please can you explain to me the relationships with the inclusion and the intramoleclar H-bond
I want to calculate a TS between SSOO, can you help me how to design this and how I can obtain this?
Thanks
Hello sir
this srinu i am very new to this gaussian(learning now) i have been trying to optimize the transition state of aldehydic hydrogen abstraction with chlorine atom. but its forming always product i am using mpwb1k level of theory 6-31+g(d,p) basis set.please help me_
Dear Dr. Joaquin,
I am trying to optimize a structure of CdCl4 with two cation at a distant apart.
Following is my input:
%chk=a.chk
%nproc=4
%mem=120MW
#p b3lyp/Gen pseudo=read opt scf(tight,maxcycle=1000)
Calculation
0 1
Cd -0.00000000 0.00000000 -0.00000000
Cl 1.86600000 1.89125000 0.29318000
Cl -0.00000000 -0.37522000 2.49421000
…………………..
………………..
C N H 0
6-31G(d)
****
Cl 0
6-31G++(d)
****
Cd 0
LANL2DZ
****
Cd 0
LANL2DZ
But I am getting a structure which is away from the crystal structure.
If I include counterpoise keyword and specify the fragment I am getting an error message
Cd atom has 48 electrons but 18 basis set is defined. This is less than minimal basis set.
Yet it is calculating the structure but the the mulliken charge I am specifying is not conserved.
Kindly help.
Ok, you have two different problems here:
1) Optimizing the structure means you will find the structure with the lowest (within reason) energy possible; crystal structures are often not since they are restrained by the crystal field. Taking them out of the crystal allows them to be relaxed which explains why both structures are different.
2) the counterpoise keyword calculates how the electrons from one fragment populate the basis set functions of the other fragment. The method doesn’t work with pseudopotentials like LANL2DZ (which replaces the core of 30 electrons so the calculation is performed faster) but the method knows that Cd has 48 electrons and only finds space for 18 so it crashes.
I hope this helps
Hi Dr.!
I’m a newcomer on Comput. Chem. I wonder if you could help me with this problem. Have you use Molden 3.4 program yet? I use this program to visualize the MO of tetraaluminium dianion but I could not obtain the HOMO, HOMO-1 or any MO pictures look like on this paper DOI: 10.1126/science.291.5505.859 despite the fact that I used the same program (G03W) and Method in my calculation. Could you help me?
Many Thanks for any Reply!
I’m not an expert on Molden but my guess is that the program can’t find the basis set and therefore can’t generate the MOs from the calculated coefficients. Try using the following options in your calculation: gfprint gfoldprint and gfinput. all of them print the basis set in different formats, molden will be able to read one of them and then generate the MOs
I hope this helps!
Hi Dr.
I’m using Gaussian with NBO analysis. I’m running optimization with NBO. But usually I got the following error message: ” NBStor is confused about NOcc. ”
I saw some questions about this on your website, so I tried to change the basis set, but it occurs some times.
Is there any difference if I do the optimization first, then do the NBO analysis? I did the optimization with NBO, which means before opt, NBO is performed, and after geometry optimization, NBO is performed. I’m using one molecule with charge 0, -1, +1. Although it works with charge 0 based on some basis set, it doesn’t work with charge -1 based on the same basis.
Is it ok to optimize for geometry, then use the optimized geometry with NBO in energy calculation?
It is correct to do it that way but you won’t find any difference in the result. You have a basis set issue which can’t be overcome and that is due to the charge. Try it your way and if it works PLEASE let me know, ok?
Have a nice day!
Hello sir
i trying to calculate Fukui function for some pyridine derivatives but i have a problem. assuming i want to calculate the Fukui function of pyridine so three calculation must be performed
first, for pyridine which is the neutral molecule to be analyzed of N electron system
second is the negative ion of pyridine (N+1) system——-???????
third is the positive ion of pyridine (N-1) system——–??????
does the input file of the second and third calculation is the same of the first but just only change the charge of the system fro 0 to -1 and +1
or what?
hello sir
sorry for the incomplete message, i just want to ask about what is he N system, N-1 and N+1 systems used for pyridine?
i tried to do the calculations using g03 at DFT/B3LYP level for pyridine its ok
but i dont know what are the N-1 and N+1 species should be calculated.
best regard
Dr Saied Soliman
Hello,
i’m trying to optimize the structure of Ir(ppy)3 and then i want to calculte uv vis spectr awith varying th density functionals…
i try to use GEN keyword to set basis sets for Iridium and the pop=(readradii) for it.
but when i run the job i get errors
this is the input file:
%chk=C:\Users\Enrico D\Desktop\Ir(ppy)3 testgrd.chk
# opt freq td rb3lyp/gen geom=connectivity int=ultrafine
pop=(readradii,mk) pseudo=read
Title Card Required
0 1
C -3.99749000 -2.98380300 0.00000000
C -4.15709000 -1.63958500 0.00000000
C -2.90822600 -0.74768400 0.00000000
C -1.67055100 -1.23449400 0.00000000
C -1.48668300 -2.76506200 0.00000000
C -2.57441300 -3.58229800 0.00000000
C -2.91748200 0.72025200 0.00000000
C -4.02164900 1.49664600 0.00000000
C -3.83063900 3.01655200 0.00000000
C -2.56850500 3.50396400 0.00000000
C -1.37319400 2.52360000 0.00000000
N -1.57201600 1.23716300 0.00000000
C -1.49898000 -2.45091700 0.00000000
C -1.65118700 2.67012600 0.00000000
N -0.28544700 -1.97986700 0.00000000
C 0.83493000 -2.88661100 0.00000000
C 0.71469000 -4.23096000 0.00000000
C -0.69702200 -4.82555100 0.00000000
C -1.75026000 -3.97629300 0.00000000
C -1.81514700 4.02072500 0.00000000
C -0.58536300 4.95399800 0.00000000
C 0.65862700 4.42015600 0.00000000
C 0.80666600 2.89257300 0.00000000
C -0.23376500 2.06410800 0.00000000
C 2.10159300 -2.14477600 0.00000000
C 2.08253600 2.16647700 0.00000000
C 3.30703300 2.73434500 0.00000000
C 4.52771400 1.80883200 0.00000000
C 4.31866200 0.47210600 0.00000000
C 2.87194500 -0.07273300 0.00000000
N 1.85736100 0.74280900 0.00000000
C 3.13809300 0.09483200 0.00000000
C 1.90442100 -0.82952500 0.00000000
C 4.38967500 -0.43867700 0.00000000
C 4.58279900 -1.97036800 0.00000000
C 3.49838600 -2.78056800 0.00000000
Ir 0.00000000 0.00005600 0.00000000
H -4.85221600 -3.62745600 0.00000000
H -5.13574100 -1.20698000 0.00000000
H -0.50258400 -3.18513500 0.00000000
H -2.44301700 -4.64421900 0.00000000
H -5.00021600 1.06382900 0.00000000
H -4.67352300 3.67566300 0.00000000
H -2.39890200 4.56043100 0.00000000
H -0.37379900 2.90579800 0.00000000
H -2.32971300 -1.77654500 0.00000000
H -2.50697900 2.02787000 0.00000000
H 1.57885000 -4.86192300 0.00000000
H -0.84629400 -5.88507000 0.00000000
H -2.74997000 -4.35772500 0.00000000
H -2.80051900 4.43781300 0.00000000
H -0.71552800 6.01603900 0.00000000
H 1.52254200 5.05147800 0.00000000
H 3.42159100 3.79819100 0.00000000
H 5.51998600 2.20913700 0.00000000
H 5.14873000 -0.20309400 0.00000000
H 2.70313200 -1.12932200 0.00000000
H 3.00995400 1.15712500 0.00000000
H 5.24367900 0.20599300 0.00000000
H 5.56755700 -2.38884300 0.00000000
H 3.61296100 -3.84442200 0.00000000
1 2 2.0 6 1.0 38 1.0
2 3 1.0 39 1.0
3 4 2.0 7 1.0
4 5 1.0 13 3.0 37 1.0 46 1.0
5 6 2.0 13 3.0 15 1.0 19 3.0 40 1.0
6 13 1.0 19 3.0 41 1.0 50 1.0
7 8 2.0 12 1.0
8 9 1.0 42 1.0
9 10 2.0 43 1.0
10 11 1.0 14 3.0 20 3.0 44 1.0 51 1.0
11 12 2.0 14 3.0 20 1.0 24 3.0 45 1.0
12 14 1.0 37 1.0
13 15 2.0 19 1.0 46 1.0
14 20 2.0 24 1.0 47 1.0
15 16 1.0 37 1.0
16 17 2.0 25 1.0
17 18 1.0 48 1.0
18 19 2.0 49 1.0
19 41 1.0 50 1.0
20 21 1.0 44 1.0 51 1.0
21 22 2.0 52 1.0
22 23 1.0 53 1.0
23 24 2.0 26 1.0
24 37 1.0 45 1.0
25 33 2.0 36 1.0
26 27 2.0 31 1.0
27 28 1.0 54 1.0
28 29 2.0 55 1.0
29 30 1.0 32 3.0 34 3.0 56 1.0 59 1.0
30 31 2.0 32 3.0 33 3.0 34 1.0 57 1.0
31 32 1.0 37 1.0
32 33 1.0 34 2.0 58 1.0
33 37 1.0 57 1.0
34 35 1.0 56 1.0 59 1.0
35 36 2.0 60 1.0
36 61 1.0
37
38
39
40
41 50 1.0
42
43
44 51 1.0
45
46
47
48
49
50
51
52
53
54
55
56 59 1.0
57
58
59
60
61
H 0
S 3 1.00
19.2384000 0.0328280
2.8987000 0.2312040
0.6535000 0.8172260
S 1 1.00
0.1776000 1.0000000
****
C 0
S 7 1.00
4233.0000000 0.0012200
634.9000000 0.0093420
146.1000000 0.0454520
42.5000000 0.1546570
14.1900000 0.3588660
5.1480000 0.4386320
1.9670000 0.1459180
S 2 1.00
5.1480000 -0.1683670
0.4962000 1.0600910
S 1 1.00
0.1533000 1.0000000
P 4 1.00
18.1600000 0.0185390
3.9860000 0.1154360
1.1430000 0.3861880
0.3594000 0.6401140
P 1 1.00
0.1146000 1.0000000
****
N 0
S 7 1.00
5909.0000000 0.0011900
887.5000000 0.0090990
204.7000000 0.0441450
59.8400000 0.1504640
20.0000000 0.3567410
7.1930000 0.4465330
2.6860000 0.1456030
S 2 1.00
7.1930000 -0.1604050
0.7000000 1.0582150
S 1 1.00
0.2133000 1.0000000
P 4 1.00
26.7900000 0.0182540
5.9560000 0.1164610
1.7070000 0.3901780
0.5314000 0.6371020
P 1 1.00
0.1654000 1.0000000
****
Ir 0
S 3 1.00
2.3500000 -1.6784642
1.5820000 2.0952553
0.5018000 0.4162934
S 4 1.00
2.3500000 1.6464467
1.5820000 -2.2748150
0.5018000 -1.0494357
0.2500000 1.2167791
S 1 1.00
0.0598000 1.0000000
P 3 1.00
2.7920000 -0.3889212
1.5410000 0.9077516
0.5285000 0.4691443
P 2 1.00
0.5100000 -0.1170669
0.0980000 1.0489002
P 1 1.00
0.0290000 1.0000000
D 2 1.00
1.2400000 0.5087022
0.4647000 0.5862102
D 1 1.00
0.1529000 1.0000000
****
! Elements References
! ——– ———-
! Na – Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985).
! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 (1985).
! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 (1985).
!
IR 0
IR-ECP 4 60
g potential
5
1 823.5880147 -0.1578014
2 364.6613336 -1517.5270446
2 55.7082801 -316.5306529
2 12.0464544 -91.8880941
2 3.5120610 -9.2241773
s-g potential
6
0 188.0490770 3.1578014
1 340.4194712 26.8322577
2 128.2373673 800.4250007
2 33.8644961 369.4050683
2 4.7560005 242.4171899
2 3.9649974 -118.2173282
p-g potential
5
0 289.7291139 2.1578014
1 87.4633789 61.9678610
2 30.4363766 269.0581986
2 4.0553412 231.1654793
2 3.5525341 -133.6952667
d-g potential
5
0 136.4017106 3.1578014
1 95.0776925 45.9349803
2 49.2258410 359.0344668
2 15.0874145 176.4740119
2 4.0405764 54.5155286
f-g potential
5
0 127.3507908 3.9546197
1 66.2364374 52.9773655
2 34.4299229 274.8643383
2 10.1995721 137.2047338
2 2.5409702 14.8633305
Ir 0.82
————————————-
and this is the output with error 2070:
Entering Link 1 = C:\G03W\l1.exe PID= 3580.
Copyright (c) 1988,1990,1992,1993,1995,1998,2003, Gaussian, Inc.
All Rights Reserved.
This is the Gaussian(R) 03 program. It is based on the
the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.),
the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.),
the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.),
the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.),
the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.),
the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon
University), and the Gaussian 82(TM) system (copyright 1983,
Carnegie Mellon University). Gaussian is a federally registered
trademark of Gaussian, Inc.
This software contains proprietary and confidential information,
including trade secrets, belonging to Gaussian, Inc.
This software is provided under written license and may be
used, copied, transmitted, or stored only in accord with that
written license.
The following legend is applicable only to US Government
contracts under DFARS:
RESTRICTED RIGHTS LEGEND
Use, duplication or disclosure by the US Government is subject
to restrictions as set forth in subparagraph (c)(1)(ii) of the
Rights in Technical Data and Computer Software clause at DFARS
252.227-7013.
Gaussian, Inc.
Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA
The following legend is applicable only to US Government
contracts under FAR:
RESTRICTED RIGHTS LEGEND
Use, reproduction and disclosure by the US Government is subject
to restrictions as set forth in subparagraph (c) of the
Commercial Computer Software – Restricted Rights clause at FAR
52.227-19.
Gaussian, Inc.
Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA
—————————————————————
Warning — This program may not be used in any manner that
competes with the business of Gaussian, Inc. or will provide
assistance to any competitor of Gaussian, Inc. The licensee
of this program is prohibited from giving any competitor of
Gaussian, Inc. access to this program. By using this program,
the user acknowledges that Gaussian, Inc. is engaged in the
business of creating and licensing software in the field of
computational chemistry and represents and warrants to the
licensee that it is not a competitor of Gaussian, Inc. and that
it will not use this program in any manner prohibited above.
—————————————————————
Cite this work as:
Gaussian 03, Revision B.01,
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria,
M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven,
K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi,
V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega,
G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota,
R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao,
H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross,
C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev,
A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala,
K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg,
V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain,
O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari,
J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford,
J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz,
I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham,
C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill,
B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople,
Gaussian, Inc., Pittsburgh PA, 2003.
*********************************************
Gaussian 03: x86-Win32-G03RevB.01 3-Mar-2003
31-Dec-2011
*********************************************
%chk=C:\Users\Enrico D\Desktop\Ir(ppy)3 testgrd.chk
Default route: MaxDisk=4gb
———————————————————————-
# opt freq td rb3lyp/gen geom=connectivity int=ultrafine pop=(readradi
i,mk) pseudo=read
———————————————————————-
Warning: this job cannot use analytic gradients
and so will do many energy evaluations.
1/14=-1,26=3,29=20000,38=1,57=2/1,14;
2/17=6,18=5,29=3,40=1/2;
3/5=7,11=2,16=1,17=8,25=1,30=1,74=-5,75=5/1,2,8,3;
4/7=1/1;
5/5=2,38=5/2;
8/6=1,10=1,27=536870912/1;
9/27=536870912,42=1/14;
6/7=2,8=2,9=2,10=2,15=8,20=101/1,2;
1/14=-1/14(1);
99//99;
2/29=3/2;
3/5=7,6=1,11=2,16=1,17=8,25=1,30=1,74=-5,75=5,82=7/1,2,8,3;
4/5=5,7=1,16=3/1;
5/5=2,38=5/2;
8/6=1,10=1,27=536870912/1;
9/27=536870912,42=1,49=4/14;
1/14=-1/14(-6);
2/29=3/2;
6/7=2,8=2,9=2,10=2,15=8,20=101/1,2;
99//99;
——————-
Title Card Required
——————-
Symbolic Z-matrix:
Charge = 0 Multiplicity = 1
C -3.99749 -2.9838 0.
C -4.15709 -1.63959 0.
C -2.90823 -0.74768 0.
C -1.67055 -1.23449 0.
C -1.48668 -2.76506 0.
C -2.57441 -3.5823 0.
C -2.91748 0.72025 0.
C -4.02165 1.49665 0.
C -3.83064 3.01655 0.
C -2.56851 3.50396 0.
C -1.37319 2.5236 0.
N -1.57202 1.23716 0.
C -1.49898 -2.45092 0.
C -1.65119 2.67013 0.
N -0.28545 -1.97987 0.
C 0.83493 -2.88661 0.
C 0.71469 -4.23096 0.
C -0.69702 -4.82555 0.
C -1.75026 -3.97629 0.
C -1.81515 4.02072 0.
C -0.58536 4.954 0.
C 0.65863 4.42016 0.
C 0.80667 2.89257 0.
C -0.23377 2.06411 0.
C 2.10159 -2.14478 0.
C 2.08254 2.16648 0.
C 3.30703 2.73435 0.
C 4.52771 1.80883 0.
C 4.31866 0.47211 0.
C 2.87195 -0.07273 0.
N 1.85736 0.74281 0.
C 3.13809 0.09483 0.
C 1.90442 -0.82953 0.
C 4.38968 -0.43868 0.
C 4.5828 -1.97037 0.
C 3.49839 -2.78057 0.
Ir 0. 0.00006 0.
H -4.85222 -3.62746 0.
H -5.13574 -1.20698 0.
H -0.50258 -3.18514 0.
H -2.44302 -4.64422 0.
H -5.00022 1.06383 0.
H -4.67352 3.67566 0.
H -2.3989 4.56043 0.
H -0.3738 2.9058 0.
H -2.32971 -1.77655 0.
H -2.50698 2.02787 0.
H 1.57885 -4.86192 0.
H -0.84629 -5.88507 0.
H -2.74997 -4.35773 0.
H -2.80052 4.43781 0.
H -0.71553 6.01604 0.
H 1.52254 5.05148 0.
H 3.42159 3.79819 0.
H 5.51999 2.20914 0.
H 5.14873 -0.20309 0.
H 2.70313 -1.12932 0.
H 3.00995 1.15713 0.
H 5.24368 0.20599 0.
H 5.56756 -2.38884 0.
H 3.61296 -3.84442 0.
NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-
NUMERICAL EIGENVECTOR FOLLOWING MINIMUM SEARCH
INITIALIZATION PASS
************************************************
** ERROR IN INITNF. NUMBER OF VARIABLES ( 0) **
** INCORRECT (SHOULD BE BETWEEN 1 AND 50) **
************************************************
Error termination via Lnk1e in C:\G03W\l114.exe at Sat Dec 31 14:28:19 2011.
Job cpu time: 0 days 0 hours 0 minutes 1.0 seconds.
File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 1 Scr= 1
…………………
for simplest calculations or for smallest molecules there is no problem.But for biggest ones…
WHAT SHOULD I DO?
IN GENERAL, CAN YOU HELP ME TO SET UP TDDFT CALCULATIONS for excited states FOR TRANSITION METALS SUCH AS Ru and Ir, what are the best settings and the corrects one?
There are errors in the input file? (Syntax, Keywords…?)…
this is the molecule: http://www.lookchem.com/300w/2010/0714/94928-86-6.jpg
i use:
GaussView 5.0
Gaussian03
ChemBio Office for structure designing
Many thanks.
Best Regards,
Enrico D’Ortenzio
Oricola (Italy)
University of Tor Vergata, Rome
Hi, I make TD-DFT with metal complex and I usually use the lanl2dz basis set with the cam-B3LYP functional for TD calculation and they give good result compared with experimental data. I suggest you to include also the solvent effect with PCM because the effect of solvent in the optimization steps and solvatochromism is important.
But it’s better that you first optimize the structure and after run TD job.
Try this for the optimization:
#p opt=tight b3lyp/lanl2dz scrf=(solvent=water) geom=connectivity pop=full
and this for TD:
#p cam-b3lyp/LANL2DZ nosym scf=maxcyc=2048 TD=NStates=35 IOP(9/40=2) IOp(8/11=1) scrf=(solvent=water)
(I used water as solvent but you can change it, the same for the number of excited state you need)
I hope this help
Please let me know if this work
Nicola
Estimado Dr. Estoy estudiando una reacción química (Diels-Alder) y quisiera los coeficientes de cada átomo en el HOMO y el LUMOm cómo puedo hacerlo? Aun estoy entendiendo este programa, gracias.
Dear Dr. Barroso
thanks a lot for your helpful posts.
I want to calculate overlap population analysis in G03.
please help me.
Best regards.
Dear Dr. Joagguin,
I am PhD student and studying with Gaussian for biological and argonometalic molecules or complexes. Can you give me some information about TDDFT calculation and Infrared-Raman calculations for this exiated state(s)? I examine some fields and help field for gaussian but I have some question… And also may you tell me system rational for gaussian?
Thank you very much, in advance…
hello ,
i do tddft uv-vis spectra of Ni(CH2S2)2, for more excited states..with g09w
but..
for some calculations i used to specify pseudopotentials with geneecp keyword to indicate the lanld2z pseudopotential for nickel…and 6-311g(3d,2p) for C,S,H
at higher frequencies, between 200-300 nm, using 6-311g for all atoms or specifying lanl2dz for Ni, i notice a split in one of the peak (the one at 270nm), i.e. the peak is split into two different peaks.
in the experimental spectrum this peak is at ca. 300nm and there is no splitting!…
what is the explanation of this effects? what are the problems related to higher frequencies states?can it depend that this is a Nickel compound? in what way it can depend by calculations?:
i do tddft calculations using b3lyp/6-311G(3d,2p), PCM for solvent(hexane)
or b3lyp/geneecp specifying lanld2z for Ni at the end of the input after the coordinates.
MANY THANKS
Enrico D.
Hi there,
i use lsda functional in my calculations on Ni, and i would use pure lda functional to compare results with lsda calculations, to understand how the spin affects (and if) the measurement.
HOW TO SET PURE LDA CALCULATION IN G09W?, since there is no pure lda in gaussview?
Best regards,
Enrico
respected sir
i am working with go3 as part of my research work. As part of my study i need to calculate Hyperpolarizability of molecule. For this, i used syntax
#p polar scf = maxcycles=500 freq = noraman b3lyp/6-311+g
finally it is giving only polar and dipolar values, but not hyperpolar.
kindly help me in this regard
thank you very much in advance
vasanth
Respected Sir,
I have done NBO calculation on diborane using standard basis set and DFT method in order to visualize the 3-centered bonds. But the NBO number appears involving 3-center bond(e.g, 1 & 4) is not matching whenever I am visualizing in gauss view rather its sum other number MO.
Kindly halp me in this regards.
Best regards,
Bijan
Dear Sir,
i am trying to do DFT calculation of TiO2 crystal for interaction qith simple molecules like water
when I’m taking / cleaving the crystal from a particular surface like 0 0 1 surface and interacting the water molecule
But in doing so using G09
the error is
“Symmetry turned off by external request
Symmetry turned off
Cannot cope with the ghost atoms or with translational vectors”
Do I have to give a PBC calculation for the crystal
Also how do I see the interacting atoms as it is a symmetrical structure and on cleaving the infinte structure still remains
Do I have to saturate the O ends of TiO2 with hydrogen/ make it a double bond?
Regards
Jyotsna
Dear Sir,
I have a quarry..
Can we do Fukui index calculation using gaussian 09 or 03?
Yes, Bijan. Gaussian can calculate Fukui indexes. Look in this blog for a post called “How to calculate Fukui Indexes” it will give you a step by step procedure on the subject.
I hope this helps
Hi
Can you pls help me to understand how these lone pair represntaion from NBO analysis means?
57. (0.22868) LP*( 6)Ru 11 s( 42.76%)p 1.32( 56.57%)d 0.01( 0.64%)
f 0.00( 0.03%)g 0.00( 0.00%)
0.0000 0.6536 -0.0100 -0.0140 0.0085
0.0009 0.0000 -0.0561 0.0109 -0.0053
0.0000 -0.7439 -0.0007 0.0019 0.0000
-0.0939 0.0024 -0.0108 0.0096 -0.0268
-0.0119 -0.0371 -0.0078 0.0078 0.0319
-0.0045 -0.0071 -0.0445 0.0216 -0.0102
0.0075 -0.0104 -0.0123 0.0047 0.0008
0.0039 -0.0028 -0.0023 0.0018 0.0017
-0.0048 0.0030 0.0013 0.0057 -0.0057
0.0101 0.0043 0.0006 -0.0004 0.0004
-0.0013 -0.0002 -0.0012 -0.0001 -0.0023
-0.0006
My question
How it is a kind of sp hybrid. I beleive usually the lone pairs are non bonding oribatals..If am wrong pls correct me..
Thanks
Rajesh
Hello Rajesh!
Lone pairs are indeed non bonding orbitals, but they can be hybridized. Think about ammonia NH3 for instance, the valence orbitals of the Nitrogen atom are sp3 hybridized, this includes all three N-H bonds but also includes the lone pair on the N atom.
Please search for my post on Pauling’s model of hybridized orbitals in this same blog. Also you could take a look at Gillespie’s VSEPR theory (well, more like a model), you’ll realize that lone pairs get hybridized too.
I hope this helps! Have a nice day
Dear Dr Barroso,
I am having trouble with molekel while analyzing a pdb file I created. The file was originally created as a trajectory / trr file by gromacs. I converted it to a pdb. I have done this dozens of times in the past. When analyzing the video in molekel, the carboxyl terminal end of the dipeptide seems to detach, specifically the carbon attached to the hydrogen. I reran this simulation many times and it is always the same way. I even ran a different dipeptide and again the same thing happened. Interesting to note, if there is a carboxyl group in the side chain of the dipeptide, the issue does not arise, only for the terminal end. I can included the pdb as an attachment in an email, so it can be examined. Any assistance with this matter would be appreciated.
Moshe Nathan
Brooklyn College – Dept. of Chemistry
Brooklyn, NY
Hi Moshe
What version of Molekel are you using? If I remember correctly, in Molekel4.x you have to go to the main interface and click on the ‘bond attributes’ button, then on ‘add bond’ and select the atoms you want to be bonded. After that you have to right-click on the main screen and then go to ‘done picking’. Well, this last bit is only if you don’t have them bonded from the start, which I think is not your case but bear with me.
On the animate/play window there are a couple of useful options “keep bonds” and “superimpose”. The first one will continue to draw all bonds throughout the movie regardless of the bond distance (which is the only criteria molekel is concerned whith when painting bonds between atoms). The second one will re-orient the molecule (or the coordinate system) to make a fluid movie. Sometimes the molecule gets re-oriented for convenience during the optimization process, depending on the case and the software used.
I hope this helps, Moshe. I hope I get to know the Brooklyn College one of these days
Best wishes
Dr Barroso,
Thank you for replying to my inquiry. I am currently using version 5.0 of Molekel. I tried your suggestion of manually adding a bond to the detached carbonyl. It worked for only one frame. If I hit the play button for the movie, the bond would be missing in all subsequent frames.
As to you other suggestion of using the options “keep bonds” and “superimpose”, I was not able to find those options on Molekel 5.0
Thank you for replying, if I do figure it out at the end I will be sure to let you know
Best,
Moshe Nathan
Sorry, Moshe, I haven’t worked with Molekel 5.0. I suggest you send an email to the developers.
Best wishes
Buen día!
Le escribo porque tengo un problema en los inputs para G09 empleando oniom y derivados del cis-platino, para la capa baja utilizo un semiempírico (PM3) y para la alta pretendo utilizar pseudopotenciales, pero al especificar la base de pseudopotenciales (SDD) no se en que parte del input esté mi error, pero no me reconoce solo para Pt dicha base. el input es el siguiente:
%chk=oniom1
%mem=512MB
%nproc=8
# opt=Maxcycle=1024 oniom(pbepbe/GenECP:PM6) scf=qc geom=connectivity pseudo=Read
oniom1
0 1 0 1 0 1
especificaciones de la molécula
C H O N Cl 0
6-31G(d,p)
Pt 0
S 3 1.00
2.5470000 -1.4739175
1.6140000 1.9115719
0.5167000 0.3922319
S 4 1.00
2.5470000 1.4388166
1.6140000 -2.0911821
0.5167000 -1.0921315
0.2651000 1.3426596
S 1 1.00
0.0580000 1.0000000
P 3 1.00
2.9110000 -0.5247438
1.8360000 0.9671884
0.5982000 0.5438632
P 2 1.00
0.6048000 -0.1061438
0.0996000 1.0383102
P 1 1.00
0.0290000 1.0000000
D 2 1.00
1.2430000 0.5598150
0.4271000 0.5511090
D 1 1.00
0.1370000 1.0000000
Gracias de antemano.
Erik Díaz
Departamento de química
Universidad de Guanajuato
Hola Erik!
Bien, pues no veo donde está el pseudopotencial. Solo veo las bases. Intenta utilizar Gen en lugar de GenECP pues tal vez esté interfiriendo con la instrucción pseudo=read pero insisto en que no veo en ningún lado el ECP, el cual lo puedes bajar de la EMSL basis set exchage site (búscalo así en google)
Saludos y ojalá nos veamos por Guanajuato un día de estos.
Dear Joaquin
Can you say the difference between binding energy and interaction energy when we handle the biomolecular system. Thank you.
Regards,
Desikan.
Hi,
Recently I have perfomed a NBO analyis on metal-alkene complex. I have found that the stablization energy (E2) given by the second order pertubation analysis on donor-acceptor interactions is very high (ranging from 30-50 kcal/mol different alkene complexes). .I don’t think I can take this value in a quantitave manner). The total binding energy for those metal-alekene complexes are ranges from 15-21 kcal/mol..Can u pls explain to me this discrepancies in these values?
respected sir
i want to study the solvent effects on my molecule. For this i used syntax
#t scf=maxcycles=1000 b3lyp/6-311+g scrf=(cpcm,solvent=nitromethane,read) freq=raman
but 1301.exe is stopped working message is being displayed after few seconds?
pl help in this regard
Sorry but I need more information in order to help you.
What is the Error message you get? maybe this is only a mistake in the input file syntax.
Send me the error and probably some more info about the input file so I know what is wrong with it.
Dear sir,
I am the new user of gaussion view 2003,while runing the optmization an error arises as Semi-Direct transformation. File extend in NtrExt1 failed; probably out of disk space. I cleared most of the things in the C Disk but again the error arises,please sir suggest me how to rectify it.
Hi Priya!
This is due to the kind of calculation you are trying to perform. The temporal files can get very big and thus your system becomes full. Please google “gaussian efficiency considerations” and go to the gaussian.com website for more information on how to set read&write files (%rwf) in order to better use your available disk.
I hope this helps but if it doesn’t send more info so I can help you better.
Have a nice day and thanks for reading!
Priya – The error is not because of the lack of hard disk space but the RAM(temporary memory) or the processor (32-bit is the one you are most probably using). There is nothing much you can do unless you reconfigure your system. Or try use those “gaussian efficiency considerations”
Hi Joaquin,
I am running some multi-reference calculations using CASPT2 in Molpro and am a little confused about orbital rotation. Is it a good idea to rotate CASSCF orbitals before passing them to CASPT2? Or is it better to try different rotations of HF orbitals to get the right orbitals from a subsequent CASSCF calculation which can then be passed on to CASPT2 without touching the orbitals?
Any thoughts you may have on this would be highly appreciated! Thanks!
Amrit
I am new to gaussian 09 and computational chemistry. I am interested in optimizing Na, K, Rb, Cs complexes. I want to use Lanl2dz and SDD. Could you please let me know if I can use Lanl2dz for Na. Please also let me, for which metals pseudo=read option is used. IF I use b3lyp 631+g(d) for these complexes, is it okay for me to do that.
I believe lanl2dz is available for Na but the only two ways of knowing for sure are using it and hoping it doesn’t crash or checking the bse.pnl.gov link.
The pseudo=read option is used if you want to declare a pseudopotential that is not already define within gaussian, in other words, if you are including specifically the pseudopotential from an external source such as the aforementioned website.
I hope this helps!
Hola Joaquín:
Qué tal todo? espero que todo magnífico. Soy Pico, estuve contigo en la secundaria y ahora buscando un tutorial para gaussian03 con gaussview para aplicar voltaje a una molécula me encontré con tu blog. Esto es, escribo para saludarte, con muchísimo gusto además, y pedirte que si tienes alguna oportunidad, puedas enviarme un totorial donde se apliquen voltajes a una molécula por fas? En el manual de gaussian viene “POLAR” (http://www.ehu.es/sgi/ARCHIVOS/g03/g_ur/k_polar.htm)? Vi con atención que se pueden marcar tamaños de paso para el campo eléctrico también (Step=N
Specifies the step size in the electric field to be 0.0001N atomic units.). Como soy nuevo en gaussian/gaussview pues me acerco a los foros para ver qué alcance puedo tener.
Gracias y un gusto saludarte,
Pico
aheredia@nucleares.unam.mx
alejandropicoheredia@gmail.com
Hola Pico, que gusto volver a saber de ti. Lamentablemente no tengo experiencia en el tipo de cálculos que comentas. Sin embargo si te apuras aun te puedes inscribir a la escuela de electroquímica teórica en Washington DC en Mayo. ( http://spring11.ise-online.org/ ) Los deadlines ya pasaron pero aun tienen espacio para el workshop según los organizadores. Tenía intenciones de asistir yo mismo pero lamentablemente no se pudo. Ahí seguro abordarán el tema de la aplicación de voltajes.
Me da mucho gusto saber de ti nuevamente. Saludos y mucho éxito!
Dear Professor;
I am interested in calculating XPS using Gaussian09. Can you tell me how to prepare the input file. Since I am new to this type of calculation, I would appreciate your help if you could also point me to relevant reference work which describes the calculation process in detail.
Thank you
Hi Mick!
So sorry but I have no experience whatsoever in calculating XPS spectra. I hope you find information soon.
Thanks for reading the blog!
Perhaps Mick, you could provide us with a link if you do find anything? I don’t have a need for the XPS currently but maybe somebody else will in the future and can reference this post.
That is a wonderful idea, my friend!
Dear Joaquin,
I’m an industrial chemist working in ink industry, currently I’m looking for database regarding complexing ability and solubility of inorganic salts in organic solvents, especially cobalt and manganese salts in organic solvents.
Do you have any links, thanks.
Regards
Abby
Dear Sir,
Greetings. We are interested to carry out the optimization and vibrational frequency analysis
for CeO2 unit cell. We couldn’t use the existing basis set in Gaussian 03. We tried with extra basis set (CRENBL ECP)from the EMSL basis set exchange. We did not get any output from log file. Can you please suggest for handling extra basis set for this.
with thanks
Sasirekha
Please take a look at my post on how to use the GEN keyword in order to introduce an external basis set and ECP, if you don’t find the info you need there then leave your question on that same post, please.
Thanks and I hope you find an answer there!
Have a nice day!
Dear Sir
please, i would like to ask you on the availability of performing solid state calculations using g03
thanks
Saied
It depends on what kind of solid state calculations you are trying to get.
Have a nice day Saied!
Dear sir,
please tell me how to provide different basis sets in the input file
Dear Joaqun Borossoo,
I am interested in knowing what literature for computational chemistry is being the most detailed (in explanation) and most useful to start studying it?
Thank you for your recomendations.
Best regards,
Aurimas
Hi Aurimas,
This is a great question! I think I will write a post about it. I would start by learning the basics of Quantum Chemistry (otherwise you only become a button pusher) so start with “Quantum Chemistry” by McQuarrie; then go to Levine’s book with the same title. This will give you a solid background on the physical and mathematical foundations of molecular modeling. Now for the operational part I would suggest using “Exploring Chemistry with Electronic Structure Methods” by Frisch and Frisch. This is a collection of exercises that you can perform on Gaussian so you get an idea of the program’s capabilities.
Please stay tuned because I will post something about this in short.
Have a nice day!
Hola Dr. Barroso!
Hace tiempo que reviso su blog y lo considero de gran utilidad ya que aquí he encontrado solución a algunos problemas que se me han presentado; sin embargo ahora no he encontrado la solución a un problema que tengo al calcular frecuencias con el método MP2 en Gaussian09. El problema es que el cálculo se interrumpe y aparece el siguiente mensaje
Error termination in NtrErr:
NtrErr called from FIOCnC.
Creí que esto podría estar relacionado con la capacidad del disco y la memoria, así que le dí cierto valor a los paramétros %mem y a maxdisk, aún así el problema prevalece. Tiene usted idea a que se debe el error, ojalá pudiera ayudarme. Gracias por su atención, le envio los comandos del input por si le sirven:
%mem=1500MB
%nproc=2
# freq mp2/6-311g(d,p) maxdisk=20GB geom=check guess=check
Hola Sara
Muchas gracias por tus bellas palabras, espero que el blog te siga sirviendo en el futuro.
Efectivamente se trata de espacio en disco. Que tipo de plataforma usas? Mi único consejo es que sigas aumentando el valor en %mem (1.5GB suenan a muy pocos) subelo a 2GB o a 4GB.
Por cierto, la paralelización de Gaussian no es muy buena, sin embargo el uso de más de 1 procesador ayuda en algo. Tienes instalado el módulo LINDA? este es el que paraleliza el cálculo. En la versión G09 la sintaxis correcta es %nprocshared=2 cuidado!
Espero que te sirva. Que tengas un bonito día!
#gaussianerror
Hello Professor,
I was trying to absorb co2 over a graphite sheet. To do this, i first made a small area of sheet, then clicked on it a =C=. then attached 2 oxygen atoms at the ends. Now, all the atoms are on the same plane. Is this right? or should I put the co2 just above the sheet in a parallel plane? I observed that, if the molecules overlap, the program doesnt run and says ‘Link died!’. If I place the co2 in such a way, the molecules dont overlap, it runs for a while and then link dies but a log file is produced this time.
What is exactly happening here?
Dear Joaqun
i am trying to calculate the interaction energies using counterpoise method at the mp2 level but i get the following error which i guess it may be due to memory or disk capacity!!!!!
plz, how can i solve this problem?
the error is:
Estimated scratch disk usage= 117863514 words.
Actual scratch disk usage= 116198490 words.
JobTyp=1 Pass 1: I= 1 to 1 NPSUse= 1 ParTrn=F ParDer=F DoDerP=F.
PickT4: no shell combinations can fit!
NKLS2p= 50 NKLS2= 50 MaxCom= 46
Error termination via Lnk1e in C:\G03W\l906.exe at Fri May 04 01:24:52 2012.
thanks
Saied
Dear Prof. Jo,
I want to calculate the Potential Energy Distribution (PED) in IR vibrational frequencies using Gaussian 09. Please help me to calculate PED. Thank you.
Regards,
Desikan.
Dear Prof. Joaquin,
I want to do IRC calculation in order to check if transition state is directly bound to reactant or product or there is any intermediate. I will be thankful if you could let me know the ways to calculate it. I tried but somehow it didnt work. Will be thankful if you could shed more information on this topic.
Thank you very much
Abdul
Hello Abdul,
IRC needs you to include a proper TS structure. This means you first have to find it by hand making sure you get one imaginary frequency in the vibration analysis. If once you perform the IRC calculation you find a stable structure, it could be related to an intermediate, you can’t know. All you know is this corresponds to a relative minimum on the potential energy surface.
I will write a post on IRC in short. Stay tuned!
I hope this helps. Have a nice day!
Hello Abdul,
IRC needs you to include a proper TS structure. This means you first have to find it by hand making sure you get one imaginary frequency in the vibration analysis. If once you perform the IRC calculation you find a stable structure, it could be related to an intermediate, you can’t know. All you know is this corresponds to a relative minimum on the potential energy surface.
I will write a post on IRC in short. Stay tuned!
I hope this helps. Have a nice day!
Dr Barroso,
We have been successfully running Gromacs (version4.5.3) simulations of tryptophan dipeptides for close to two years now. We build the dipeptide using PyMole and use the Gromacs command pdb2gmx in order to create at Gromacs topology file. We use the OPLS-AA force field with the suggested tip4p water model. For the first time we decided to run a tryptophan residue by itself. While the zwitterion simulation went without incident, the positively or negatively charged form of the residue repeatedly gave an error message.
The message we received was:
ERROR 1 [file topol.top, line 228]:
No default Ryckaert-Bell. types
ERROR 2 [file topol.top, line 229]:
No default Ryckaert-Bell. types
Excluding 3 bonded neighbours molecule type ‘Protein’
Excluding 2 bonded neighbours molecule type ‘SOL’neighbours molecule type ‘SOL’
We are at a loss as to the meaning of this message as well as how to correct it. We narrowed down the error to the terminal carboxylic oxygens (line 228 – 229), but we do not understand what is wrong with them. In addition, it is the same terminal carboxylic oxygens as for the zwitterion species, in which the simulation ran well.
We suspect that the error is due to the fact we are running a single residue and not a dipeptide.
As a control, we tried running a simulation of single residue of tyrosine and it too produced a similar error message.
Any help or advice as to circumvent this issue would be appreciated.
Sincerely,
Dr. Azaria Eisenberg and Moshe Nathan
Brooklyn College – Dept. of Chemistry
ps
Dear Prof. Joaquin,
I am fairly new to using gaussian. I want to know two things
1. How to determine whether a uv-vis transition from TD-DFT is n -> pi*/ pi -> pi*/ d-d transition ?
2. How to study reaction mechanism steps using gaussian ?
Sincerely,
Arnab
Student, Dept of Chemistry
Tripura University, India
Dr. Barosso,
I am facing one issue regarding PCM input. It said H 11 has 2 bonds. so i asked it to create cavity explicitly by specifying “SPHEREONH=11” and also i gave read with that scrf keyword. After that it gave error “End of line while reading PCM input files”….Can you please quickly drop solution to this….Thanks a Lotzz!
Dr. Barosso,
I am trying to calculate NMR for a molecule. I am through the calculations…but the NMR spectra that I am getting is no worth to conclude. So I tried the way of substracting the isotropic values of protons from that of reference isotropic values (TMS) ran under same basis set but still I am not getting the chemical shift values to the mark.
Please can you guide where I am going wrong or just tell me any other way
Thanks.
Dear Dr.Jacquine,
I’m asking if it’s possible to calculate the spectral band width from Gaussian vibration “IR” frequency output…
Thanks
Marawan
Dear Marawan,
Unfortunately it is not possible since quantum mechanical calculations pertain to single molecules therefore you will get the frequencies to which each normal mode of a molecule gets excited. The with of the band is associated to the relaxation mechanisms which might involve the surrounding media or any other intermolecular pattern, all of which are not taken into account into the IR output.
Hope this helps! Have a nice day
Hi
I’m working with gaussian ‘9 and I’m doing a zmatrix scan of two molecules, my script works nicely with HF but it crashes with MP4 complaining
“CALL FROM INITNF: BAD IC ENTRY FOR VARIABLE 2”
do you have any ideas?
Have you tried using a Cartesian scan? How many steps are accomplished by MP4 before it crashes? I need a little more information to help you.
Have a nice day
Hi Dr,
thanks in advance for your kindly help. my Q is how to use EMSL to get best initial gauss of basis set, for a system that it contains B and N atoms(almost 40 atoms ).
I imagine you are trying to build a guess, right? I don’t think you can use the EMSL for that. Remember the guess is only the starting point of the SCF, of course a good one will yield better and faster results but with a BN cluster like yours, provided you have a chemically reasonable geometry, almost any guess is as good as the next. Choose the basis set according to your needs, i.e., to the quantity you want to calculate.
I hope this helps. Have a nice day
I wish to study in detail about the structure, vibrational spectra and all the electronic properties of a biomolecule using a Gaussian program.In this regard I would like to know that what are the possible descriptors which i can calculate/study , which can make my study a complete one. I would very much appreciate if there is a paper in this regard or any other related reading material.
Thanks
Hello,
How do I calculate the percentage of each conformer of all conformers obtained from a potential energy surface scan done using Gaussian 09?
Thanks
Hi Yang, you can to use Maxwell distribution equation.
Bye
dear Dr.
i ran bis-indole using g03 in hf and b3lyp. in the bond lengths, bondangles and dihedral angles section, almost hf and b3lyp values are nearer in estimating the values of bond lengths and bond angles, but, whereas, in case of dihedral angles, in few values there was huge difference.
Ex: hf= -177.6 b3lyp = 177.5
what may be the reason for this. kindly help me in this regard
Try taking a look at the structures because this could only be a matter of definition between one structure and the other, i.e., a reverse numbering definition which makes the sign of the DA change. If that is the case then the absolute value is not different at all.
I hope this helps. Have a nice day
Thank you very much for immdt reply.
Actually in case of hf and b3lyp if we compare, the bond lenghts and bond angles, the diff is very less(it is around < 0.2 to 0.6), where as in case of dihedral angles there is a diff in few values around 2 to 3. why it is? kindly help me in this regard.
Ex: hf = 69.9 b3lyp= 71.25
hf = 86.93 b3lyp = 83.90
i went throughly through the numbering of structure. Numbering was given is same order.
But maybe the dihedral angle was defined in reverse. I mean, the DA(1,2,3,4) = – DA(4,3,2,1) Check the structures again and if you don’t find this issue send me the files so I can take a look at them.
Best wishes
Hi Dr,
how we can have full optimization out put results,but in frequency it ended with error, plz advise.
thanks
Hi Jacquine
I use MOLDEN to view the gaussian output. How can I see the NBOs using MOLDEN? Please advise
Thanks
Subrato
I’m sorry but I have no experience working with MOLDEN. Try to contact the software developers.
Thanks for reading!
Dear Jacquine
Thanks for very useful blog, it is really interesting
i want to ask about the CCSD(T)-F12 method using gaussian 03. I want to make CCSD(T)-F12 calculations on some H- bonded complexes using G03 version C01 running on PC of 1G RAM/core2du processor. Is such calculations is possible to run on PC having such configuration????? please give me the keyword line, i tried to use
#n CCSD(T)-F12/6-31G(d,p) Opt
but there is something wrong ??
best regards
Saied
Dear Prof.Jacquine
Would you tell me about GVB calculation in gaussian program?? I read few articles on web. However, i cannot clearly understand. I want to know detailed information for GVB calculation.
Sorry SunWoo,
I have no experience working with GVB. I suggest you try the Gaussian website and their help desk.
Hope this helps!
Dear Dr.Jacquine,
I’m asking how can we determine the vibration mode associated with a certain vibrational number..In Gaussview, one wavenumber may have contribution from different functional groups, shall we take the highest contribution to simplify the argument, or we have to go to a more sophisticated technique…????
Regards
Marawan
Hello Marawan,
If I understand correctly you want to know to which functional group corresponds each vibrational mode, right? Well you have to take the entire vibrational mode, all atoms involved, if you only take the largest contribution you can have an idea of what you are looking for, however this is not theoretically correct. I’m not aware of any other technique but your approach seems to be interesting.
Best wishes!
Hi Joaquin,
I want your expert opinion regarding a problem that I am failing to figure out. I am trying to get an expression for a given MO (say HOMO, LUMO etc.) out of electronic structure calculation. What I could figure out is an option with the “CMO” keyword for NBO calculation, however, I really don’t follow the output in that case in terms of functional. I want to get a mathematical expression for a given MO of a molecule. How can I do that?
Thank you,
Regards,
Bijan Paul,
Dept. of Chemistry and Biochemistry,
University of Colorado at Boulder, United States.
Hello Paul,
An MO is in fact a mathematical construct which we interpret in a certain chemical or physical way. Every MO is a linear combination of atomic orbitals (in Gaussian’s case these AOs are linear combinations of -gaussian- basis functions). The explicit form of these basis functions is described in Gaussian’s website under tech support, somewhere under the manual section. From your output you get the coefficients which form that linear combination. In short, the mathematical form of every MO is already given; G09 merely displays the coefficients.
I hope I understood the question but if you feel I didn’t, please let me know so I can provide you with better help.
Have a nice day!
dear sir,
i want to transform my IR spectrum obtained by gaussian which is IR intensity Vs wave number into %transmittance Vs wave number. How can I do it? how to compare it with experimental one
Hi Joaquin,
Probably I follow what you said about my problem regarding a mathematical expression of MO. However, I don’t really understand the meaning of that expression in terms of functional. I want to get an expression for a given MO (e.g., HOMO/LUMO etc.) in terms of functional so that I can operate an operator on that, say if I want to operate a Coloumb operator (or anything other) on the functional form of the MO.
Can you please give a clue to this?
Thank you very much,
Bijan Kumar Paul,
Department of Chemistry and Biochemistry,
University of Colorado at Boulder, United States.
Hi Joaquin,
I am a graduate student from India. I want to optimize pi-stacks of large molecules to look at their properties. But since the molecules are mostly flat, the potential energy surface is flat and hard to optimize. Also, since these are weakly bound systems, capturing such weak interactions is important. I tried using Gaussian-03 and 09 without much success. Also the plane wave codes become extremely costly because of the enormous box size required (50-60 Angstrom). Is there any package which captures these weak interactions as well as scales well to perform such large calculations.
Thanks.
Hi Chidambar,
I don’t think your problem lies on the package but on the level of theory employed. Remember DFT methods don’t do a good job in describing dispersion forces such as pi-pi stacking. You’ll need to use a large basis set with polarization and diffusion functions, specially the latter. Plane wave codes are very high quality but have a very slow convergence, well at least those I know about.
Gaussian can do this if you provide the appropriate level of theory.
I hope this helps! Have a nice day!
Dear Dr. Joaquin,
Many thanks for your quick reply. I agree with you that the level of theory plays a major role in capturing the interactions. But the bottleneck I am facing is that, even with HF/6-31g the amount of time taken on 8 distributed cores for a system with 300 atoms is exceeding 20-25 days using G-09. Also it is not ending up in a minima. I heard that TURBOMOLE and NWChem performs faster and also scales better with the number of nodes. Is that a good option?
Thanks in advance.
Chidambar
NWchem should work better for you since it is highly parallelized, just make sure you have the proper parallel machine to run it.
I hope this helps!
Have a nice day!
Thank you Sir.
Chidambar
Dear Sir,
Could you please help me out regarding how to perform ELF calculations.
I have only access to Gaussin09 and 03.
Looking forward to you.
regards,
Bijan
I’m sorry, I don’t know what ELF calculations mean. Can you describe more extensively what is that you want to accomplish?
Have a nice day
Hi,
Your blog is very nice- came across it when trying to figure out something regarding relaxed PES in Gaussian 09. I wanted to scan a certain distance between an atom and a dummy atom but get an error because dummy atoms are not numbered. Can I do this? Also, is it possible to scan two variables at once? I thought this was possible but can’t seem to find it in the manual
Thanks
Hello Elizabeth!
Thanks for your kind words about my little blog!
Unfortunately dummy atoms cannot be used for scanning, sorry! I’ve written to Gaussian’s help desk a couple of times on the matter but so far I haven’t received any clear answer as to why not.
You can scan as many variables as you want, you just need to use the same procedure described in my post on PES scans twice or thrice or as many variables you want, line after line. Just bear in mind that this will produce all possible combinations for both variables. I’ve received questions from people who want to scan two variables simultaneously (i.e. obtaining the diagonal elements of the matrix they actually get). Of course this procedure can become quite time consuming.
I hope this helps.
Have a nice day!
puede poner la liga al post de PES scans? Saludos
Espero que te sea de utilidad
Hi.
At first, i would like to mentioned that it is nice blog, very usefull for begginers.
I decided to write because maybe some of you had this problem.
I have an really strange problem with gaussian09.
I am trying to obtain the transition states, mainly but problem is also with minimas ( not so often).
After reading the input program is do not do anything, without any error… In the queue it is looknig like running but only looking like, it stops everytime in the same line:
(Enter /usr/local/gaussian/gaussian09/g09/l101.exe)
——————-
Title Card Required
——————-
Charge = 1 Multiplicity = 2
Symbolic Z-Matrix:
N 2.44738 -0.63559 0.02773
H 2.68288 -1.24697 -0.76198
C 3.18296 0.63045 -0.03616
C -1.95635 0.02025 -0.00257
H 4.19904 0.58991 -0.39588
H 2.72271 1.48159 0.44
O -3.09388 0.17289 -0.03424
O -0.79474 -0.13526 0.03065
H 0.63811 -0.36246 -0.00116
H 2.65737 -1.16661 0.88635
The following ModRedundant input section has been read:
I was trying to change the geometry of the molecule, but if i change it a lot i obtain the things that i already have and i am not interested. If i change a little i got the same.
I am using the same key words so this shouldn’t be a problem.
Any ideas?
If you have some ideas, i will gbe greatfull!!
PS. Nice blog.
Best regards
Darek
Wow! This is very strange indeed! Please tell us what kind of platform are you using, linux? windows? You say you can see it in the queue, but do you see the gaussian process or just the script with which you send it to the queue?
Sorry for the lateness of my response. If you send me more information I might be able to help you more efficiently.
Have a nice day!
sir
Sir,
is this possible to optimize a molecule at a higher basis set and calculate its frequency at a lower basis set. e;g if a molecule is optimized at 6-311++G(d,p) and calculate its frequency at 6-311++G(d,p),6-311G(d,p),6-31G(d,p) respectively
I’m afraid it’s not possible. In fact it is conceptually wrong. Your geometry optimization generates a potential energy surface at a certain level of theory, computing frequencies over a different PES won’t correspond to the values on the other surface.
Have a nice day
thanks sir
Dear Sir,
Greetings. I am in need of detailed explanation for the optimization of CeO2. Because of greater atomic number we couldnot optimze with the avialble basis set ofGaussian.So we tried to use gen and extra basis set.But we could not run the program.Please give a detailed procedure for the same.We tried as maximum as possible with all available references and examples.please help us for optimization and vibrational analysis.
thank you sir.
Hello Sasirekha,
Please search for a post in this blog which is titled something like The Use of an External Basis Set (GEN keyword). something like that.
In order to work with Cerium, I strongly recommend using a pseudopotential or ECP from the family published by Amlof et al. Try finding it at the BSEL which is in the links section of this blog.
I hope this helps!
Dear Sir,
I am a freshman on the kinetic calculation using Gaussian 09. As you know, according to the transition state theory, rate constant can be calculated using
k=κ(kBT/h)*(q≠/qR)*exp(-△G≠/RT).
I opitimized the reactants, TS, and products. The ZPE corrected G were obtained. If I use these corrected G, should I further consider the partition function for k calculation? (Becuase another professor told me that G containing the information of partition function). Is it right?
If the partition function is necessary, which one should be used?
Q Log10(Q) Ln(Q)
Total Bot 0.718377D-66 -66.143648 -152.301378
Total V=0 0.353068D+24 23.547859 54.220948
Thank you for your suggestion.
Buen día Dr. Joaquín,
Le agradecería mucho si pudiera orientarme con lo siguiente:
Necesito justificar el por qué de mi preferencia por utilizar los índices de Wiberg en lugar de utilizar algún otro análisis. Cuales podrían ser las ventajas de los índices de Wiberg respecto a otros índices de orden de enlace?? Busco una explicación sencilla para discutir en mi tesis. Saludos
Hola de nuevo Abril!
Te recomiendo que leas el artículo original de Wiberg: K.B. Wiberg, Tetrahedron 24 (1968) 1083
Quizá el análisis de población más popular, por su simplicidad, sea el de Mulliken, sin embargo por su construcción se pierde mucha información (De acuerdo a la naturaleza de los átomos enlazados reparte la densidad para uno y para otro, el sobrante lo reparte democráticamente a la mitad, lo cual no refleja la electronegatividad de c/átomo correctamente), además es muy dependiente de la base, i.e., si calculas los órdenes de enlace de Mulliken con 3-21 obtendrás valores muy distintos que si lo haces con 6-311. Wiberg es más estable ante cambios de base, y por tanto más confiables.
espero que te hay sido de ayuda.
Saludos!
Hello Sir,
I am trying to calculate NMR( EFG and magnetic shielding) for my compound, For the ligand of my compound I did not have any problem going from 6-311g to higher basis sets. For complex which is Indium is included I have an issue. I tried to have different basis sets for different atom but does not work !!!
This is my input file
k=00000001troy
%mem=128MB
#p B3LYP/gen nmr Test iop33(10=1) prop=efg scf(MaxCyc=150)
Molecule Name
0 1
molecule coordinate
blank line
O P 0
6-311g
************
I 0
6-311g
************
In 0
3-21G
******************
Could you please let me know what I am doing wrong here .
Thanks so much
Rosha
Hello Rosha,
It would be very helpful to know what kind of error you are getting from the program so I know what the problem is.
Is this input the one you actually used? You are using a small basis set on a heavy atom and a large one on the lighter ones. I don’t think the 3-21G basis set is defined all the way to that row (In) but even if it is, I think the whole calculation is conceptually wrong. Check at the Gaussian website the availability of the basis set (for which elements is it defined) or check it at the EMSL website (check out the links section in this blog). I’d suggest you used the pseudopotential approach.
I hope this helps. Have a nice day!
Hi Sir,
Thanks for comments this is what I get:
Rotational constants (GHZ): 0.0366304 0.0187492 0.0187492
Leave Link 202 at Wed Oct 24 14:31:05 2012, MaxMem= 16777216 cpu: 0.0
(Enter /global/software/gaussian/g09.c01/l301.exe)
General basis read from cards: (5D, 7F)
Centers: 5 6 69 70 71 72 73 74 7 8
6-311g
************
Centers: 1 3 4
6-311g
Atomic number out of range for 6-311G basis.
Error termination via Lnk1e in /global/software/gaussian/g09.c01/l301.exe at Wed Oct 24 14:31:05 2012.
Job cpu time: 0 days 0 hours 0 minutes 0.2 seconds.
File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1
I checked the EMSL website there is lets say basis sets for I for 6-311G** like this:( the problem is I do not know where I have to put these lines in my input file and what change I have to do to my input file)
“BASIS “ao basis” PRINT
#BASIS SET: (15s,12p,7d) -> [10s,9p,5d]
I S
444750.0000000 0.0008900
66127.0000000 0.0069400
14815.0000000 0.0360900
4144.9000000 0.1356800
1361.2000000 0.3387800
I S
508.4400000 0.4365900
209.5900000 0.1837500
I S
81.9590000 1.0000000
I S
36.8050000 1.0000000
I S
13.4950000 1.0000000
I S
6.8859000 1.0000000
I S
2.5520000 1.0000000
I S
1.2088000 1.0000000
I S
0.2734000 1.0000000
I S
0.1009000 1.0000000
I P
2953.6000000 0.0122100
712.6100000 0.0858700
236.7100000 0.2949300
92.6310000 0.4784900
I P
39.7320000 1.0000000
I P
17.2730000 1.0000000
I P
7.9570000 1.0000000
I P
3.1529000 1.0000000
I P
1.3328000 1.0000000
I P
0.4947000 1.0000000
I P
0.2160000 1.0000000
I P
0.0829300 1.0000000
I D
261.9500000 0.0314400
76.7340000 0.1902800
27.5510000 0.4724700
I D
10.6060000 1.0000000
I D
3.4217000 1.0000000
I D
1.1370000 1.0000000
I D
0.3020000 1.0000000
END
There is a post in this blog about the GEN keyword and its usage, which is pretty much the same thing you already did before, you use the gen keyword in your route section and then at the end of the file you write the following lines:
AtomSymb 0
I S
444750.0000000 0.0008900
66127.0000000 0.0069400
14815.0000000 0.0360900
4144.9000000 0.1356800
1361.2000000 0.3387800
I S
508.4400000 0.4365900
209.5900000 0.1837500
…
…
…
****
AtomSymb2 0
…
…
****
Notice I deleted the first two lines and you should also delete the last one (END)
I hope this helps!
PS Maybe you could also try B3LYP/lanl2dz straight at the route section, this will use a quasirelativistic pseudopotential in heavy atoms like I and In (if it reaches the fourth row, which I’m not sure of) while using a double zeta quality basis set (close to the number of functions you’d get with 6-31G). I am not aware of the quality of this level of theory when it comes to calculating nuclear shielding tensors, so I can’t be liable if it doesn’t provide accurate results 😀
Dear Joaquin,
I would like to post here a question that is blowing up my mind. This question is related with TD-DFT in Gaussian: I want to compute the energy of the first singlet excited state of ethene, so I have optimized the geometry of ethene in its fundamental singlet state (B3LYP/6-311+G(d) OPT, charge 0 multiplicity 1) and, taking the last geometry of the optimization, I have launched a TD-DFT calculation with a simple header (B3LYP/6-311+G(d) TD(singlets,root=1,nstates=1), charge 0 multiplicity 1). Until here, all is quite normal, but some questions arise from now on:
1.- I mispelled the TD-DFT calculation header writting down “UB3LYP” in place of “B3LYP” and the results were quite different in both cases. What is going on here, then? Gaussian website http://www.gaussian.com/g_tech/g_ur/k_td.htm states that TD-DFT singlets option is only effective for closed-shell systems. From this sentence, I understand that Gaussian does not matter about computing a TD-DFT an UHF system of a RHF system since it will take RHF wavefunction so, which is the origin of this difference?
2.- Since I want to know the energy of the first singlet excited state, can I optimize the geometry of the triplet ground state of ethene (UB3LYP/6-311+G(d), charge 0, multiplicity 3) and then, launch a TD-DFT calculation with the header UB3LYP/6-311+G(d) TD(singlets,root=1,nstates=1), charge 0, multiplicity 3)? If this is correct, which energy would be more accurate for the first singlet excited state: that calculated from the ground singlet state or that computed from the ground triplet state?
Thank you in advance for your response and your time!
Jose
Dear Dr.Jacquine,
I have a nuclesoides with a first solvation shell i got from an MD run. Can i compute the IR spectra in Gaussian of the nucelsoeds only without the accompanying cluster of water molecules.?..Also, which is better, when optimizing the geometry first with Gaussian, shall i constrain the water molecules, or treat them as MM using the ONIOM method or optimize the whole lot at the QM level with which i’m going to produce the IR spectra.
Thanks
Marawan
Hi there
I am quiet new to using gaussian/gaussview and currently I am facing a bizarre situation.
I have done a Scan (relaxed using Opt and modredundant) by gaussian 09 and everything was fine. But when I am trying to open .log file in gaussview (both 3 and 5) it complains about the redundant coordinates (specificly those lines that I have defined the range of values for scan). finally it says that the structure is incomplete and just shows the final geometry. It is obvious that in results menu non of the scan and optimization are active.
I appreciate if you can help me out
Abn
———————————————————
%chk=C:\Users\abnnor\Desktop\temp\Job1.chk
%mem=4000MW
%nprocshared=4
# opt=(modredundant,maxcycle=1000) rhf/6-31g(d) nosymm
geom=(connectivity,cangle,cdihedral) scf=tight test trackio
First Optimization of the ButanDiOl
0 1
C 1.74509157 -2.25272303 -0.88406810
C 0.92534837 -1.08869149 -0.34995131
C 1.66130851 -0.23438183 0.68531752
C 2.85550967 0.54920221 0.14892945
O -0.22690557 -1.65983209 0.22552993
O 3.47738020 1.30641706 1.15367746
H 2.61468044 -1.91225658 -1.43507074
H 1.13442131 -2.85144139 -1.54934156
H 2.07583182 -2.88660068 -0.06758621
H 0.63355875 -0.45464397 -1.18788653
H 1.98386020 -0.88526917 1.49620406
H 0.96496602 0.48000684 1.11940626
H 2.53423145 1.25923231 -0.60302454
H 3.57742218 -0.11384424 -0.32100020
H -0.80412139 -0.97382491 0.53144329
H 3.85073556 0.72328780 1.79986761
1 2 1.0 7 1.0 8 1.0 9 1.0
2 3 1.0 5 1.0 10 1.0
3 4 1.0 11 1.0 12 1.0
4 6 1.0 13 1.0 14 1.0
5 15 1.0
6 16 1.0
7
8
9
10
11
12
13
14
15
16
B * * A
A * * * A
D * * * * A
D * 3 4 * R <————-gaussview complains about this two lines.
D 2 3 4 6 S 24 15.000000 <————-
—————————————————————————————————–
these two lines are looking like this in .log file
B * * A
A * * * A
D * * * * A
D * 3 4 * R <————-
D 2 3 4 6 S 24 15.000000 <————-
Try eliminating the first three lines of the scan input, i.e.
B * * A
A * * * A
D * * * * A
Do you have a specific error message in the log file?
Hope this helps
Hello Dr. Barroso:
I have come across a paper [J Comput Chem 30: 2752–2763, 2009] regarding various Density Functions for use of determining geometric parameters for zinc complexes. In one of their tables (2) they describe five different basis sets together with the valence basis set considered for each of the atom types that make up the Zinc complexes. For example using
6-31G(d) All Electron, they go on to describe valence basis set of:
6/6631/31/1 for Zn;
6/631/1 for S and Cl;
6/31/1 31 for C, N, O;
and
31 for H.
I am wondering if you might be able to help me understand the meaning of this? Did they apply different basis sets to each atom during their calculation and is this possible in Gaussian using the GEN command? IF so, could you provide any guidance on how this type of job might be set up?
Thank you for your time and knowledge!
brian
Dear Brian,
I’m very sorry for the delay of my response. What you have there is the full expression of a basis set; they all correspond to 6-31G(d) but for every atom you need different amounts of basis functions. They all use 6 primitive gaussian functions for all core electrons (contracted all in the first part, “6/”). The rest of the numbers indicate how many primitive functions are used in each shell.
For a detailed explanation I suggest you to check Levine’s book “Quantum Chemistry”. Chapter 15
I hope this helps
Estimado Dr.
Estoy haciendo un cálculo de un TS en el gaussian y el resultado que me da con HF y DFT es una frecuencia imaginario que es la que no necesito y la que quiero me da positiva, al aumentarle el nivel al calculo como un MP2 ya me salen casi 4 frecuencias imaginarias incluyendo la que necesito.
Le agradecía su ayuda
Diana
Estimada Diana,
Encontrar TS’s es prácticamente un arte, y un arte obscuro diría yo. Te recomiendo que partas de una estructura minimizada en la que puedas deformar la variable que te interesa a modo que en un segundo cálculo lleves la estructura al TS deseado. Yo lo probaría con ambos niveles de teoría si tienes las instalaciones adecuadas.
Otra manera de hacerlo sería partir de tu 2o archivo, con 4 freqs imaginarias, y arreglar las 3 que no te interesan para que en el cálculo subsecuente te quedes solo con la necesaria. Sin embargo, recomiendo el uso de un nivel alto como el MP2.
Espero que te sirva!
Saludos!
#Gaussview-error
Dear Joaquin,
When trying to load the checkpoint file of a calculation in GaussView sometimes I get the message error “CConnectionGFCHK::ReadFile()” Cannot find File”.
It looks like I get this error message somewhat arbitrarily. I mean, on the same machine, using the same versions of Gaussian and Gaussview, the same kind of job (i.e. different molecules with the same keywords) sometimes Gaussview reads the .chk file and sometimes not. At least the results are consistent in as much as the same input file generates a .chk file that gives the same error message.
Have you find this kind of problem?.
I use Gaussian 03 + Gaussview 4.1. on a Windows XP PC.
Thanks.
Pedro Alberto.
P.S. Following your recipe to visualize the NBO orbitals, I run a test with one badly behaving .chk files and found that Gaussview loads the .fch file without problems. Magic?.
Hola Pedro,
I have found that same error when trying to move a chk file between computers with different architecture (64 vs 32 bits). It would be very useful if you track all the variables that make a file easy to open or not by gaussview.
Maybe you should try to always work with fch files and not with chk ones. Could this be it?
I hope this helps!
Dear Sir,
I have tried to calculate the exact polarizablity values by giving the keyword ‘polar’ using g09. In the output file, I am getting ‘*******’ instead of the numbers as shown below.
Exact polarizability:******** 0.0001794.519 0.519 -0.063 278.533
Approx polarizability:******** -0.0033140.674 6.210 -0.113 469.161
Please tell me how to solve this problem and get the numbers.
Those stars ******** mean the number you are getting is out of range and therefore cannot be printed. This usually means the level of theory you are using is too low or too incomplete. Try searching in the literature similar calculations performed on similar systems to yours and use their reported level of theory.
I hope this helps!
thankyou
Dear Dr.Joaquin,
I’m asking how can i get the vibration spectra from a QM/MM MD trajectory using ORCA and 0.5 fs timestep. I’m saving the dipole moment at each step then finally i got a .dat file contains the time step with the 3 dipole moment coordinates (mux, muy, muz). I’m using the AMBER ORCA interface for a nucleoside dissolved in a box of water and the nucleoside is the QM part. There’s a tool in VMD but as i can understand it does not require the dipole moment.
Full of respect
Marawan
Dear Marawan, I have no experience working with orca. Im sorry but I can’t help you this time
Have a nice day
Dear Dr.Joaquin,
Could you please even suggest a pathway. I guess it’s a common procedure from all softwares and not directly connected to ORCA. From what i can understand i have to calculate the dipole-dipole correlation function then Fourier transform. I didn’t find any tutorial for such procedures unfortunately.
Full of respect
Marawan
Dear Dr.Joaquin,
I’m a regular reader of your blog and found it really useful in solving many of the tricky things associated with gaussian.
I have a problem in viewing the output file for a gaussian calculation in gaussview 5.0. The calculation have been done in g09.
I have optimized the structure of my compound(polar) in both vacuum as well as solvent(IEFPCM model) using b3lyp/6-31G++ basis set and got a normal termination of gaussian process for both the jobs.
But when I load the output file of the solvent optimized compound in gaussview I got the following error immediately after opening the file in gaussview:
CConnectionGLOG::Orient_Dipole_Derivative()
Unable to orient dipole derivatives.
Kindly help me in this regard.
Thanks in advance.
Hello Aravindan
I have never seen this error before. This kind of messages in gaussview are usually related to some kind of error termination in the log file; I suggest you check the log file for any error messages. It could also be a bug that could be overlooked but it would be better to check. Remember that gaussview is not the important thing to look at but the log file.
If I find a better solution I will let you know.
Have a nice day!
Dear Dr.Joaquin,
Thanks for your immediate reply and will definitely see the log file for errors.
Have a nice day.
I am also facing same issue, although it’s Normal terminated. I could not able to collect Gibbs free energy from Frequency calculations. please send me solution.
Good afternoon sir,
we are running TD-SCF energy calculation on a particular molecule. Sir, what would be benefits if we calculate it by for more states, e.g N= 6. 12 ..100 and so on.
Another comment regarding my above question is that what is the importance if we also mark the state of interest, root =1, 2…( option given in gaussian)
thanks sir,
waiting for your comment sir.
Hello bhat,
The more states you include the better is your description of the available space but it will take longer to calculate, much longer. Sometimes it is not necessary to have such a detailed description of the excited states and that is why gaussian allows you to focus on a particular state that is close to the phenomenon you are studying.
I hope this helps
Good evening.
Please can you help me how to calculate solvation energy in Gaussian 09?
I know, that it is difference between the gas phase and the solvent phase.
But, there are many energies in Gaussian 09 outputs.
Which of these are correct for solvation energy calculation?
Thank you very much for your help.
# genecp keyword
Dear Dr Barroso
I have done full geometry optimization and frequency calculations for Ru-NAMI-A (an anticancer drug)at UB3LYP/(LanLD2Z+6-31G(d))level in gas phase by employing the Gaussian 03 package.
Input file for geometry optimization and freqency :
# ub3lyp genecp fopt freq
Title
0(charge) 3(multiplicity)
Atomic coordinates
…
…
C N S Cl O H 0
6-31G(d)
****
Ru 0
LANL2DZ
****
Ru 0
LANL2DZ
The result was HF=-2714.1754994 that is very different from that obtained by RHF/3-21G (for all atoms)which is -7022.352913 in atomic units reported by Knapp-Mohammady et al on quantum-chemical study of Ru–NAMI-A. I don’t know if this difference is normal or something is wrong with my calculations. I would grateful if you could help me.
I look forward to hearingg from you.
Yours sincerely
Yes, of course it’s normal. You have used a higher level of theory; your calculations are more accurate. I guess the reference is an old one. To begin with you are using many more basis functions plus a quasi relativistic ecp.
I hope this helps
Dear Dr.Joaquine,
I’m struggling to perform a simple ONIOM calculations in Gaussian. My system is a nucleoside with a few water molecules. I’m using B3LYP/AMBER for the QM/MM systems respectively. Becasue some MM parameters are not availbale with official amber shipped with Gaussian, i’m defining an external parameters file (gaff.parm) using the hardfirst option, but i always got the following error:
Read MM parameter file:
Define OM 1
Expected a string in RdPar
Error termination via Lnk1e in /apps/gaussian/g09c01/g09/l101.exe at Tue Dec 18 15:27:57 2012.
Here’s the first few lines of my input:
%nprocshared=8
%mem=5gB
%chk=test
#P opt freq oniom(b3lyp/6-31g(d,p):amber=hardfirst)=embed scrf=(solvent=water,oniompcm=x,pcm) geom=connectivity iop(6/7=3,6/79=1) scf=tight
Displayed atoms
0 1 0 1 0 1
c-CQ
N-NC 1 1.36021158
C-C 2 1.34303418 1 119.42324725
N-N* 3 1.42424438 2 118.19798996 1 0.64340879 0 H
C-CM 4 1.36872655 3 118.81644680 2 -0.93789134 0 H
N-NC 5 1.31200307 4 124.04723261 3 0.58490013 0 H
C-CT 4 1.47797132 3 120.19317849 2 176.38518847 0 H
O-OS 7 1.41809007 4 108.81074718 3 -133.87546007 0 H
and here are the last few lines:
59
60 61 1.0 62 1.0
61
62
63 64 1.0 65 1.0
64
65
@parm99.dat
Could you please comment.
Full of respect
Marawan
Dear sir,
How to write input file for dimer calculation of hydantoin-5-acetic acid in guassian-03
with regards
Devi
hello,
i would like to carryout counterpoise calculation for the interaction energies of a dimer using gaussian09. I have calculated the individual monomer’s energy separately and i calculate the interaction energy
IE= total energy of the dimer – {Emonomer1+Emonomer2}
i have also calculated the energy of the dimer with counterpoise=2 keyword in gaussian, it gives the counter poise corrected total energy and it also gives the energy of monomers. my question is whether a single calcuation using counterpoise keyword is enough to calculate the interaction energies? or as i tried earlier by calculating the Emonomer separately and then i need to take energy of the dimer from counter poise calculation?
thanks in advance
vijay
Hello Vijay,
When you calculate the energy of a two component system, as you did originally, there is a slight error due to the superposition of the basis set on each of the components. This Basis Set Superposition Error (BSSE) is corrected through different methods like the Counterpoise method you used. This corrected energy is the one you want to use in your equation:
IE = total corrected energy – (Emon1 + Emon2). Check if the energy of the monomers in the counterpoise calculation matches the ones you calculated separately; it is crucial that you have maintained the same level of theory or the comparison will make no sense.
Hope this helps. Happy new year!
dear Dr.Joaquine,
many thanks. and i can understand that and again i would like to ask, does a single counterpoise calculation enough to calculate the interaction energy? if so, then there is no recessary to calculate Emon1 & Emon2 separately. Right?
cheers
vijay
Hello again, Vijay
If you indeed obtain the separate energies of the monomers within one single calculation then yes you can only carry out the counterpoise calculation and the do the substraction on your own
EI = Corrected_dimer_energy – (Emon1-Emon2)
I don’t remember that Emon(i) is given within the counterpoise calculation but if you say its there then I believe you.
Have a nice day!
thank you…. Dr. Joaquine
Hai,
I have a small confusion. I did optimization for both monomers and dimer using G09W. I did IE calculation by simply E(Dimer)-(E(Monomer1+Monomer2)) and the calculated value is 5.43 kcal/mol. I did counterpoise calculation also and the output is as below,
Counterpoise corrected energy = -5908.087362190423
BSSE energy = 0.009082833853
sum of monomers = -5908.081030077537
complexation energy = -9.67 kcal/mole (raw)
complexation energy = -3.97 kcal/mole (corrected)
Now, If i want to calculate IE which is counterpoise corrected, which energy i have to use for dimer i.e. Counterpoise corrected energy( -5908.087362190423) or sum of monomers(-5908.081030077537) .. ?
or simply IE=(Counterpoise corrected energy)-(sum of monomers )
Hi Shivanand,
The slight difference you are noticing (5.43 against 3.97 kcal/mol) is most probably due to a slight difference in monomers conformation from the isolated state to the dimer.
In other words: If you optimized A and B separately and then you optimized AB, the conformation of A in AB might be slightly different to the conformation of isolated-A because of the influence of B in AB. Same holds for B.
The first procedure you mentioned is called supermolecular method and the way I like using it is backwards from what you used: I first optimize AB and then manually isolate A and B and calculate their separate energies WITHOUT optimizing (so their respective conformations already carry the influence of the other monomer).
In short you should use the counterpoise corrected energy but notice that the CP calculation is doing what I stated above, calculating the separate energies at their conformations INSIDE the dimer.
I hope this helps. Have a nice day
Dr. Barroso,
I am currently investigating several high spin complexes and am trying to optimize the main groups separate from transition metals using genECP option. I am able to achieve a “converged” calc, however if perform a subsequent stability calculation on this “converged” structure the output reads, “wavefunction has internal instability”. Is it possible for you to explain how one is able to achieve a global minimum from this state? Thanks for your help!
Dear Dr. Barroso,
I truly appreciate your running this wonderful blog. I bet this site will make a legacy among Gaussian users!
I am confronting with a technical issue in TD-DFT calculation.
When I would like to calculate the optimized structure of the 1st triplet state
(starting from the optimized singlet ground state),
1. perform “td(triplets,…) opt” calculation with spin multiplicity of 1.
2. perform usual “opt” calculation with spin multiplicity of 3 (instead of 0).
Which one should be correct for getting optimized T1 structure?
What is the difference between scheme1 and scheme2?
And it would be also great if you will post a simple tutorial on
NTO analysis sometime in 2013 🙂
Thank you again for your blog.
from a huge fan of yours 🙂
Dear Dr.Barooso,
I’m asking how can we do Potential energy distribution (PED) analysis for vibrational spectroscopy.
Regards
Marawan
Hello:
I’m trying to optimize the geometry of 4-Iodosalicyclic acid at B3LYP/6-311++G** but the gaussian o/p is link dying with the error: “Atomic number out of range for 6-311G basis.
Error termination via Lnk1e in C:\G03W\l301.exe at Fri Jan 25 14:40:03 2013.”
Can you give me a suggestion how to get rid of this.
Bijan K Paul
Department of Chemistry and Biochemistry,
University of Colorado at Boulder, USA.
Hello.
It means the atomic number is out of range for the 6-311++G** basis set as defined in Gaussian; in this case, it is pretty obvious that it refers to the Iodine atom. Go to http://www.emsl.pnl.gov/forms/basisform.html
and retrieve the appropriate form of this basis set for Iodine (I believe this link is in the ‘Links’ section of this blog). Then, search another post in this blog on Gen and ECP keywords so you know how to insert it in your input file.
Have a nice day!
Dear Dr. Joaquin Barroso
Is this the correct input file for calculating the single point energy of a Ru-based complex at the UB3LYP/LanL2DZ(f)+6-311++G(3df, 2pd) level:
# ub3lyp genecp scf=tight
Title
(charge) (multiplicity)
Atomic coordinates
…
…
C N S Cl O H 0
6-311++G(3df,2pd)
****
Ru 0
LANL2DZ(f)
****
Ru 0
LANL2DZ(f)
Best regards
Brier
Yes, the input seems fine. If this is the input to the calculation you wrote about in the other comment, the one where you have a crash after 19 hours, then I insist on using SCF=QC
Have a nice day!
Dear Dr. Joaquin Barroso
I hope I’m not bothering you with my questions. My Gaussian geometry optimization and frequency calculation at the UB3LYP/(LanL2DZ+6-31G(d)) level fails with this error message:
Error termination request processed by link 9999.
Error termination via Lnk1e in C:\G03W\l9999.exe at Wed Jan 23 09:50:20 2013.
Job cpu time: 0 days 19 hours 42 minutes 50.0 seconds.
File lengths (MBytes): RWF= 77 Int= 0 D2E= 0 Chk= 8 Scr= 1
I’ve tried increasing the number of optimization steps by specifying OPT=(MaxCycle=500)that I chose the number 500 without rhyme or reason and I got the same error at the same point (i.e after 19 hours 42 minutes). I don’t know how to choose the number of optimization steps and If it is useful for this error or not? How about OPT=(restart,MaxCycle=n)?
Best regards,
Brier
Hi Brier,
That error you wrote above only means that the calculation is being aborted but it doesn’t say why. Just above it, in your output file, there must be a bit more of information as to why the computation crashed. After almost 20 hours, even on a small processor, I can say that your calculation is well set but maybe you are running out of disk and not out of memory; maybe the geometry is not converging to a minimum, have you checked how your molecule looks like after crashing?
I’d need a little bit more of information to help you but just for the sake of trying something, use scf=qc. If there is a problem with the SCF convergence then this might be helpful, but as I said, I need more information about the output in order to point you in the right direction.
Hope this helps!
Dear Dr. Joaquin Barroso
The input file for the calculation that I got error is here:
# ub3lyp genecp opt freq
Title
(charge) (multiplicity)
Atomic coordinates
…
…
C N S Cl O H 0
6-31G(d)
****
Ru 0
LANL2DZ
****
Ru 0
LANL2DZ
and the error message includes this too:
Optimization stopped.
— Number of steps exceeded, NStep= 144
— Flag reset to prevent archiving.
Best regards
Brier
I am trying to change the theshold for the Wiberg indices to another decimal point. I have NBO 3.0 on gaussian 09
can anyone write how hyperpolarizablity is calculated in Gaussian 03
I am Goutam, currently doing PhD in India. I am a regular visitor of your blog and find it quite useful.
I have a molecule containing Ge-O single bond. On doing NBO analysis in Gaussian 03 it does not print the hybridization of Ge-O bond. Is there any specific command in NBO which will enable me to the same.
Dear Sir,
Greetings. After the excited state optimization i could get the UV spectrum. How can i get the fluorescence spectrum for the same. Can you please tell me how should i modify the route section to get both at the same time in TD-DFT excited calculation.
And also i would like to know how to draw nano cluster structure easily, and with various size.
thank you sir.
Dear sir,
How to give the route section to get the information about density of states of the dye molecules.
thank you
I assume you are asking about Gaussian, right? Well, as far as I know there is no way to calculate DOS with it. Maybe you should contact Gaussian’s help desk.
Sorry. Have a nice day
Hello Sir,
I got Error # 2070 while submitting the input file
ASH
Gaussian (I’m assuming you are using it) has very cryptic error messages. I need more information to be able to help you.
Have a nice day
Hello Sir,
I need to calculate the optical absorption of molecules complexed with iron, I would ask for some references on how to perform this calculation in gaussian. Could you help me?
Many thanks,
José Gadelha
Hello José,
Since this is not yet my current area of expertise I can’t point out to the best references possible. However I do recommend to look for the book “Exploring chemistry with electronic structure methods” by Frisch & Frisch. In it you will find a comprehensive tutorial on this kind of calculations.
I hope this helps!
Hello Sir
I will calculate the binding energy between polymer and drug with oniom (DFT:UFF) in solution , but error occures :
Out-of-memory error in routine PCMQM2 (IEnd= 207619281 MxCore= 196195310)
Use %mem=199MW to provide the minimum amount of memory required to complete this step.
Error termination via Lnk1e in d:\l502.exe
also %mem up 200 error 1101.exe
thanks
You seem to be running out of memory. Try splitting the read/write files with the use of the %rwf utility. Search in google “efficient use of memory site:gaussian.com”
It may not work if you are using a very small computer. I would need more details about your working system to help you.
Have a nice day!
thank you
Dear Dr. Barroso:
It is niceto find this kind of support for Gaussian users. Thanks for that!
My question, althogh related to the use of Gaussian, might be a little off from your research. No harm done by asking though, right?
Is there a “symple” way to print out or extrac off the kinetic energy associated with a configuration interaction calculation (that is, the correlated kinetic energy)?. I have checked and tried different links and overlays with no success.
Your help on the matter will be greatly appreciated.
Thanks again!
Rogelio
Hola Rogelio!
That is an interesting question (which means I don’t have the answer to it). Gaussian usually displays a separate line with the kinetic energy, i assume you have tried finding it. I’m sure the guys over at gaussian help desk will be more helpful.
Sorry. Have a nice day!
Dear joaquin,
I have a question regarding QMMM calculation in Gaussian and would be grateful if you can kindly help me.
I am trying to do the frequency calculation with ONIOM in Gaussian. For the MM part I use UFF because I don’t want to go each to atom type specification. At the same time I wanna impose UFF to read the charges that I am giving as input. (I know we can give charges as input in AMBER but as I said I don’t want to go through atom type determination). I’d grateful if you can guide me on how to use customized UFF in ONIOM.
Many thanks in advance,
Tara
Hello, I’m trying to convert a .chk file to .fchk file. I tried to use the formchk utility in Gaussian 03. but whenever i select the .chk file, it shows error like NtrErr from FileIO like this. usually i submit my jobs at supercomputer using g09sub command. all my files are there. i tried “formchk -3 filename.chk filename.fchk cmmand” there. but the supercomputer does not recognize this command. it says-not a typo, command not found – like this. but I really need this thing. how can I do that?? I’m new at computational. would I get some help please??
Have your calculations finished with an error or were they completed successfully? The message you are getting seems to suggest they didn’t finish properly. Try to only type formchk file.chk file.fchk also try using formchk -3 file.chk file.fchk without any further command.
Also, maybe the formchk utility is not properly installed in which case you need to talk to your system’s administrator or the holder of the Gaussian license at your institution.
I hope this helps! Have a nice day
Dear Dr. Barroso,
I am trying to calculate the valence IPs of a radical species using OVGF/6-311++G** model. Since it is a radical, it has alpha (55) and beta (54) spins. When i tried to run the calculation, i found that the job was incomplete, but without any error messages. I found that the job exactly stopped after printing the summary of results for all the alpha spin-orbital in the radical and when exactly i started print the beta orbitals. A brief snapshot showing the last few lines of the output are as follows:
—–
Summary of results for alpha spin-orbital 41 OVGF:
Koopmans theorem: -0.21098D+00 au -5.741 eV
Converged second order pole: -0.10502D+00 au -2.858 eV 0.854 (PS)
Converged third order pole: -0.17828D+00 au -4.851 eV 0.927 (PS)
Outer Valence Approximation: -0.15376D+00 au -4.184 eV 0.910 (PS)
DD1Dir will call FoFDir 12 times, MxPair= 408
NAB= 1640 NAA= 820 NBB= 780 NumPrc= 8.
Summary of results for alpha spin-orbital 42 OVGF:
Koopmans theorem: 0.15147D+00 au 4.122 eV
Converged second order pole: 0.13696D+00 au 3.727 eV 0.985 (PS)
Converged third order pole: 0.13850D+00 au 3.769 eV 0.983 (PS)
Outer Valence Approximation: 0.13828D+00 au 3.763 eV 0.983 (PS)
Orbital window will be selected automatically
Beta HOMO is orbital 40
GREENY has selected a window containing beta orbitals
11 through 41
from symmetry group number 1 of the 1 total symmetry operations
————
I did not find any error messages in the logfile. I gave sufficient wall time and memory.
I shall sincerely appreciate if you could kindly help me to handle this issue. Also, I shall be grateful, if you could kindly share with me some of your suggestions when calculating the IPs for the radical anion species. Is there any particular model do you suggest?
Thank you….
Hola Profesor, hace un tiempo que estoy trabajando con gaussian, y tengo unos resultados experimentales de XAS de complejos de metales de transición, estuve leyendo algunos papers sobre cálculos para simular los espectros de XANES, hay varios que usan TDDFT, quisiera saber o ver algún ejemplo del input para realizar dicho cálculos,
Gracias!
Hey there,
I was interested in freezing all the bonds in 2 molecules and studying the van der waals forces. I can’t seem to massage Gaussian enough to do this without finding an error. Any tips?? thanks. ( I want to use experimental values for the bond lengths instead of Gaussian opt)
Could you please provide more information about the error produced? If you are not studying any H bond interaction, I would advise you to relax the positions for all H atoms, i.e. just optimizing those atoms, since their locations obtained from an Xray diffraction experiment are somewhat bogus. In order to do so include the following keyword after opt: opt=(readfreeze) and then after a blank line at the end of the file include the following line:
noatoms atoms=H
–blank line–
I h ope this helps!
I had been trying to optimize the structure of B2H6 (at B3LYP/6-311++G(d,p) level). While giving the input, I saw that even if I didn’t specify any bond between the two B atoms, it’s taking a single bond always. If I delete it and save the corresponding file as a new input, it still shows the same. Even after optimization, the B-B bond remains intact.
I’ll be highly obliged if I get any solution regarding this.
Thanking you in advance…
I assume you are building the molecule with gaussview, if so I wouldn’t worry about that bond since its just a line GV draws between two atoms whenever the distance is below a certain threshold. However, if your route section specifies geom=connectivity it would be advisable to go the connectivity matrix at the end of your input file and delete the line wherever it specifies a single bond is to be considered between B1 and B2. Say B1 is atom number 1 and B2 is atom number 5 in your coordinate section, then a line looking like
1 5 1.0
must be deleted from the connectivity matrix.
I hope this helps, thanks for reading!
Dear Sir,
Thank you so much for your response. That will help me a lot!
Have a good one……..Cheers!
-BKP
Dear Professor,
I’m new to QSAR.. Can you share your materials to learn QSAR from scratch?? I saw in one of your post that you sad you are preparing the materials for students… Though, I got the basics from kubinyi and other articles… I don’t find any materials that direct us to improve the model predictivity… I followed tutorial in sybyl and my predicted R sqaure is low 0.308. Now how to proceed? can you guide me with any materials or solution?
Thank you..
Pavithra.
Dear Pavithra,
Unfortunately I use the old blackboard approach so I don’t have any slides or powerpoint presentation to share with you; if I had it I would have uploaded it a long time ago. Kubinyi’s articles are a great place to start. I think I will try to prepare something and post it on the blog but for sure it won’t happen soon.
Sorry. Have a nice day and thanks for reading the blog!
Thank you professor…
Dear Sir,
I would be grateful if you could explain me that how can I calculate Fukui functions on different atoms of a molecule using B3LYP 311-G ++ dp basis set G03 program. I have been successfully run the DFT of the organic molecule 2,2’-(1Z.1’Z)-(4,4’-methylenebis(4,1-phenylene)bis(azan-1-yl-1-ylidene))bis(methan-1-yl-1-ylidene)diphenol and now i want to calculate Fukui function on each atoms of this organic molecule. Please advise me how can I calculate fukui function.
Thanking You
Vinay Jaiswal
Palease read the post titled ‘how to calculate Fukui function’ in this blog for detailed instructions. You can search for it with google.
Hope this helps
Hi
Sometimes there is a warning in molecular orbital calculation like “Largest MO coefficient is 0.138235 x 10^3^, be careful about the interpretation….”
them after finding of the different segments contribution by GaussSum2.2 software in a molecule the percentage is not correct, for one segment is -31%, for the other one is 123%.
How can I get ride of this warning?
What level of theory are you using? This could be related to the use of the wrong basis set (too large or too small depends on the problem and the method employed)
Send me more info so I can help you properly.
Have a nice day!
Dear Dr.Joaquin,
I’m trying to get the pure DFT binding energy for a ligand using ORCA. If an anion is included, i should use diffuse functions in the basis set. I’m asking if this statement is also true if i want to use a very large basis set such as the def2-QZVP to get rid of the basis set superposition error.??..I have read that Triple Zeta quality basis gives a BSSE of 10-20 % so, i want to use the Quadruple Zeta type.
Full of respect
Marawan
Dear Sir:
Can you please give me some instructions about how to calculate the aromaticity indices: average two center indices (PDI), average two center indices (ATI), aromatic fluctuation index (FLU)?
Bijan.
Dear Sir:
Can you please give me some instructions about how to calculate the aromaticity indices: para-delocalization index (PDI), average two center indices (ATI), aromatic fluctuation index (FLU)?
Regard,
Bijan.
Dear Joaquin,
Thank you for such a terrific blog! I just started using Gaussian recently, and your blog has provided me very useful information. I have a question about relaxed PES scan. Gaussian prints a summary towards the end of the output file which gives the eigenvalue (energy, I suppose?) and geometry (all the bond distances, angles, dihedrals) for the structures optimized at each step during the relaxed scan. In some of my output files, however, the eigenvalues appear to be “******” instead of any numbers. For example:
……
Summary of Optimized Potential Surface Scan
1 2 3 4 5
Eigenvalues — **************************************************
R1 1.86918 1.86755 1.86649 1.86702 1.86595
R2 1.09213 1.09178 1.09142 1.09080 1.09049
R3 1.09229 1.09183 1.09150 1.09259 1.09178
R4 1.09746 1.09680 1.09597 1.09437 1.09370
…….
I could not find a proper solution to this through googling. Do you know how I can extract the energy for the final optimized structure in each step? I want to plot the energy vs. bond distances (that I constrained for the scanning), and I figured out how to extract the distances. Also, do you know how I can avoid such problems in the future?
I’m desperately looking for an answer, and would appreciate any insight you could offer. Thanks a lot!
Jen
I will calculate thermochemistry and frequency of a polymer with method : freq b3lyp/6-31
but the result is ” No file to extend for
IUnit= 1 — out of disk space.Error termination in NtrExt: NtrExt called from
NtrExt.”
I have coefficient space and only 8% occuped,
Hello!
I have a question which is bugging me for a while now:
How do you visualize ESPs using contour lines (just like your header up there).
I don’t have any problems visualizing it in general I just would like to use this type of visualization. Do I need a special program for that or is GaussView capable of doing that?
Thanks a lot!
Great blog btw!
Philipp
ok, Molekel 4.3 does the trick… anyway, is there a possibility to do the same with Gaussview 5? I don’t think so…?
I have done a relaxed PES scan on a dihedral angle and everything is fine (:D). now I want to extract the geometry of system in every step of the scan (the optimized one) to do the MM calculation and compare them with QM results. Regardless of the type (z-matriz or cartesian) is there anyway to force Gaussian to print out geometries? I know this information is there even in the .log file (when we open the log file in gview it shows the transition between each step). I tried to extract data from gview (exporting data from edit menu) but it would get cumbersome soon as I have 73 scan point in one of my 10 different molecules. so manually doing this in gview is not an option. I tried to read the log file to see where the information regarding the geometries is printed but it was unsuccessful. any comment on that!
Hello Sir:
Can you please let me know about the interpretation of an IRC plot? What does an IRC calculation indicate and how important is it?
Waiting for your response
Have a good day!
Bijan.
It is very important! An IRC plot will display the energy profile during a chemical change/reaction; i.e. the change in energy during the course of a structural modification that will lead to a chemical transformation whether it be monomolecular or polymolecular.
Minima on this plot will correspond to chemically available structures (reagents, products, intermediates) while maxima correspond to transition states (which cannot be isolated).
Thus IRC calculations are performed to study reaction mechanisms.
I hope this helps. Have a nice day!
Hello Joaquin,
Sorry for a very basic question: what review, book or blog would you recommend to someone who wants to use computational biochemistry as instrument (not for research in this field), and who tries to quickly grasp limitations and successes of methods used to model chemical reactions? Something that answers following questions:
– which methods provide the most precise correlations with physical measurements, for which types of bonds, forces, molecules, reactions?
– which methods are the most suitable for organic molecules/reactions, especially enzymatic?
– which approximations and heuristics are the source of modeling errors?
– which simulations are the most computationally intensive and why?
– what is the usual size of molecule(s) participating in reaction, like a dozen of atoms, or, as in molecular dynamics, a few hundred-thousands?
Overall, I’m asking for the most appropriate source to begin with, your answer is highly appreciated and will save tons of time for sure.
Thank you in advance,
Igor
Hola Joaquin.
I’m Alessandra and I’m trying doing anharmonic calculations using g09. Do you have any experience with those? Do you think it is possible to start over an anharmonic analysis reading the derivatives from the chk file and specifying different threshold values for Fermi and DD resonances?
The documentation on the G09 website is quite obscure about it.
Many thanks in advance!
Suerte
Alessandra
pa: your post on relaxed PES scan is a pearl!
Hi Alessandra,
Sorry for the lateness in my response. I have no experience working with anharmonic frequencies but I would encourage you to take your question to Gaussian’s help desk. They are very efficient and prompt to help their users.
Thank you very much for your kind words about my blog!
Have a nice day
Dear Sir:
I’ve been reading a nice article on intramolecular H-bonds in malonaldehyde: J. Phys. Chem. A 2007, 111, 8519-8530 (10.1021/jp073098d). The article describes a method of calculating IMHB energy as:
E(HB) = – (a03/2)VCP
In which a03 is described as the atomic volume element.
I have been finding difficulty in understanding the meaning of this term. Can you please let me know what does this mean (I mean the physical significance of the term) and how can this parameter be calculated in Gaussian?
Does it refer to H atom as such or is it different for the H atom in the molecule from an isolated H atom?
Your response will immensely help me in clarifying my doubts and better understand the matter
Looking for your response
Thank you very much
Regards,
Bijan.
Hello Joaquin,
Do you know how to construct a 2D-plot consisting of two rotors (i.e 2 dihedrals)? I’ve already extracted the values from my G09 output file. I’m baffled about how to plot the values. When I look at other examples, their Eigenvalues (on the y-axis after converting to kcal/mol) are all positive.
Why?
I don’t understand how the plotted values can all be positive when all of my Eigenvalues are negative.
My dihedrals are positive and negative, which is understandable because I did a 360 scan.
Thank you for your help,
Gail
You can always define a positive system by applying a unit transformation to your dihedrals, i.e. plot only the change in angle after each step, or in other words, use the original dihedral angle as your 0.0° value.
Also you can use relative energy values instead of the actual eigenvalues; if you started from the lowest energy conformation then all the energy values will become positive by definition.
I hope I’m not missing something from your question; if I did please do not hesitate to contact me again, I promise not to take so long this time 🙂
Have a nice day!
Dear Sir,
I am chethan, currently working on Sugar Chemistry using G09 suite (DFT calculations). The molecule contaisn more than 25 atoms with elements such as Sn, C H O Si etc. Currently am using LANL2DZ for Sn and 6-31g for C H O Si. (3-21g also used before). But these calculations are running for a long time and ended up with a some error related to symmetry or Berny optimization etc. It consumes lot of CPU hours without any fruitful results.
Following are my doubts
1. Is it possible to use only ECP with lower basis set for this kind of calucations, so that it save the computaional time and to get some rough optimized structure.
2 Is it possible to use only ECP for the calculations
Thanks in advance
Chethan
I have used the ECP+All electron basis set approach successfully before. If you specify lanl2dz for Sn as an ECP and also as its basis set while the rest of the molecule uses any kind of Pople basis set you should be doing fine.
Turn off the symmetry by including the NoSymm keyword in your route section, that ought to work!
Have a nice day
Buen día profesor Barroso. Felicidades por este espacio que seguro ha sacado a más de uno de muchos aprietos.
Estoy interesando en estudiar en enlace de varios complejos Metal-carbonilo. Para esto he visto que a traves de NBO se puede cuantificar el ‘bonding’ y el ‘back-bonding’ entre un metal de transicion y un ligando sencillo como el CO.
Acaso sabría usted como hacer esto ?. He leído sus previos post sobre NBO, así que creo que más o menos entiendo el resultado de mis cálculos. Sin embargo, no tengo idea de cómo calcular dicha cuantificación.
Le agradezco toda la ayuda posible.
Francisco Nuñez Zarur
Lo más sencillo es incluir la keyword BNDIDX en el espacio de NBO con NBORead en el route section. De ese modo tendrás una matriz con valores de indices de enlace entre todos los átomos de la molécula.
La otra (y que más recomendaría) es revisar la sección Second order perturbation analysis para ver las transferencias de carga CO -> MT
Genera un archivo de entrada para una molécula pequeña y córrela para observar estos resultados. A lo mejor y hago un tutorial en este blog.
Gracias por leernos!
#problem in optimization of metal complexes of phthalocyanine
Hi Dr. Joaquin
I have a master degree in organic chemistry and I have a little background on Gaussian and how to run small jobs like optimization and calculation of HOMO and LUMO energy gap in small organic molecules.
Now, I am trying to optimize metal complexes of phthalocyanine derivatives by using b3lyb/6-31+G (d,p) method. I completed optimization of Zn-Phthalocyanine with HF/3-21. But I couldn’t optimize the compound with the larger basis set.
Calculations were run on Pc [core i7-3840 QM cpu 2.8 GHz ,RAM (32), 64 operating system].
Could you help me to understand why it doesn’t complete?
I saw a question on your homepage related to ZnPc optemization and your advice to use LANL2DZ, I will be highly appreciated your help about this method?
Regards,
basma
Hi Bazhma,
What is the error you are getting? My guess is your PC is running out of memory. HF calculations will not get you published anymore. Try using that HF optimization as input for B3LYP optimizations and search for a page in gaussian called something like efficiency considerations; you can just google it. Therein you will see instructions to use %rwf (read write files) in order to partition your calculation in a more suitable way.
Hope this helps! Have a nice day
Hello
I am trying to calculate the HOMO LUMO for my system ! in some publication I saw they calculate the percentage like dxy energy -0.355 eV 12% !!!
publication figure 10 of ooms et al, Inorganic chemistry, 2007, 46, 9285-9293
I have system like VOCl3 , interested in vanadium , what do u suggest me to do !?use NBO?…. what command give me these percentage ?! I have read in your blog a comment back to 2010 that the calculations on G09 can not be seen by gaussview 03 this is the problem I have so I calculate on g03 ! I see some picture but can not be saved on Gaussview !!!! no save or copy icon !!! could you plz suggest another graphic software comparable to gaussview .
I do really appreciate your help.
Thanks
I would suggest either chimera or chemcraft. About the percentages, please send me a copy of the article so I understand better, because I’ve never heard of such a thing. Maybe its just the percentage of the dxy orbital into the hybrid which forms either the HOMO or the LUMO but I’m not sure if they indeed used NBO or not.
Have a nice day!
Hi Thanks for your reply !
I downloaded chimera, kinda confused it shows something but I am interested in getting like gaussview that show the MO surface for each level of energy ! is it possible with chimera?!
In chemcarft I have tried it asked for formatted file after doing that just show me energy level no MO surface ?! what should I do ?
I have pdf file of that article how I can send you !
Thanks again
Rosha
Thanks for your reply,
I already use the HF optimization as input for B3LYP optimizations and I have no error but the pc is stopped for 2 days at this step:
The electronic state of the initial guess is 1-A.
Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
Requested convergence on MAX density matrix=1.00D-06.
Requested convergence on energy=1.00D-06.
No special actions if energy rises.
The input for the calculation is
%chk=ZnPc_Br.chk
%mem=200mw
# b3lyp/6-31+g(d,p) opt optcyc=400
Title
(charge) (multiplicity)
Atomic coordinates
Does you mean I have to add (%RWF=1,1GB,2,1GB,3,1GB,4,1GB,5,1GB,6,1GB,7,1GB,8,1GB,8,1GB,9,1GB)
Regards,
Yes but mind your computing capacities. Try to contact a scientific computing facility near you to help you run these larger calculations.
Best wishes
Thanks for your kindly support, but I don’t have a scientific computing facility on my faculty. Can I complete this calculation on my pc or it’s impossible?
And could you kindly tell me with the best computing facility to complete our project?
Best Regards,
I’m not aware of any public computing facility because here at UNAM we have our own supercomputing favilities; try google for some place that can help you.
It is possible to finish it on your pc but it will take a lot of time. You just have to be very careful about how to distribute the memory and all.
Best wishes!
Hi Sir,
i am interested to calculate LDOS for ethyl benzene.
I dont know the keyword by which i can calculate LDOS of each atom in ethyl benzene.
Please help me sir.
Thanks
Prabhakar sharma
Hi Sharma,
I don’t think there is a keyword for calculating LDOS in Gaussian. Try another software like AOMIX.
Have a nice day!
Thanks so much for your kindly support;
I optimized the metal complexes of phthalocyanine derivatives using:
%chk=ZnPc-Br.chk
%mem=200mw
%rwf= 1,1GB,2,1GB,3,1GB,4,1GB,5,1GB,6,1GB,7,1GB,8,1GB,9,1GB,
# opt b3lyp/3-21g* geom=connectivity
Then, I do single point calculation using:
%chk=ZnPc-Br.chk
%mem=200mw
%rwf= 1,1GB,2,1GB,3,1GB,4,1GB,5,1GB,6,1GB,7,1GB,8,1GB,9,1GB,
# b3lyp/6-31g* geom=check guess=read
But, I have an error on frequency calculations due to size and I try many trials like (optcyc=400 or scf=xqc) and it doesn’t solve yet.
There are 438 degrees of freedom in the 1st order CPHF.
No file to extend for IUnit= 1 — out of disk space.
Error termination in NtrErr:
NtrErr called from NtrExt.
I will be highly appreciated your advice about this error about frequency calculation as I need to calculate the NMR theoretically.
Best Wishes
Dear Sir,
I am a beginner in the field of research and using gaussian03w.
Please suggest me,how i can calculate emission wavelength for a compound?.
Thank you
Hi,
I am beginner of gaussian09. I want to optimize a structure of isopropylphosphate. The isopropylphosphate contains -2 charge. However, when I don’t consider the -2 charge then I am getting expected bond angle, bond length and dihedral angle(close to experimental observation). My input file looks like this
%chk=isopropylphosphate1.chk
%mem=4GB
%nprocshared=8
# opt b3lyp/6-31++g(d,p) geom=connectivity
B3LYP
-2 1
C 0.02563200 -1.04646600 -0.06925500
C -0.22829000 -2.45701400 -0.57448600
O 1.17729100 -0.53167300 -0.83050600
P 2.46250500 0.12547100 -0.18386700
O 3.46510700 0.58633300 -1.14869600
O 2.08982600 0.87247900 1.21037700
O 2.79203000 -0.56586700 1.24942000
H 0.28518400 -1.06389900 0.99306300
H -0.47283000 -2.45333600 -1.64068100
H -1.05360000 -2.91582800 -0.02482200
H 0.66551000 -3.06743500 -0.42440900
C -1.13753943 -0.06386962 -0.29976870
H -1.12874945 0.26680910 -1.31735129
H -2.06543956 -0.55460743 -0.09221688
H -1.02660650 0.77890229 0.35010005
1 2 1.0 3 1.0 8 1.0 12 1.0
2 9 1.0 10 1.0 11 1.0
3 4 1.5
4 5 2.0 6 1.0 7 1.0
5
6
7
8
9
10
11
12 13 1.0 14 1.0 15 1.0
13
14
15
Therefore, I want to use -2 charge but I want to get the result of neutral molecule. How can I do that.
Any suggestion will be appreciated.
Thanks in advance
Sudipta
Hello Sudipta!
Maybe I’m not following but how can you expect to get the structure of a neutral molecule for a charged one? They are two different species!
If your experimental results were obtained for a neutral molecule then forget it, the charged calculation will never resemble the experimental (neutral) conformation.
If your experimental results were obtained for a charged molecule and you can’t reproduce the structure (but strangely you do it with the neutral calculation) then you might try to change the basis set which is highly polarized; I’d try 6-311G(d,p) (i.e. drop the polarization functions).
I hope this helps!
Hello Sir,
I tried to get the vibrationally resolved electronic spectrum using gausiian 09 program, but after some time it shows the error given below. If it is able to open the file, sir please suggest how to overcome this error. I also tried by generating .fch file. but it is showing the same error. Thanks
**********************************************************************
Generation of the Franck-Condon spectrum
**********************************************************************
Approx. of the electronic transition dipole moment: FC
Type of transition requested: ONE-PHOTON ABSORPTION
Data for initial state taken from current calculation.
Passed-in normal modes used.
Data for final state taken from checkpoint file “acetone initialfreq”
Error termination in NtrErr:
ntran open failure returned to fopen.
It seems to me you are making a call to either a corrupted or an non existing file. Please send me your input file and a copy of these last few lines in your output file so I can help you in a better way since yoiu don’t quote here the method for vibrational calculation.
Best regards
Hi,
Thank you very much for the reply. You have correctly followed what I meant. However, I tried with 6-311G(d,p) basis set but it doesn’t improve the result. Actually, I am at critical situation to explain my result properly. Otherwise, I need to prove that the results for two cases are same. Please help me out in this regard.
Sudipta
How can the results be the same for two different molecules??? Despite the fact they are very much related in their structure, double deprotonation would cause the electron density to rearrange in an unpredictable fashion! I still don’t know why would you expect to have the same bond angles and lengths between a neutral and an anionic species.
Try sending me an email with more (way more) information on what you are trying to accomplish.
Have a nice day!
I sent an email to you at this address jbarroso@unam.mx. please let me know if you need any further information from my side.
Hi Sir, I am doing gaussian calculations for C2H4, in output there is a place says “Population analysis using the SCF density: and show the orbital symmetry like AG, B1U,… .which is great !
I am doing same calculation for VOF3 belong to C3v symmetry.
E 2C3 (z) 3σv linear,rotations quadratic
A1 1 1 1 z x2+y2, z2
A2 1 1 -1 Rz
E 2 -1 0 (x, y) (Rx, Ry) (x2-y2, xy) (xz, yz)
I would like to assign each energy level with the 3a1, 2e, 4a1, …. like figure 3 of this publication http://www.sciencedirect.com/science/article/pii/0368204886800536
how I can get this information from output that which energy level is 3a1, or 2e or 4a1,… since I want to do the same assignment for VOCL3, and VOBr3.
I do really appreciate if someone can help me to out of this confusion.
why everybody ignored me !!!!!!plz i am so helpless!
Hi Rocha,
Sorry if I haven’t replied to your question promptly. I assume you are using Gaussian, right? Are the energy levels in the aforementioned paper electronic levels? If so, you are mixing things! Those lines you reproduced in your question are eigenvalues to the rotational operator, your electronic energy levels should be labeled the way you want in the population analysis section. I’m probably not understanding your question properly, if this is the case please send an email to help!at!gaussian.com they are always very helpful and friendly, not to mention quick, they don’t even verify who is sending the question, *wink*wink*
I hope this helps! Have a nice day
Hi ,thanks for your reply I sent you email to this address
Have you received it ?
Thx
Hello there, I have received your email but please give me some more time; I have an enormous pile of things to do 🙂
Have a nice day!
%nprocshared=3
%chk=C:\Users\sheeraz\Desktop\acetoneoptinitial.chk
%mem=500MB
#p freq=(FC,SaveNM) NoSymm b3lyp/6-31+g(d,p) guess=read geom=allcheck
acetone initialfreq
%chk=C:\Users\sheeraz\Desktop\acetoneoptfreq.chk
0 1
C
C 1 B1
O 2 B2 1 A1
C 2 B3 1 A2 3 D1 0
H 1 B4 2 A3 3 D2 0
H 1 B5 2 A4 3 D3 0
H 1 B6 2 A5 3 D4 0
H 4 B7 2 A6 1 D5 0
H 4 B8 2 A7 1 D6 0
H 4 B9 2 A8 1 D7 0
B1 1.51825460
B2 1.21898800
B3 1.51825460
B4 1.09623380
B5 1.09701567
B6 1.09107769
B7 1.09623314
B8 1.09701559
B9 1.09107760
A1 121.59065096
A2 116.81869809
A3 110.72986117
A4 109.82078001
A5 110.05968071
A6 110.72984506
A7 109.82073423
A8 110.05968234
D1 180.00000000
D2 127.06161404
D3 -115.16467550
D4 5.30687972
D5 -52.93842394
D6 64.83529815
D7 -174.69317594
1 2 1.0 5 1.0 6 1.0 7 1.0
2 3 2.0 4 1.0
3
4 8 1.0 9 1.0 10 1.0
5
6
7
8
9
10
Sir, this is the input file.
The last few lines of the output file are
Eckart Orientation
———————————————————————
Center Atomic Coordinates (Angstroms)
Number Number X Y Z
———————————————————————
1 6 -0.697824 -0.001075 -1.293268
2 6 0.097509 0.000000 0.000000
3 8 1.316497 0.000000 0.000000
4 6 -0.697824 0.001075 1.293268
5 1 -1.427424 -0.819227 -1.299428
6 1 -1.266491 0.932929 -1.381012
7 1 -0.024597 -0.096576 -2.146553
8 1 -1.427424 0.819227 1.299428
9 1 -1.266491 -0.932929 1.381011
10 1 -0.024597 0.096575 2.146553
———————————————————————
**********************************************************************
Generation of the Franck-Condon spectrum
**********************************************************************
Approx. of the electronic transition dipole moment: FC
Type of transition requested: ONE-PHOTON ABSORPTION
Data for initial state taken from current calculation.
Passed-in normal modes used.
Data for final state taken from checkpoint file “acetone initialfreq”
Error termination in NtrErr:
ntran open failure returned to fopen.
I’m not familiar with this kind of calculations, however it is clearly trying to read something from a checkpoint file which the program believes to be named “acetone initialfreq” but this is only the Title Card line, right?
I don’t understand your input file, it looks as if you defined two different chk files at two different places in it.
If I understand correctly, you should try something like the following:
%nprocshared=3
%chk=C:\Users\sheeraz\Desktop\APCHKFILE.chk
%mem=500MB
#p freq=(FC,SaveNM) NoSymm b3lyp/6-31+g(d,p) guess=read geom=allcheck
acetone initialfreq
0 1
C
C 1 B1
O 2 B2 1 A1
C 2 B3 1 A2 3 D1 0
…
… etc.
In which APCHKFILE stands for Appropriate (or correct) CHK file, in which ever you have previously calculated your initial set of frequencies, either acetoneoptinitial.chk or acetoneoptfreq.chk
I’m not exactly sure what else could be but it seems interesting, so please share the right answer with me if this works, ok?
Have a nice day
hello sir,
I think the only problem is that I am not able to open the .chk file. after optimization. If I can be able to optimize it, I think the problem is solved. Kindly suggest.
The error shown is
CConnectionGFCHK::ReadFile()
Cannot find file.
please suggest how to overcome this error, please dont suggest to create .fch file
I already told you! You have two %chk lines in your input file, delete one! I believe the second one, the one out of place, the link0 that is, is the one that should be deleted. The error you are describing above is not a Gaussian error but a Gaussview error in which the molecule cannot be read.
Hi sir,can u give me a idea and concept about vibrational spectroscpy analysis used in drug designing?
Hello again!
Well of course Infrared spectroscopy is always useful in any kind of synthesis not to mention that is a cheap and fast technique for identifying certain functional groups that might be of interest in a lead compound. I’m not sure Raman spectroscopy is that helpful. I think Circular Dichroism must be fundamental in identifying chirality of leads and other compounds.
I hope this helps!
Thank you so much for ur info sir…
#Hello Sir,
Can you give me suggestion for protein-ligand complex simulation in GROMACS 4.5 software.
I gave the following command
grompp -f hdac1em.mdp -p hdac1dr.top -c hdac1drwater.gro -o hdac1drgion.tpr.
Then, I got response of Atomtype SDMSO not found.
Please give me your valuable suggestion.
Sorry but I don’t know how to work with Gromacs.
Have a nice day and thanks for reading!
hello Dr,
can u pls tell me tat which value should I take to calculate dipole moment and second hyperpolarisability from Gaussian 09 output?
Hi,
Can you please suggest how can I perform single point energy calculation at different dihedral angle.
I can perform the optimization at different dihedral value by using opt=modredundant option. I don’t find such kind of option for single point energy calculation. Any help will be appreciated.
Thanks
Perform a rigid scan. Find more information in this same blog on a post about rigid and relaxed scans.
Best wishes
hI Dr,
Im not quite sure, have you ever used “q-chem” before? Recently, I’m running TDDFT calculation, but I got the error that I cannot solve it. below is my input file and error information:( the coordinate is the optimized structure with solvent which I got from solvatiion calculation before this one)
$molecule
0 1
C -0.049505 -1.24475 -0.056378
C -1.302811 -0.689786 -0.020935
C -1.273506 0.741986 -0.005695
C 0.001451 1.246114 -0.030377
S 1.18586 -0.023895 -0.072382
H -2.159818 1.366411 0.02211
H -2.21391 -1.27791 -0.005902
H 0.223637 -2.291459 -0.074281
H 0.317395 2.280912 -0.026538
$end
$rem
JOBTYPE OPT
BASIS 6-31G+(d,p)
EXCHANGE B3LYP
CIS_STATE_DERIV 1
CIS_N_ROOTS 1
CIS_SINGLETS TRUE
CIS_TRIPLETS FALSE
SOLVENT_METHOD PCM
RPA TRUE
POP_MULLIKEN 2
$end
$pcm
Theory CPCM
Method SWIG
Solver Inversion
Radii Bondi
vdwScale 1.2
$end
$pcm_solvent
Dielectric 4.00
$end
=======================
error output:
Q-Chem fatal error occurred in module /home/scratch/qc40release/qc40c/qchem/libmdc/newfileman.C, line 326:
Error reading in TMP file 99/0 (8)
p0_3952: p4_error: interrupt SIGx: 6
“1ringopt.out” 238L, 9816C
Initially, I thought this probably was space problem, so I tried to add mem_static, but still got same error. or the space of the scratch is full? I’m not quite sure what causes this problem. and how to troubleshoot this.
Best, Hao
Dear Sir,
I am doing excited state study ( # cis/6-31g(d) geom=connectivity) using gaussian 03w for my compound.
and every time the link has been died showing
” Transformation cannot fit in the specified MaxDisk.
Error termination via Lnk1e in C:\G03W\l804.exe at Sat Sep 07 12:03:48 2013.
Job cpu time: 0 days 0 hours 4 minutes 50.0 seconds.
File lengths (MBytes): RWF= 2292 Int= 0 D2E= 0 Chk= 10 Scr= 1″
.
Please suggest me what should do?
and how we can increase iteration for the calculation in gaussian 03w?
Thank you.
with regards
PP
I am currently calculating dynamic Hyperpolarizabilites using the coupled-perturbed Hartee-Fock method in Gaussian09. Calculation seems to work fine. My problem is, that the output contains now 18 terms for the \beta-tensor instead of 10. The Gaussian manual only describes the order of the \beta-values for 10 terms which is:beta_xxx,beta_xxy,beta_xyy,beta_yyy,beta_xxz,beta_xyz,beta_yyz,beta_xzz,beta_yzz and beta_zzz.
I assume the addtitional 8 terms should be: beta_xxz,beta_yxz,beta_yxx,beta_zxz,beta_zxy and beta_zyz.
I just do not know the ordering of those terms in the output. I hope u can help me with this problem.
Greetings
Mopp Zilla
Hi Sir,
I am trying to find methodology to use Gaussian to predict fluorescence of any small molecule. i have read many papers but none of them tell the methodology. Everyone discuss about the basis set they have used which of course differs from case to case. I tried learning it from the example of acetaldehyde (http://www.gaussian.com/g_tech/g_ur/k_scrf.htm) but i am unable to understand it.
Can you help me with it ?
Hello Ankita,
I suggest you find online a copy of “Exploring Chemistry with Electronic Structure Methods” by Frisch and Frisch for a step by step introduction to photochemistry calculations. The procedure is rather lengthy for a comment, perhaps I should write a full post on it 🙂
Have a nice day
Hello again Dr. Joaquin!
I tried to visualize HOMO and LUMO for an optimized metal complexes of a halogenated phthalocyanine (B3LYP 6-31G(d)) but I have error termination in cubegen formation:
Error termination via Lnk1e at Mon Sep 16 16:29:47 2013.
Cubegen Job Completed (PID = 1b38, status = 2057)
Cubegen Series Job Completed
Could you kindly tell me how to increase the grid file?
And please suggest me a book or a tutorial to learn more about this kinds of calculations,
Best Regards for your continues support,
Basma
Use the following comands:
cubegen MO=HOMO file.fchk npts file
where you should change npts for the number of points to be set on each side of the grid. so if you change npts for 100 you will have a grid with 100³ points (1,000,000 points).
Hope this helps!
Estimated Prof. Joaquín
#gaussianerror
I would be very gratetful if you could help me with an optimization in gaussian 09. I Tried to optimized a Noble gas compound using CCSD(T) an i get the next error:
HESSIAN DOES NOT HAVE THE DESIRED LOCAL STRUCTURE
TAKING SIMPLE RFO STEP
SEARCHING FOR LAMDA THAT MINIMIZES ALONG ALL MODES
*****************************************
*** UNABLE TO DETERMINE LAMDA IN FmD114 **
******************************************
Error termination via Lnk1e in /usr/local/g09/amd/g09/l114.exe
Could you help me
Cheers,
Said.
Try it again with the option freq=calcall it will take a long time but probably will help you.
Let me know if it doesn’t
Cheers
Ok, thank you very much. I will let you know.
Bye Bye.
my question may silly.
is there any way to find out the energy of the individual atom in molecules?
Hi Uma
I’m sorry for the lateness of my response. I think you could use the NBOdeletion scheme to eliminate all the interactions from the atom under consideration with the rest of the atoms in the molecule.
The NBODel manual is located at the NBO website from the Wisconsin University.
May I ask what are you trying to study or prove?
I hope this helps
#NBO
Saludos!!
Tengo tres preguntitas con respecto al análisis del NBO. Es válido hacerlo para sistemas de capa abierta con multiplicidad 1? Como por ejemplo dirradicales. Y si es así, tiene sentido analizar los índices de Wiberg para estos sistemas?. Lei en un sitio web que se puede especificar en Gaussian con el iop(5/14=2) para que el análisis poblacional se haga con la función de onda corregida (spin annihilated). La verdad es que los resultados no me parecen mejores, pero no he encontrado nada al respecto!
Gracias por este blog!!
Hola Beatriz,
Mil perdones por la tardanza de mi respuesta, a veces con tanto trabajo soy un poco negligente del blog.
Claro que tiene sentido usar NBO en sistemas de capa abierta, pero cuidado ya que el análisis se hace por separado para la densidad con spin alpha y la densidad con spin beta, del modo que se haría con los métodos no-restringidos.
Algunas propiedades son sumadas (como la población total) pero hay que en general estar al pendiente de lo que leemos en el archivo de salida.
Saludos y gracias a ti por tus palabras
Gracias por responderme Joaquín! Tendré cuidado con la densidad de spin alfa y beta, un gran saludo!
Hello Sir,
As mentioned in your blog I used the following input to calculate free energy of solvation, b3lyp/6-31+g(d,p) scrf=(smd,solvent=water, DoVacuum) nosymm geom=connectivity polar
I dont see energy for vacuum. I see SCF but how can we say that it free energy for solvation. I will be grateful if you help me to under stand this.
Thank you,
Mohan
Just run a single point on your geometry of interest separately.
Have a nice day
Hello,
I will be very grateful if you step-wise explanation for the calculation of pKa using gaussian 98 (which value needs to be extracted). As my knowledge and using the formula reported in JACS 123, 7214 (2001), I try to calculate but I did not get similar values. The process is very straight forward according to that paper. My main problem is to get solvation free energy. Gaussian 98 does not print directly in the .log file.
Thank you.
Bharat
Hi,
I am a regular visitor of your blog. I have a query regarding nbo calculation. On calculation of bond order of borazine with G09W at b3lyp/6-31G*, I found that B-N wiberg bond index is 1 for all 6 B-N bonds in borazine. However, the table showing the occupancy/bond orbital/coefficients etc. showed that 3 B-N bonds have pi-pi bonding, while the other 3 B-N bonds have only sigma bonding. This means that B-N bond order should be 2 (for those which has pi-pi bonding), or if 1.5, if average is taken. However, as mentioned earlier the B-N Wiberg bond index is 1 for all the 6 B-N bonds in borazine. They seems to contradict. I am confused and looking forward for your help.
Thank you.
Sameer
Hi Sameer
This is indeed confusing and I’m not sure where is this discrepancy coming from. However you should note that while the NBO program provides Wiberg bond indices, these are defined in a different way than the NBO bond orders. I wouldn’t mix both definitions, specially if you are observing such different values. Use the BOAO option in your NBO keyword section so you get also the Bond Orders in the Atomic Orbitals basis and compare those values to Wiberg’s
I hope this helps
Hi Dr Joaquin,
I am wondering if you can tell me if is a way or method that can calculate the interaction between two small molecules using Gaussian. i.e A + B = A.B
Otherwise the interaction energy that hold the two molecules together.
Thank you
Rean
I can think of two methods:
1) First calculate the energy of the AB pair (I guess you might need an optimized geometry for the interacting pair). Then delete the A molecule and save it as a new input file (e.g. b.gjf) and do the same for the B molecule and calculate a single point for each. The interaction energy would be then calculated as:
Eint = E(AB) – {E(A) + E(B)}
2) Another method is to use the NBODel implementation. Run a geometry optimization of the AB pair then run the NBODel calculation on that geometry by using pop=NBODel on the route section. The added input should read
-blank line-
$NBO $END
$DEL
ZERO 2 DELOC FROM 1 TO 2 FROM 2 TO 1
$END
blank line
Please search the NBO deletion post on this blog for futher details.
HAve a nice day!
# End of line while reading pcm input #
hello sir,
I’m a new computational chemist. I’m trying to calculate fluorescence for tryphenylamine molecules. as they have given in g09 manual i started with acetaldehyde molecule. but in 3rd step I’m getting the following error.
The first two steps (Step 1: Ground state geometry optimization and frequencies; Step 2: Vertical excitation with linear response solvation) just using Water instead of Ethanol working fine. Step 3: State-specific solvation of the vertical excitation – Part II (Link1) quits with the following message:
SC-PCM: Self-consistent PCM reaction field calculation.
Using the following non-standard input for PCM:
NonEq=Read
End of line while reading PCM input.
Error termination via Lnk1e in xxx/GAUSSIAN/g09/l124.exe at Sun Jun 12 17:02:49 2011.
Job cpu time: 0 days 0 hours 0 minutes 0.1 seconds.
File lengths (MBytes): RWF= 36 Int= 0 D2E= 0 Chk= 56 Scr= 4
This is the Jobfile:
%mem=8GB
%nprocshared=8
%chk=03-calc.chk
# B3LYP/6-31+G(d,p) SCRF=(Solvent=Water,Read) Geom=Check Guess=Read
DMABE: prepare for state-specific non-eq solvation by saving the solvent reaction field from the ground state
0 1
NonEq=Write
–link1–
%chk=03-calc.chk
# B3LYP/6-31+G(d,p) TD(NStates=6,Root=1) SCRF=(Solvent=Water,StateSpecific,Read) Geom=Check Guess=Read
DMABE: read non-eq solvation from ground state and compute energy of the first excited with the state-specific method
0 1
NonEq=Read
Any suggestions on how to solve this problem?
thanks in advance.
Hi. Did you make sure to leave a blank line at the end if the input file? If you didn’t then the program will think there is more to be read but the File is abruptly ended. I’m sure it might be more complex than that but it might be a good idea just to check it. Let me know, ok?
Best regards
yes sir…that was the mistake i made…now am able to run the programme successfully.
thankyou very much sir
Dear Niveditha,
Could you please help me to get step 3 and 4 successfully terminated? My molecule is 36 atoms and i got job error due to exceeded walltime.
Dear Sir/Madam
I am using Gaussian G09 and also using Gauss View 5.09 for the visualization. I want to visualize the NBO orbitals using G09 Calculation and Gauss View program. I am looking every one suggestion regarding this.
Please refer to the post on how to visualize NBO’s with Gaussian, provided in this same blog. Use the search box. You will find everything you need to know about the matter.
Best regards
Hi Dr Joaquin,
I use G09 and Gauss View 5.09 for my PhD studies. I use the b3lyp/genecp method to activate an alkane using vanadium-based catalysts (e.g. H3VO4 model). The mechanism I am trying to follow involves a two step dehydrogenation:
H3VO4 + R-H (alkane) = H3VO4H + R. = H3VO3 + R (alkene) + H2O
My challenge is that I do not get a maximum on a relaxed PES scan for the first step, i.e. scanning between H of alkane and O of catalyst. I have tried a different algorithm (scf=qc) without success.
Any suggestions on how to model dehydrogentaion reactions?
So you are trying to get a maximum? This means you are trying to get to a transition state structure. Please search for the usage of the QST2 or QST3 keywords in Gaussian. You may also look for the IRC keyword at Gaussian’s website.
Best regards
#convergencefailure#
Dear Dr Joaquin,
I have problem with calculation of solvation energy using IPCM solvation model for an anionic system at m06l/6-311++G(d,p) level of theory using G09. The optimized geometry from gas pahse calculation was used for IPCM single point calculation. The job did not converge and terminated with an error: Maximum number of iterations exceeded.
I tried to increase the number of iterations to 600, with [iop(1/6=600)]. But this did not solve the problem of convergence and the job terminated with the same error.
Regards
Just increase the number the iterations by using scf=maxvycle=1000
Best regards
Just use scf=maxcycle=1000 and that should increase the performance.
Hope this helps
Dear Dr Joaquin,
Thanks for your reply.
I tried using scf=maxcycle=1000 but still i get the same error message.
Regards
Try even more iterations scf=(QC,maxcycle=10000)
Hope this helps
Dear Dr Joaquin
I optimized ethanol molecule. After that, frequency calculation was performed. The calculations were done successfully. I didn’t have any imaginary frequency (NImag=0) and four YES options were obtained that confirmed my structure is stable. But in thermochemistry section, there is this warning:
Warning — explicit consideration of 3 degrees of freedom as
vibrations may cause significant error
Can you help me about this problem? Is it important?
No it’s not important. This is only a warning that is issued as a sort of disclaimer. So carry on!
Have a nice day
Dear Dr Barroso
Thank you so much for your answer.
Have a nice time
Dear Sir,
I wanted to ask about this as well, since it’s appearing in many of my calculations. I want to optimize my molecules both in gaseous phase and solvatated so I can calculate DeltaG. But some calculations present this warning and some don’t.
I’m very grateful for you taking the time to keep this Blog and help people around the world!
María Fernanda Muñoz,
Universidad Central de Venezuela.
Muchas gracias, María Fernanda! Espero poder seguir siendo de utilidad. Saludos hasta Venezuela!
Dear Dr Joaquin
I am considering to calculate transfer integral by using splitting method. So I guess the g09 zindo calculation would be a good option. By my experience, some people will add the command z=N to give a certain electric field for getting a more accurate calculation. Im curious If i am only concern homo, homo-1, lumo, and lumo+1 in dimer scheme, adding Z=N is that necessary? besides, are the eigenvalues can be trusted ? or I only can believe the total energy for certain root?
Hao
Hello,
I just read the blog entry about hybridisation of atomic orbitals (the standard way proposed by pauling) to sp2 or sp3 hybrid atomic orbitals. I can’t find a theoretical justification of this concept anywhere. This is what I mean: the orbitals are just combined in a some way and there is never an explanation provided for why it is actually allowed to do that (why it actually fits the real electronic structure). Also, they don’t have the right symmetry to combine (if this a combination like in MO theory). I’m looking for a theoretical underpinning of the concept and a justification for why it is actually more or less realistic/true/whatever. You mentioned something in the blog entry but it was rather short. Could you please elaborate on that and maybe suggest a source where I could find what I am looking for?
Thanks
Hello John,
This is actually a great question! I think the blog entry on the matter was one of the firsts I ever wrote back in 2009; I guess I never really expected anyone to pay much attention to it.
Ok so on to your questions:
p orbitals don’t have the right symmetry because they were obtained as a solution for a Hamiltonian with spherical symmetry (that of a hydrogenoid atom) but the set of three p orbitals (solutions with l =1) is indeed spherical when summed all together. Using hydrogenoid orbitals as the basis for MO construction is a huge leap but it is justified under the mean field approximation (each electron ‘swims’ in the field produced by the electron density ocean produced by the rest of the N-1 electrons) which can be proven to be *cough*sort of*cough* spherical (Weissbluth – Atoms and Molecules).
As I remember writing in that particular post, once a set of solutions of any given Hamiltonian is found, any linear combination of them will also be a valid solution of the same H (obviously, since H is a linear operator!); therefore a symmetry ADAPTED linear combination can be found in which orbitals “point” to wherever we need them to in order to ‘explain’ any geometry (‘describe’, would be more accurate).
The general procedure for performing this adaptations under a given group point (Td in the case of methane) can be found in D. Harris – Symmetry and Spectroscopy (Dover).
Orbitals are a tricky thing, they don’t quite actually exist, they are functions, but they do work really well as a model to explain both chemical structure and reactivity. This is why DFT methods are so conceptually popular because the one ‘tangible’ thing is the electron density but then you go into the v-representability problem (cleverly solved by Levy) in which the quantum effects (spin of all of them!) is taken into account. Of course the DFT problem lies in finding THE functional and ultimately we fall back to Kohn-Sham orbitals and so on…
So in short the justifications are purely of mathematical consistency but they do adapt really well to our chemical knowledge.
Thank you very much for this thought provoking post, I hope I understood and answered your question but if I didn’t I’m open for further conversation and maybe I’ll post some more on the matter.
Have a nice day!
Dear Dr. Barroso,
thank you very much for your reply, the fact that a linear combination of solutions to a particular hamiltonian is also a valid solution is enough to justify the use of hybrid atomic orbitals to explain a given geometry.
I wonder whether the description of bonding using hybrid atomic orbitals is of any use, other than explaining the geometry. How accurate is it, qualitatively, to explain reactivity, in inorganic and organic chemistry? The concept of hybridisation is so widespread in organic chemistry, but there is not a single textbook that really justifies the use of it. sp3 and sp2 hybrid orbitals are used even in higher-level textbooks to construct MO-like orbital diagrams. For inorganic chemistry, I never see an explanation involving hybrid atomic orbitals, its always MO. Why the difference?
As you said in your blog entry, hybridisation can only explain the geometry after it was determined. But nearly everywhere, a carbon atom with 4 bonds to different atoms is taken to be 1. tetrahedral and 2. sp3. If hybridisation can only be used after the fact, and if we ignore non-QM theories like VSEPR, what is the theoretical explanation for a tetrahedral carbon atom? Don’t get me wrong, if I see a methyl group in some structure, I also directly assign a tetrahedral geometry. But there has to be a quantum chemical explanation for that, which does not rely on VSEPR or hybridisation.
I have used these concepts for quite some time now, but in my undergrad course I am now for the first time confronted with theoretical chemistry, and I’m really trying to see the consistency of all these things.
best regards
(For some reason I cannot reply to your latest comment, there seems to be a limit to nesting in this thing)
It is indeed a very interesting question. I guess, in inorganic chemistry (IC) the use is not as widespread because the canonical atomic orbitals of any metal atom (d orbitals) usually point to the vertexes of most found geometries (squares, octahedrons, etc.) (USUALLY and MOST are key words in the previous sentence since this isn’t always the case!). A funny thing occurs in the borderline between OrgChem and IC, and that is P (phosphorous). There is a cute paper from the 1980’s entitled something like “no d orbitals but welsh diagrams and possibly banana bonds in hypervalent P compounds”, I should have it somewhere at home (oh those crazy pre-PDF times!); in order to keep a consistent case of hybridization in orbitals for P one must ‘invoke’ the usage of d orbitals (which is questionable in most molecules with not-electronegative-enough substituents on P). Then again these are just models; ways we wrap our heads around problems in order to find a description that makes sense for MOST systems in MOST of the times.
Now, your question about why is CH4 tetrahedral goes far deeper than I can possibly assess in a blog comment! It seems only logical that the arrangement of least energy is a tetrahedron but then again, why is BeH2 bent if it could be linear. This is a real headscrather! (well, actually there are many models on why is BeH2 (or was it BeF2?) linear, all in accordance with VSEPR and hybridization).
This is a very enthralling conversation, I hope we might keep it up!
Best wishes
Dear Barroso,
Could you kindly answer my little query.For berny T.S optimization of a T.S guess structure,does the nature of the bond between the reactants , i.e., dashed,solid or double influence the final geometry?What kind of bonds should I use for partially formed or broken bonds in the T.S?
The connectivity matrix only provides an initial clue to the software about the molecular graph. It makes little difference in the results so I would use no dashed bonds
Have a nice day!
Dr. Barroso
Mi nombre es Patricia, y me tomé el atrevimiento para escribirle, ya que tengo un inconveniente, y no lo he podido resolver. Yo actualmente trabajo con el g09 y gv para visualizar las moléculas, pero en plataforma windows. Conseguí el gv para linux, pero no he podido instalarlo, porque venía sin el protocolo para instalar las librerías. Le escribo para pedirle su ayuda al respecto, ya que en ningún lado he conseguido el protocolo para la instalación. De ante mano, le agradezco su tiempo y si es es posible su ayuda al respecto, y espero no importunarlo con mi pregunta.
Cordialmente,
Patricia
Dear Dr Barroso
I optimized acetate and trifluoroacetate at M052X/6-31+G(d) and M062X/6-31+G(d) level of theories using Gaussian 09 program. To confirm that my molecules are on a local minimum position, I performed frequency calculation at the same level of theories used in geometry optimization. Unfortunately, I observed one imaginary frequency in my output files (-30) for each molecules . I used many ways to remove that :using of Opt=calcall keyword, rotation of molecules and creation of many structures, using of optimized geometries at higher level of theories such as CBS-QB3 or G3 that didn’t have any imaginary frequency. But, these ways couldn’t solve my problem. Can you help me?
If you calculate a structure at a certain level of theory, you must calculate the frequencies at the same level of theory.
If you found an imaginary freq you must first try to visualize it and distort, just a little, the molecule in the direction of the vibration because it is in this direction that the molecule “wants to be distorted”; after that you should try once again the optimization followed by a new frequencies calculation.
I hope this helps
Dear Barroso,
Could u kindly suggest me how to convert my structure files into .lib or .frcmod format?
I’m not sure if those are supported by OPEN BABEL but you could try using it 🙂 Google it for their home page
Have a nice day!
but they aren’t supported..:(
Hi Barroso,
I’m an undergraduate just starting out on a computational chemistry project using Gaussian 03. I’ve been skimming through your blog these last few days (it’s really useful by the way!) and I was hoping you could help with some naive questions about what I’m trying to calculate (very sorry if these are obvious):
I want to look at PES and UV/Vis spectra of transition metals in helium nanodroplets, but things I’m unclear about:
– For solvation I can either use SCRF or draw the solvent molecules around the molecules of interest manually (in something like Chemcraft). The latter is computationally expensive, however using the former would give the results in bulk liquid helium, so manually might be more accurate?
-So I run Opt with minimum basis set, then do Scan, then repeat in the solvent, but I’m still unclear how to modify things like pressure/temperature…? Surely I need to specify the temperature of the helium nanodroplets and the fact that they’re in a vacuum, or won’t it just compute for He gas?
Many thanks for continuing to write this blog!
Hi David,
Thank you very much for your kind words about this little blog of mine.
The SCRF procedure in Gaussian is limited to a -somewhat large- number of solvents, but I don’t think liquid He is parametrized in G03 and introducing the parametrization by hand is too troublesome since it requires knowledge of the dielectric constant, the molar volume, the electric permitivity and some other characteristics of the solvent. Therefore, your only way of using Gaussian is by using explicit solvent but this would be computationally demanding as you’d need to set a very large number of He atoms.
You can change the Temperature of the simulation by including temperature=300 in the route section (in this example you are requesting a simulation at 300K)
I’d strongly suggest you either look for a different approach or a different software. If you have any knowledge about the solvent and if you may find a solvent that resembles liqHe then try the SCRF procedure with that solvent.
I hope this helps.
Have a nice day!
Hi Barroso,
Many thanks for your advice. Unfortunately I think I’m fairly stuck with Gaussian 03 for the time being, so I’ll have to make do…
Something I’m still not that clear about is the construction of a Z matrix for PES calculations. From what I understand this is generally to give relative coordinates of atoms with respect to each other in a molecule, however Z matrices can also be constructed for a number of atoms? If so, does the ordering impact how the PES scan is calculated? For example I tried building up a nanodroplet of 100 He atoms, and used Chemcraft to build up a Z matrix through assigning distances/angles/dihedrals, however this was merely in an arbitrary order of choosing the nearest atoms and I’m unclear if this is the correct way for specifying a Z matrix for such a system..
Any advice would be great!
Dear Sir,
I’m trying to do a TDDFT OPT job in G-09 and my job is getting link died with the error message:
“You need to solve for more vectors in order to follow this state.
Error termination via Lnk1e in d:\gaussian\l914.exe ”
I also tried maximizing the # cycles but that resulted in same error.
Please suggest me a way-out at your earliest convenience!
Regards,
Thank you in anticipation,
-Bijan (bijan.paul.chem.cu@gmail.com).
Hi,
I do have a problem with saving high-resolution image. I can generate a high-resolution image in gaussView but saving it as TIFF makes the resolution as low as 96 dpi. How can I save an image in 300 dpi.
Thank you very much,
Jameel
Hi Jameel,
There is a small check box at the bottom of the save image window (sometimes this window is too small so the check box is not visible and you may have to enlarge the window to see it) that says something about enlarging the image; by default it is set to 3 times, I think. Maybe playing with that value could help but I’m not sure.
I hope this helps
Have a nice day!
Respetcted sir,
Due to power failure, my anharmonic gaussain job failed after 23 days. Kindly help me how to restart the job
Respected sir
Wish You a very happy New Year 2014. If I have to Scan a molecule through dihedral angle, please hep me how to fix the atoms which are not to be scanned. Please help by some example.
thanking you.
The problem of power failure question is solved now.
If you completely fix them then you will break them, what you want to do is to have them move along with the dihedral you have defined. Please find a post in this blog of mine entitled Potential Energy Surface Scan. In it you will find detailed instructions to accomplish what you are asking.
Have a nice day!
Dear sir,
I will be very thankful if you can explain me how the interaction energies will be corrected to the basis (BSSE)
Thanks in advance.
Hi Rayen,
You should look for the original papers by Boys et al. but the short story is the following. if you have two molecules interacting the energy you obtain for the AB system is different from the sum of the individual energies for A and B, it tends to be way lower (i.e. much more stable) this, among other things is due to the BSSE which arises when the electrons of A have a larger basis comprised of the orbitals of B and viceversa. In other words, the electrons of A occupy orbitals in B and the other way around. BSSE then leads to an overestimation of the interaction energy and that is why it should be corrected with methods such as Counterpoise.
I hope this helps
Dear Sir,
Please give me an input file to rum in Gaussian 09 for calculating emission (fluorescence) spectra. How is it done by TD-DFT? Any molecule would do. I want to know exactly what does such an input file look like.
Thank you
Estimado Dr. Joaquín Barroso:
Durante unos cálculos de unos sistemas, al estar observando los orbitales frontera, me he dado cuenta que el LUMO tiene un valor negativo. Use el función de M062X y una base 6-311++G(d,p) en G09 W. ¿El valor es erróneo o que pudo llevar a este resultado?
De antemano le doy las gracias
Hola Antonio,
Un valor negativo de LUMO significa que este puede ser poblado de forma estable, es decir, se trata de un estado ligado. Nada de que preocuparse. La pregunta entonces sería, es tu sistema capaz de aceptar electrones y formar así una especie estable?
Saludos
sir, in order to calculate fukui functions, i am in a dilemma about the q value to be taken and N+1, N,N-1 values also…could you please elaborate, how we can get these q and N values(i.e., from gaussian output or any other mode. if they are from gaussian output, how we can find them from output file)??
Dear Dr Barroso,
How do I solve this error message for a transitions state optimization (both Qst2 and Qst3): “Gradient too large for Newton Raphson, using scaled steepest decent instead, convergence failure!”
Regards,
Nkululeko
hola,
Ɗeboo reconocer que antes nο me interesaba demasiado elblog, pero ahora estoy siguiedolօ mas vees y me esta gustando mas.
😉
I’m having trouble to run the program in python to graph free energy vs reaction coordinate. I copy paste the program, changed the path to the file, but I’m getting this error: ‘plot’ is not defined.
Hello Magally,
You probably only need to update the gnuplot program.
Try from your terminal:
sudo apt-get update gnuplot
Look for more ways to update your unix system in google, there are many resources out there.
I hope this helps
I have tried to study a Ruthenium(III) complex and I don’t know What is correct, to use the keywords: opt ub3lyp/basis scrf=(solvent=water) pop=full or separately: opt ub3lyp/basis scrf=(solvent=water) and after optimized, to calculate the population: ub3lyp/basis pop=full. I need to use the solvent effect (PCM) to calculate the population, or It doesn’t matter?
Hello!
The first option is correct. You will get the population analysis performed before and after the optimization process so be careful which one you are reading!
Doing it as a separate job is also valid but seems to me as a waste of time and disk space.
Hope this helps. Have a nice day!
Can anyone tell me “B3LYP/6-31++G(d,p) 5d ”
what is 5d in this?
Hi Vinothan,
5d specifies the usage of pure d functions not cartesian d functions.
Regards
Eric
Hi Dr. Barroso,
I want to output kinetic, coulomb, exchange and correlation energies out of a dft calculation in gaussian 09. By default, it only outputs total energy of the system. I searched through all iops, especially 9999, but I couldn’t find an answer. Any guess would be helpful.
Thanks
Hi Dr. Barroso,
I have a very strange problem in NBO visualization. I did NBO calculation for a molecule using gaussian to show the strength of a n-pi* interaction. I found the interaction is strong enough because the second order perturbation energy E(2)=3.96 kcal/mole which is pretty high. However, I saw strange thing when I visualized it using gaussview. The picture shows that there is a overlap between positive lobe of n orbital and negative lobe of pi* orbital. I think that is weird because the strength of interaction between n and pi orbital depends on the sign of the lobe and if the signs are different then the strength of interaction is very weak. But here I am getting opposite observation.
sudipta
Hi Sudipta,
3.96 kcal/mol is not that much. Run a calculation with a phenyl ring and you’ll notice that pi-pi* interactions are much much higher.
The antiphase overlap indicates a destructive antibonding interaction; sort of (probably) a retrodonation pattern as that observed in metallic carbonyl systems.
Have a nice day!
Thank you very much for the suggestion. I had taken few literature on the n-pi* interaction. I found that the value of E(2) between 1 to 4 kcal/ mole is reasonable for n-pi* interaction. For phenyl ring, may be the pi-pi* interaction is strong. I definitely do that test.
Hi Dr Barroso,
I have bother you before several times. Now, one of my result really puzzles me. I don’t figure it out still what is going on.
I was trying to analyze a phosphothreonine residue using gaussian. My aim was trying to show the energetics of PO4 group rotation. Therefore, I had chosen a dihedral angle which is associated with that bond and then I did relaxed and rigid scan for that which is very usual procedure. I varied the basis set but the result doesn’t change too much. I found a minima in potential energy surface at a eclipsed configuration. But I want to figure out the origin of such minima in terms of orbital interactions. To do that I perform NBO analysis. I thought some donor acceptor interaction favors that configuration. But I didn’t see such type of stabilization energy is associated with it and there is no substantial NBO overlap when I visualize it. Moreover, I summed all the stabilization energies those are associated with that bond but I didn’t see any trend. Do you have any suggestion how to explain the origin of minima in potential energy surface in terms of orbital descriptions. Or any other clue that can explain the origin of minima in potential energy surface in a naive way.
Thanks in advance
Sudipta
Hello Dear Dr Barroso
I study fluorinated compounds properties using high level ab initio methods such as
CBS-QB3 and G3 methods. I performed CBS-QB3 calculations on (CF3)3COH and C6F5COOH
molecules using Gaussian 09 program under window on the system (8GB, Processor: Intel(R)
Core(TM) i7-2700K CPU @ 3.50GHz).
My input file:
%rwf=D:\SCRA,50GB,E:\SCRA,-1
%NOSAVE
%Chk=1.chk
%nprocshared=4
%mem=200MW
# CBS-QB3
.
.
.
Unfortunately,this error was occurred:
My output file:
Internal consistency error detected in FileIO for unit 1 I= 6 J= 0 IFail= 1.
.
.
.
Number 0
Base 20480
End 67072
End1 67072
Wr Pntr 20480
Rd Pntr 20480
Length 46592
Error termination in NtrErr:
NtrErr called from FIOCnC.
The above error was occurred in this step:
#N Geom=AllCheck Guess=TCheck SCRF=Check CCSD(T)/6-31+G(d’)
The size of RWF was 18 GB in the end of failed job. Also,the same error was occurred
when I performed G3 calculations. I will be very happy if you can help me to solve this
problem.
With best reqards
Ali
#visualization
Hi,
I am a chemistry Ph.D. student at University of Delaware. I will be grateful if you can help me on some NBO calculation.
I used Gaussian 09 (DFT) to optimize my molecules, and I often add NBO calculation to the job as well. I am wondering what is the difference NBO will show if calculate NBO with close shell (restricted) or open shell (unrestricted). I was told once that NBO shouldn’t be done with open shell, but I didn’t ask the reason. I have searched on web for a while without finding answer.
Thank you.
Hi Jia-Ming,
It is possible to perform the NBO analysis with open shell systems, however some results are not reliable. The core reason is that the NBO population analysis is based on electron pair description (such as Lewis, that is why it has become so popular). There is also a problem with the re-orthonormalization of the basis set for an unrestricted calculation if I recall correctly. Go to the NBO official website and download the manual, I’m positive that a more thorough answer can be find there.
Have a nice day!
Hello Dear Dr Barroso
I study fluorinated compounds properties using high level ab initio methods such as
CBS-QB3 and G3 methods. I performed CBS-QB3 calculations on (CF3)3COH and C6F5COOH
molecules using Gaussian 09 program under window on the system (8GB, Processor: Intel(R)
Core(TM) i7-2700K CPU @ 3.50GHz).
My input file:
%rwf=D:\SCRA,50GB,E:\SCRA,-1
%NOSAVE
%Chk=1.chk
%nprocshared=4
%mem=200MW
# CBS-QB3
.
.
.
Unfortunately,this error was occurred:
My output file:
Internal consistency error detected in FileIO for unit 1 I= 6 J= 0 IFail= 1.
.
.
.
Number 0
Base 20480
End 67072
End1 67072
Wr Pntr 20480
Rd Pntr 20480
Length 46592
Error termination in NtrErr:
NtrErr called from FIOCnC.
The size of RWF was 18 GB in the end of failed job. Also,the same error was occurred
when I performed G3 calculations. I will be very happy if you can help me to solve this
problem.
With best reqards
Ali
Dear Dr Barroso,
I’m Ning. I’m now working on the H-bond interaction of the catalytic residues to the cofactor of the enzyme. I’d like to know how these interactions can modulate the NMR isotropic chemical shift on the enzyme cofactor. The way I did was:
1) I use the crystal structure (pdb.) to run ONIOM (DFT/B3PW91/6311++G(d,p):AMBER) with freezing all atoms 20 A from the active site.
2) After ONIOM, I re-optimize the QM region on higher level of basis set. I freeze all five catalytic residues (except H-atom) and some of the enzyme cofactors’ atoms).
#p opt b3pw91/6311++g(2d,2p) nosymm geom=connectivity.
3) I used the output chk. to run NMR calculation and NBO analysis. Do you think I should perform NBO analysis at this step or at the step in which opt was run (step 2)? I try to correlate the electron density of NMR with the NBO analysis.
#p nmr=giao b3pw91/6311++g(2d,2p) nosymm guess=read pop=nbo geom=AllCheck
In the route, I have to use pop=nbo or pop=(full,nboread)?
4) To better understand the interaction from each catalytic residue to the enzyme cofactor, I have remove 4 catalytic residues out and re-optimize the structure (now I have 1 catalytic residue and enzyme cofactor). I did re-optimize the structure because I want the wavefunction to be polarized on the cofactor in order to get the NMR and NBO calculation. Am I right? We can’t get new wavefunction after remove 4 catalytic residues for NMR calculation without optimization? or I can just remove other residues and then run NMR/NBO calculation without opt? I have a little bit confuse because the NMR calculation typically benefit from an accurate geometry and a large basis set.
I’m not quit sure which step I should run NBO and do I have to re-optimize the structure after I remove other residues out in order to get the new wavefunction for doing the second job on NMR/NBO?
many thanks for your help in advance!!
Cheers,
Ning
#NBO change treshold for printing (because here is a common place for all questions – I post here as well this question that was posted at NBO section)
Hello, I would like to ask how to change for Second Order Perturbation Theory Analysis of Fock Matrix in NBO Basis the Threshold for printing of 0.50 kcal/mol to a lower value. I mention that I work in Gaussian for windows (both G03 or G09)
Thank you in advance
Isabela Man
Hello Isabela,
I’m afraid you cannot change the threshold for printing. You would need access to the source code (which I think is not a problem) but even then I wouldn’t know where to make the changes. Sorry.
Have a nice day!
Dr. Joaquín Barroso:
Antes que nada le envío un cordial saludo. Quisiera saber: ¿cuál es la forma adecuada de mandar un cálculo de Full CI en Gaussian?, ya que no sé si sea a través de CASSCD, o CISD o de otra forma. De antemano le doy las gracias.
Dr. Joaquín Barroso, I am doing transition state optimization of a organic system having 60 atoms by opt=qst3. The frequency also match -1680 cm(-1) that indicate a proton shubtle between carboxylic carbon and amino hydrogen. The problem arises when, I do the IRC, optimization of last points in both reactant side and product side results almost same result. I am unable to solve this problem.
Please help.
Yours
Partha Sarathi Sengupta
Respected Professor,
I want to perform calculations to investigate the adsorption properties of a molecule [binding properties on different metal surfaces in a medium (solvent)]. Kindly help me in this regard.
Here is the link for further reference
Click to access 80810839.pdf
Thank you
Dear Dr. Barroso,
I want to perform a computation of NMR in a molecule that it has to be deuterated in some positions (not all atoms), i want to know the effect of the deuterium in the rest of the molecule, I already specified the isotope and nuclear spin, but i dont know if gaussian recognize deuterium?
The error is:
Illegal nuclear properties clause: “H(iso=2,spin=2)-0.896327000”
Nuclear properties must come at end.
Best regards
Hi Said,
I would need to take a look at the input in order to help you. Check the gaussian website to find out how to specify isotopes for particular atoms.
Have a nice day
#CASSCF
#Counterpoise
Hi Joaquín,
Very quick question that I can’t seem to find any information on.
Is it possible to run a counterpoise correction calculation on a CASSCF calculation on Gaussian 03, or am I being a bit naive with how a CASSCF works?
I’m trying to calculate a PES for the dissociation of an Al dimer, but I get multiplicity errors regardless of which state I input.
For example, inputting
#CAS(6,10)/3-21G Counterpoise=2 SCF=tight Scan temperature=0.37 pressure=0.0
CAS small basis set scan of Al-Al Potential.
0 1, 0 2, 0 2
13,1
13 1 R12,2
Variables:
R12 = 2.00000000 280 0.05
Gives the error:
Illegal values: Multiplicity= 2 CAS( 6,10),
while inputting a singlet state for the individual Al atoms gives the familiar error saying a combination of 13 electrons and singlet state is impossible.
Any help would be very much appreciated, and thanks for maintaining a very helpful blog.
Hello David,
I’m sorry for the lateness of my response.
I think the problem is that CASSCF by definition evaluates all different ways in which N electrons can be distributed in M orbitals preserving the spin multiplicity; hence disrupting the multiplicity of the CASSCF wavefunction with the CP method might be causing the problem. I’m pretty sure that is it. Have you found information on a successful calculation of this kind? If so, please share it!
I hope this helps. Have a nice day!
11. LP ( 3) N 2 23. LP*( 4) C 1 1360.80
What does the above list mean in an NBO Secondary Perturbation mean?
The eleventh NBO, which is a Lone Pair (the third one) on Nitrogen atom number 2, donates electron density to the 23rd NBO which is an empty Lone Pair type orbital located on Carbon atom number 1 with a 1360.80 kcal/mol energy
Hope this helps
Could you please explain the nature of this transition sir? How to understand if a transition is sigma/ pi?
51. LP ( 3) F 26 / 52. RY*( 1) C 1 0.61 1.40 0.026
Thanks
These are not transitions, these are delocalization (if I understand correctly the output section you copied here, I believe this is the second order perturbation delocalization energies requested by the E2PERT keyword). This says that a Lone Pair on F (namely lone pair no.3) is delocalized to a Rydberg orbital on C.
Even if they were transitions, I’m not sure you could use the sigma pi nomenclature for these are Natural Atomic Orbitals (NAO) and not Natural Localized Molecular Orbitals (NLMO).
I hope this helps
Hi!
I have quite specific question:
I have successfully performed scan of 2 different dihedral angles (5 degrees step, 72 steps to cover 360 angle). As a result I got 3D plot, where X and Y are angles phi1 and phi2, and Z is energy. It’s cool, but I open it with Gaussview and don’t like how it looks (colour, fonts, etc). More than that I would like to make a view of energy using isolines – it’s like the geography map where you look from the height and see mountains encircled with lines where height is given with a number.
As far as I understand, I need to extract parameters of angles and energy from output file and put it to Excel or Origin… but how to do this? I cannot do it manually because of too many numbers (72*72 steps). So, I am stuck…
Can you advice how to extract all this data or maybe another Viewer (soft for Windows) where it is possible to work with plots in different ways?
I’m sorry if this question is a little bit far from the main topic…
All best,
Denis
Hi Denis,
I’m not aware of how to change the settings in GV and I don’t think its even possible. Try using other software like Chimera. Maybe even VMD.
I don’t have a specific answer but if you share it with us that would be great. I’ll look into it and get back to you.
Have a nice day!
Hi,
I’m a new comer to this field.but this is a kind of interesting field for me now.i got irc plots successfully.i have save the vedio as a gif file but the problem is when i open it from windows it plays from end to begin.but i want to play it from begin to end.can you please give me some advice to do it properly.
thank you
charitha
Hi:
I’m trying to run a TDDFT Optimization job in Gaussian 09 at B3LYP/6-311++G**. There was an error “Warning!!: The largest alpha MO coefficient is #########” and my job went down. Can you please help me fix this problem and show me a way about how to get this job running?
Regards,
BIjan.
Hi once again!
First of all I would like to say many thanks to you for your blog and answers!
Nevertheless, I have one more.
I performed a relaxed scan, rotating one group (NH2) using dihedral angle and noticed that at one point structure has a huge jump in the structure (and energy) what can be seen using GaussView05. Looks like programm moves one of the atoms trying to optimize, and when angle between two hydrogens becomes too large just move second hydrogen to another side… To avoid that I tried to decrese convergence and stepsize, moving to both sides (negative and positive s 72 -5. and s72 +5), but no result. Usage of different basis sets and methods (HF instead of DFT) didn’t result in something usefull..
Maybe explanation is not awesome at all, but if you have a chance to look at .gjf and .out files you definitely will understand and maybe give me some help… Can I send it to you somehow?
Thanks!
Denis.
Sure! Send them over and I’ll take a look at them. It’s probably nothing but an unfortunate change in the coordinate system, I’d call it spurious but lets check it first.
Have a nice day!
Hi once again!
I also think that it is just a change of a coordinate system, but how can I avoid it? I also haven’t found your direct e-mail, so if you get this e-mail, please confirm it, if it is not too hard.
I attached .gjf and .out files, please, have a look at a spare moment.
All best and thanks again, Denis.
Dear Dr.Joaquin,
Did you have a chance to look trough my files? The problem with change in coordinate system that I am still struggle with…
Here is a link to download them, in case previous time they were unavailable somehow:
https://www.dropbox.com/sh/fim7cn4vx9r7p7z/AACpwYzy3OOV9lv_FyeTcHl-a
In case it has very ugly formatting (looks like long strings if open with Windows basic Norepad), I open it with Notepad++. I do not understand why, but after work at cluster it always has such format… sorry if iy is inconvenient.
Desperately waiting for your opinion!
Thanks!
I replyed to the e-mail I got from this blog (I’m subscribed), but not sure that you recieved it. I haven’t found your direct e-mail… So, what is the best opportunity to send you files?
Have a nice day!)
Well, now I see what was result from my reply directly to that e-mail.
Sorry for mess in your blog…
https://www.dropbox.com/sh/fim7cn4vx9r7p7z/AAA6CZb6d6QcZ2RZFBrxdbfLa
Well, this is a link to my dropbox files.
Thanks!
Respected Sir,
Good Morning.
I got an interesting problem in my output file…
I was optimizing my compound (i.e. aluminosilicates). using b3lyp/631-G/d.
it took 7 days to optimize with the following output…]
Item value Threshold Converged
Max For. 0.000004 0.000450 YES
RMS 0.000001 0.000300 YES
Max Displ. 0.005040 0.001800 NO
RMS 0.000665 0.001200 YES
Optimization Completed on the basis of negligible forses
Stationary poinnt found…
Please suggest me how to proceed now……
Thank you in advance.
with regards
PP
INDIA
Hi,
I’m trying to run a TDDFT Optimization of di Iodo Benzoic acid in Gaussian 09 at B3LYP using 6-311++G** for H, C, and O and LANL2DZ for I. During this It was showing the following errors:
(1) EOF while reading ECP pointer card.
Error termination via Lnk1e in /opt/apps/gaussian//g09/l301.exe
(2) You need to solve for more vectors in order to follow this state.
Error termination via Lnk1e in /opt/apps/gaussian//g09/l914.exe
Can you please give me some suggestion to fix this problem?
With regards,
Ramakanta
olá professor, o senhor pode me ajudar nesse erro? o meu arguivo de entrada é :
%Mem=10GB
%NPROC=8
# B3LYP/6-311+G(d,p)scf=fermi opt freq=raman
C48H20
0 1
….
e o erro é:
The electronic state of the initial guess is 1-AG.
Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
Requested convergence on MAX density matrix=1.00D-06.
Requested convergence on energy=1.00D-06.
Level shift goal 0.100 maximum shift 0.100.
No special actions if energy rises.
Dynamic level shift is on during FON iterations.
Restarting incremental Fock formation.
Restarting incremental Fock formation.
Restarting incremental Fock formation.
Restarting incremental Fock formation.
Restarting incremental Fock formation.
Restarting incremental Fock formation.
>>>>>>>>>> Convergence criterion not met.
SCF Done: E(RB+HF-LYP) = -1841.80450269 A.U. after 129 cycles
Convg = 0.2639D-06 -V/T = 2.0047
S**2 = 0.0000
Convergence failure — run terminated.
Error termination via Lnk1e in /usr-local/gaussian03/l502.exe at Thu May 29 13:09:45 2014.
Job cpu time: 4 days 7 hours 28 minutes 6.0 seconds.
File lengths (MBytes): RWF= 634 Int= 0 D2E= 0 Chk= 32 Scr= 1
Hi!
I’m having problem with calculating counterpoise corrected Gibbs free energy.
I got the optimized geometry from my previous geometry optimization and put this in my input file. During the counterpoise calculation, Gaussian ’03 performs 5 separate single point energy (SPE) calculations at the level specified in the route section. Once these 5 electronic energies are determined, a Counterpoise correction and Counterpoise corrected energy is calculated.
Before performing the counterpoise calculation, I just used the “Sum of electronic and thermal Free Energies” from frequency calculation as Gibbs Free Energy.
I was wondering if adding the Counterpoise correction to the previous Gibbs free energy gives the CP-corrected Gibbs free energy or I should perform an extra frequency calculation for getting “Thermal correction to Gibbs Free Energy”?
Thanks!
Dear Dr. joaquin,
I am really glad to see this nice blog for learning and sharing ideas.
I have a problem in calculating the atomic condensed fukui indices for some compounds. when i want through the literature, i was confused to find two equations for the same f+ and f- values. the first equation is:
f+ = qk(N) – qk(N + 1) AND f- = qk(N-1) – qk(N)
where N is the number of electrons, q is the atomic partial charge.
but, i found other pair of equations (also in the blog here):
f+ = qk(N+1) – qk(N) AND f- = qk(N) – qk(N-1)
could you please tell which one to use..When i used the first pair from NBO charge scheme, the f+ were positive, and it is obvious that the signs will be reversed if i use the second pair.
Thanks
Sridhar
Hello Sridhar!
I stick to the set of equations that are written in this post. However you can use either and just pay attention to the relative values obtained, thus, the atoms with the highest change in total population will be the most affected by the entrance or leave of an electron.
Have a nice day
Hi, Dr Joaquín,
For calculate fukui indices, i need the atomic charges to each atom, but there are many population analysis. For you and according to your experience,
Which population analysis is the best for computing transition metal complexes?
I’m trying to work complexes with lanthanum and cerium, what is your recommendation?
Thanks for your help.
Carlos G.
Hello Dr Joaquin.
Im having some problems when i try to find a stability in my wave function of an optimizaed copper phthalocyanine, the output at optimizating is good, also i did using the D4h point group for adding symemetry, but i have the strange exception that the second derivative matrix have a lot of eigenvalues that are 1000; the calculations runs ok, but when i try to stabilize the wavefunction it appears this: Error termination via Lnk1e in C:\G03W\l914.exe I dont know why, this structure is well optimized and also when i make some frequency or excited states calculation it also breaks the code, this is the keywords: # stable=opt ub3lyp/genECP geom=connectivity, using an ECP for the copper atom.
I would appreciate very much your answer for my problem.
Hello:
I am using following keywords:
#m062x/6-311++g(2d,2p) opt(zmatrix,maxcyc=300) field=x+10 nosymm geom=checkpoint scf=(direct,maxcyc=300)
This job is going too slow. Can something be done in this regard.
Please help me with this. Thank you in anticipation.
Hello sir,
With regards,
I am trying to optimize the single crystal unit cell(Zn2SnO4) which is in cif file. When optimized by using genecp, I get the following results:
Small interatomic distances encountered:
3 2 0.00D+00
Atoms too close.
Please help me sir and also could you please tell me the format to run genecp for nano single crystal cluster.
Hello sir,
I have read your suggestion regarding the problem of fchk.file and could not understand how to perform it . I have the same problem you mentioned and using gauss view 5.0.8.
Will you please clarify how to tackle the problem since I am using 6311+ and 6311++ bases sets.
By the way for smaller molecules like butadiene I do not have problem with fchk.file when using 6311++.
Regards
I assume you mean you can’t open your fchk file with gaussview. Open it with a text editor and perform the changes I wrote about in the posts (actually the second one is better, the change from independent to independant), then save the file again and now you should be able to open it.
Have a nice day!
Hello Dr. Barroso,
I would like to get .wfn file and densities in g09 revision c.01 in a ccsd(t) calculation. However, when I try:
#P CCSD=(T,MaxCyc=100,SaveAmplitudes)/aug-cc-pVDZ Density=Current Output=Wfn Test
I get the error saying:
Post-SCF densities or gradients only with
Real MP2, MP3, MP4SDQ, CI, CCD, and QCI.
However, gaussian website is saying that ccsd(t) density is possible calculate:
http://www.gaussian.com/g_tech/g_ur/k_density.htm
Release notes (in page 1) are saying that it should be possible if some options are used:
Click to access rel_notes_g09_c01.pdf
However, I still get the same error, I would appreciate any help.
Best
Bir yazılım uzmanı olarak sizin bunun gibi kişilerin bu sistemde daha
fonksiyomel hallerde olabilecekleri koşullar ѕağlanabilseydi
Һerşey çok daha farklı olabilirdi diye düşünüyorum.
Maalesef bir insanin іçki içipiçmemesi
bundan sonra çɑlışmalarından daha önemli !
I’m going to run code NBO 5 in g09 or g03 but I can not?
or convert NBO3.1 to NBO 5?
I’m going to run code NBO 5 in g09 or g03 but I can not?
or convert NBO3.1 to NBO 5?
I would buy this code.
Dear Sir,
I’m a Beginner in computational chemistry. I started Two photon absorption studies. I’m confused with 1PA and TPA. In many journals they have calculated 1PA using TD-DFT and for 2PA probability by using someother programme. why cann’t we find 2PA in Gaussian..?? And i’m trying to calculate the TPA cross section. How to calculate this using Gaussian 03..? Please guide me sir..
Thanks in Advance.
Hi Sir,
Myself Prabhakar Sharma and i am using Gaussusm 2.2.4. I am interested to know that how i may calculate the PDOS for a particular atom in a catalyst or in a group of atom. I want to work which is much similar to this work by Y j Du.
DOI: 10.1016/j.molcata.2013.08.011
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Alguem poderia me dizer a estrutura do Fe3O4 para o gaussian?
Które majątkowy użytkownika natomiast przypadku felg konsekwencja finalny.
Come perdere peso. Bezsprzecznie na ich wyglądu sposób życia.
przyciąga spojrzenie innych na tym rynku doskonale umie jak skończony samochód, azaliż sportowy – następstwo jest
uzależycie troszczyć się. Come perdere
peso. Systematyczne pielęgnowanie wypycha ze stopów aluminiowe, tuning,
auto, bądź sportowy – efekt jest nałogowiec od momentu właściwie dopasowania parametrów, np.
pod w stosunku do parametrów, np. Come perdere peso.
pod spodem w stosunku do parametrów, np. u dołu w stosunku do parametru ET,
podczas gdy skończony fura, jednakowoż sportowy
– pokłosie.
Good day! This post couldn’t be written any better!
Reading this post reminds me of my previous room mate!
He always kept chatting about this. I will forward this write-up to
him. Fairly certain he will have a good read. Many thanks for sharing!
Dear Dr.goaquin ,
This is Fatemeh Sabzalizade a M.Sc student in cell and molecular biology, Shiraz university, Iran. I am working on biomolecule intraction. I have optimized the structure of two my compound in both vacuum as well as solvent(PCM and cpcm model) using b3lyp/6-311++G** basis.for cpcm model I using syntax
# b3lyp/6-311++g** opt freq scrf=(cpcm,solvent=H2O)
I have several questions about using from Gaussian:
1. I am asking weather this order is correct or not?
2. can I use a solvent except solvents in gaussian09?
3. How I can study biomolecule intraction in natural condition?
4. How I study exchange structural?
am having difficulties in getting the chk file kindly help
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Hello Dr. Barroso i have a problem with mi calculation but i don’t know if is the program (gaussian09) or mi calculation itself. I run one molecule of 146 atoms in HF/cc-pVTZ and pseudopotential because I have Sn in my molecule. I run the calculation but it never pass through the read of the molecule it never begin with the calculation, but it never show me an error and i have to kill the calculation because it never pass through.
I really appreciate your help
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Hi, there kindly help me to set transition state calculation for associative mechanism
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Dear Dr Joaquín,
Do you think that there is a limitation of the number of basis functions for freq calculation in Gaussian 09?
I have 2 freq calculations, one has 879 basis functions and the other one has 1047 basis functions. Gaussian 09 couldn’t finish the 1047 basis function calculation no matter how much memory I gave the job.
Here is my input file
%nprocshared=1
%rwf=Mol1.rwf
%nosave
%mem=31GB
%chk=Mol1.chk
#p freq=noraman rb3lyp scrf=(check,solvent=methanol) nosymm
guess=tcheck chkbas genchk geom=allcheck
I’d optimized the molecule at the same level of theory, so I used the check point file to do freq calculation and every time, I get 2070 link die message. There is no additional useful error message in the output file…The last line in the output file is:
” Leave Link 1110 at Sat Jul 12 17:32:22 2014, MaxMem= 1744830464 cpu: 3662.0″
I’ve searched Google and posted the question on a couple forums but it didn’t seem I could find an answer. I’ve been working on this calculation and other calculations in the past couple months, but this one calculation just keep holding me off, or every time I need freq calculation of more than 1000 basis function, I hit this brick wall.
I appreciate any input/ thought to this question!
Cheers!
Tue
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#energy_minimization_error..
hello sir,
i am kurshid basheer and working with gromacs ona membrane efflux protein AcrB. in gromacs 4.6.3 i an ecountering the error:
“Fatal error:
Bond length not finite.”
all the previous steps have been executed properly..
i would also like to tell you that in the first command line “pdb2gmacs” I had used the attribute -missing because it prompted the followimg erroe
“305 residues missing from proteikn_chain_A”
is the energy minimization error due to the first command :pdb2gmx” ? if so how can i overcome it.. or is their any other solution.. please help!!!!
regards
kurshid
Dear Kurshid,
Unfortunately I’m not a GROMACS expert so I’m afraid I can’t give you a good answer on this matter. I’d suggest you to contact directly the GROMACS people or an appropriate forum.
Sorry for not being able to help.
Hello, i am Mr krid Adel from Algeria, i am preparing a doctoral thesis in theoretical chemistry. I am a teacher of quantum chemistry in the university, i got my Magister in 2008 in the same field. My question is: is there an opportunity to make and prepare a thesis in your lab? a possibility to make stages, cooperate, collaborate together? if yes i wish to know how? with all my respect and all my salutations. THANKS ALOT
Dear Adel,
Thank you so much for your interest in our laboratory. We do have space in it for people like you, however we don’t have the enough resources to actually bring you over. If you come up with a source of finance that could allow you to come to Mexico, I’d be happy to receive you. Also, if I find out of any other source I will let you know.
Sincerely,
Dr. Barroso
Dear sir,
We are working with G09W software,functional/basis used (B3LYP/6-31G(d))… at time of optimization for some structure we get imaginary frequencies(1,2,5,6,8 and 10) among them for 2 structures G09W is unable to minimize the maximum and r.m.s displacement, for one structure except the maximum force all three parameters are converged, for the rest it shows we get the stationary point. and yes for another investigated structure we are unable to get a stationary point but the structure hasn’t any imaginary frequency.
Can we proceed to Raman and mulliken charge distribution studies with our results?
Hello sir,
i am RAMESH iam biggning in gaussion( g 03) ,i run opt and i face trouble in transition state opt (qst2,qst3) ,kindly provide any guidence for that .
Respected Dr. Joaquin barroso…
I got clarified few doubts long back through your blog….and able to continue my work..
I have a small doubt..
1. The thermochymistry writes about thermodynamical properties. How does one list ZPVE and rotational constants as thermodynamical properties?
2. This is the data I found in output file of a molecule under study.
Molecular mass: 280.13107 amu.
Principal axes and moments of inertia in atomic units:
1 2 3
Eigenvalues — 2302.09149********************
X 0.99998 -0.00548 -0.00253
Y 0.00547 0.99998 -0.00355
Z 0.00254 0.00354 0.99999
This molecule is an asymmetric top.
Rotational symmetry number 1.
How to calculate the moment of inertia for this molecule and How to calculate rotational contribution of the molecule through it moment of inertia?
Tahnking you very much in advance….
Hi Joaquin,
Thanks very much for putting up your WATOC2014 presentation – always interesting to read more detail into what you’re up to! I was wondering if you had any tips on maintaining symmetry in Gaussian (03).
I’m working with a system that converges to a 2-Sigma state, and I want to run some calculations of it in the 2-Pi state.
After using Guess=alter, I make what I think is the correct switch of orbitals (switching an sp alpha orbital to the lowest virtual orbital that is not a rydberg orbital – a BD* orbital, using the pop=NBO output).
In the initial guess after alteration, no statement is made about the electronic state, and after analysis (guess=only) or calculating the single point energy, I get
Unable to determine electronic state: an orbital has unidentified symmetry.
I’ve tried using scf=qc and symm=loose, and tried switching the equivalent beta orbital, or selecting rydberg virtual orbits with simiular hybridization values etc….Any help would be very much appreciated!
Thanks
David
Not to worry I think I’ve solved it.
Thanks for keeping up such a great blog!
Dear Sir,
In one of your blog article “Analyzing Natural Bond Orbitals (NBO) results from Gaussian ’03 & ’09”, you mentioned that “Sometimes you’ll get numbers larger than 3 for an sp^x hybrid or even s^yp^x hybrids (for y>1 and x>3), this has to do with the basis set employed and the number of functions used to describe each atomic orbital.” I can’t find the rest part of this story! What if my result shows something like sp5.82 hybridization, how should I interpret this data? Or should I make any modification on my calculation?
Thank you very much and have a nice day ^^
Kai-Ti Chu
Hello Chu
What I meant to say is that you probably have a double or even triple zeta basis set and thus you probably have a near sp3 hybrid orbitals with two functions on each p orbital. What bases set are you using? And what kind of hybrid orbitals you were expecting to observe?
Best wishes!
Dear sir:
I have tried several basis set and basis function. The following are the Gaussian output results:
Job 1 # pop=(nbo,savenbo) b3lyp/gen scrf=(pcm, solvent=ch2cl2) pseudo=read gen=LANL2DZ(Fe)/6-31G**(O, S, P, C, N, H)
12. (0.97264) BD ( 1) S 4 – H 61
( 72.90%) 0.8538* S 4 s( 14.59%)p 5.84( 85.20%)d 0.01( 0.21%)
0.0000 -0.0007 0.3819 0.0080 0.0003
0.5770 -0.0258 0.0000 -0.3751 0.0197
0.0000 0.6141 0.0084 -0.0110 0.0340
-0.0165 0.0137 0.0177
( 27.10%) 0.5206* H 61 s( 99.90%)p 0.00( 0.10%)
0.9994 -0.0101 -0.0192 0.0127 -0.0227
Job 2 # ub3lyp/6-31G* scrf=(solvent=ch2cl2,pcm) pop=(nbo,savenbo)
14. (0.97361) BD ( 1) S 4 – H 61
( 72.80%) 0.8532* S 4 s( 15.03%)p 5.64( 84.77%)d 0.01( 0.21%)
0.0000 -0.0005 0.3876 -0.0005 0.0012
0.0003 0.5656 -0.0231 0.0000 -0.3807
0.0220 0.0000 0.6180 0.0024 -0.0109
0.0333 -0.0176 0.0118 0.0197
( 27.20%) 0.5216* H 61 s(100.00%)
1.0000 -0.0097
Job 3 # ubp86/gen scrf=(solvent=ch2cl2,pcm) pop=(nbo,savenbo) pseudo=read
gen=LANL2DZ(Fe)/6-31G**(O, S, P, C, N, H)
12. (0.96928) BD ( 1) S 4 – H 61
( 72.59%) 0.8520* S 4 s( 14.18%)p 6.04( 85.63%)d 0.01( 0.18%)
0.0000 -0.0008 0.3765 0.0080 0.0003
0.5692 -0.0256 0.0000 -0.3760 0.0190
0.0001 0.6244 0.0082 -0.0093 0.0327
-0.0140 0.0130 0.0173
( 27.41%) 0.5236* H 61 s( 99.91%)p 0.00( 0.09%)
0.9995 -0.0086 -0.0177 0.0121 -0.0208
I am curious about the bonding situation between sulfur atom and proton in my complex. These three calculations show similar results! However, I expected it would be a sp hybridization based on the HOMO. Should I use a simple basis set?
Thank you very much and have a nice day ^^
Kai-Ti Chu
Dear Dr. Barroso, I´m a student of a master degree in food technology from Chihuahua, I´m glad to find a blog like this, firt let me congratulate you, and then I have a question: I have been working with a Pd cluster for ethanol oxidation process and I have to handle it to diferent pH scales, Would be possible to do this with Gaussian 09? whereas also have to work with the reactants and products (mainly ethanol, OH and H3O +).
Beforehand thanks a lot.
Dear Johan
Thank you so much for your kind words thoughts. I’m glad to know this blog has been helpful to your research.
Unfortunately this is not possible with G09. You must explicitly protonate or deprotonate all species. You could use explicit solvent molecules and their corresponding ions, however your calculation seems pretty big as it is, maybe adding just a few molecules of solvent at the requested PH value could help you approximate the answer.
I hope this helps. Best wishes
how to optimize a radical cation? how to specify the +ve charge and a radical at a time?
please help me regarding this issue.
Just define the charge and make sure that the multiplicity matches that of the radical. For example lets say you have an organic molecule with charge = 0 and multiplicity 1 and you want to homolitically break a C-H bond, thus, your new charge is still 0 but your multiplicity has change to 2 (because that unpaired electron left behind can take two spin states)
I hope this helps!
Yes, it is help me a lot . Thank you.
Hi Dr. Joaquin
The titled the following article is ab initio but the method used is TD- DFT is that title correct?
http://link.springer.com/article/10.2478/s11532-010-0058-3
(An ab initio simulation of the UV/Visible spectra of substituted chalcones)
Thanks
There is some controversy as to whether or not DFT methods may be considered as ab initio, bit is a little one. The general consensus is that they are not ab initio and thus the title of thos paper is, at the very least, misleading.
Hi Sir, kindly help me how to restart qst2 job i have checked the check file optimization it is nearly there!!
Hi Dr.
How do i use gaussview for linking two methods consecutive manner, for example if we take the ethylene molecule
the initial calculation geometry optimization
and for the subsequent calculation uv , how can and What are the steps?
Thanks
Hello Sir,
This is Tamil from IIT madras, Chennai. Currently I am working in transition metal complexes. I have used G09. I need to calculate percentage contribution of atomic orbitals to HOMO and LUMO. I would be grateful if you advise me how to calculate it.
How do we incorporate the scaling factors in gaussian calculations to reach the experimental result ? Specially in getting UV-Visible spectra. please help me regarding this issue.
Thank you.
You can’t incorporate them within the program. You must do it manually after the calculation was performed.
I hope this helps. Have a nice day!
How one can put the negative charge along with a radical over a molecule? plz help me
If you have an organic molecule with a close shell configuration and you want to turn it into a radical anion, just increase the multiplicity and decrease the the charge. -1 2
The same procedure holds true for whatever electron configuration you start from.
Hope this helps. Have a nice day!
Dear Sir,
I would like to optimize the molecule which contains Iodine atoms.
How to give the gaussain basis set, a split valence (SV) of 433321/43321/43 with two polarization functions with exponents of 0.105 and 0.334.
please help me in the input of Gaussain.
Bull. Korean Chem. Soc. 2010, Vol. 31, No. 8 page 2228
Chang Kon Kim et al.
DOI 10.5012/bkcs.2010.31.8.2228
sir, i am trying trying to optimize ce3+ using lanl2dz and b3lyp bt it is showing me error.can you please suggest me the appropriate basis set.
#gaussianerror
Hi. Dr joaquin barroso. How Can I define Ortho and Para Hydrogen molecule in Gaussian 03W?
I used the following input:
******************************************
%chk=ortho.chk
#n B3LYP/ 3-21G Pop=full
ortho H2, Wave Function
0 1
H(Iso=1,Spin=1) 0.0 0.0 0.0
H(Iso=1,Spin=1) 0.741 0.0 0.0
**********************************************
and same input for para, but Spin=0
The problem is that the output files of both(para and ortho) were same. In fact, the wave functions of ortho and para hydrogen are different, so the molecular orbital coefficients which we get from gaussian also must be different.
Thank you, Have a nice day.
Dear Sir,
I am trying to find interaction between a metal ion and a phenol using gaussian 09. but it shows an error when i try to optimize the geometry. so i gave the keyword pop=readradii and in the end of input file the covalent radius of the metal ion as M 1.45 (read in Angstrom). so i want to ask will it give a valid interaction now?
Dear sir,
I am trying to calculate gibbs energy of solvation for organic fluorides using B3LYP/6-31G(d) basis set. My values do not match the experimental ones but show large deviations. I am not able to figure out what went wrong with the computations. Can you help please?
Gibbs energy/Ha GAS Gibbs energy/Ha WATER ∆Gsolv/Ha ∆Gsolv/kJmol-1
CH2F2 -238.964087 -238.968799 -0.004712 -12.371356
CHFCl2 -1058.929382 -1058.937746 -0.008364 -21.959682
Calculated (∆Gsolv/RT) Experimental (∆Gsolv/RT)
CH2F2 -4.990826479 -5.44911
CHFCl2 -8.858928834 -3.7528
Hello Monisha
Sorry for the lateness of my response. Have you tried to change the level of theory? B3LYP is a small and deficient functional and for calculating free energies you need a more sophisticated method.
Have a nice day
Sir, I got the polarizability andhyperpolarizability for a molecule as
Polar=269.2266404,
-21.2799287,
239.9810706,
-13.2687335,
-10.4386215,
201.0602443|
Which data correspond to αxx, αyy and αzz ?
HyperPolar=-29.6709602,
21.0802085,
17.142304,
-74.1961901,
56.492484,
-53.9660375,
47.6376838,
111.8904511,
-38.2762556,
58.4032979|
Which data correspond to
βxxx, βxyy, βxzz,
βyyy, βyxx, βyzz,
βzzz, βzxx, βzyy,?
Waiting for reply,
Yours sincerely
Partha S. Sengupta
Estimado Joaquín
Tengo una duda que en la página de Gaussian con el manual no puedo resolver.
Quisiera saber si al utilizar ModRedundant (o algun otro keyword), puedo en lugar de fijar la distancia de dos átomos, darle un rango mínimo y máximo.
Muchas Gracias!
Nico
Hola Nico
Si lo que quieres hacer es un barrido de la energía al variar un enlace entonces puedes usar ModRedundant para optimizar el resto de la molécula mientras que la distancia entre esos dos átomos se mueve entre tus valores mínimo y máximo (necesitas definir el paso, es decir, cuanto se modifica el enlace en Angstroms de una optimización a la siguiente). Creo que tu pregunta es algo diferente pero yo haría primero el barrido para encontrar el mínimo de energía a lo largo de ese enlace.
Espero haber entendido bien tu pregunta pero si acaso no fue así escríbeme nuevamente.
Saludos y gracias a ti por leerme!
Estimado Dr. Barroso:
No soy quimica computacoinal pero he estado tratando de calcular la fluorescencia de una molecula para predecir el efecto PET (Photo induced electon transfer). Hice calculos de optimizacion con la base semiempirica PM6 para despues poder hacer calculos de energia con ZINDO para ver los estados de excitacion. Despues para poder ver la fluorescencia de la molecula ahora optimizo el estado de excitacion con TD DFT B3lyp 3-21g en el cluster de la universidad pero ha tomado mucho tiempo (mas de dos dias) solo busco por una aproximacion, no sera un trabajo que sera publicado. Es posible guardar los calculos que hasta ahora ha realizado el cluster y detenerlo para despues proceder al calculo de energia?. Tiene alguna otra sugerencia?
Aprecio mucho su tiempo y su respuesta.
Gracias.
Hola Paulina
Disculpa la tardanza de mi respuesta. Lamentablemente los cálculos TD DFT toman muchos recursos computacionales, y el nivel de teoría tan bajo que estás utilizando no te permitirá observar nada interesante ni siquiera de manera cualitativa. mi sugerencia es que consigas a un químico computacional que pueda trabajar contigo en realizar esos cálculos.
Saludos
Dear Dr joaquin barroso
greetings
I am working in G09 .I want to study TD DFT for my molecule in different solvents. because it is very solvent sensitive molecule.
In G09 SCRF method shows, IEFPCM, SMD, CPCM, SCI-PCM model.
Which model is suitable for studying the solvatochrmoism effect?. and How it can be selected ?
thank you
hi will someone help please, i need to write 0.000143 in words. can anyone help
One hundred and fortythree millionths (?)
First off love the site. Great work!
Had a new problem/error that came about and can figure it out.
Looking to calculate the ionization potential for a organic molecule.
#p b3lyp/6-31g(d) EPT pop=full
The error that keeps occurring is:
Internal consistency failure #1 in ROv08.
Any help would be great!!
Thanks
This is probably related to a problem with the structure. Try to optimize it first.
Have a nice day!
Hi. Dr joaquin barroso. Please, answer me:
Is there any way to define Ortho and Para Hydrogen molecule in Gaussian 03W?
Thanks so much
Please ellaborate. Im not sure what you mean
I used the following input:
******************************************
%chk=ortho.chk
#n B3LYP/ 3-21G Pop=full
ortho H2, Wave Function
0 1
H(Iso=1,Spin=1) 0.0 0.0 0.0
H(Iso=1,Spin=1) 0.741 0.0 0.0
**********************************************
and same input for para, but Spin=0
The problem is that the output files of both(para and ortho) were same. In fact, the wave functions of ortho and para hydrogen are different, so the molecular orbital coefficients which we get from gaussian also must be different.
Hi, I’m still not sure what do you mean by “ortho” and “para” hydrogen, I’m sorry.
From what you just wrote I think you want to assign different spin states to different molecules but defining them atom by atom. To the best of my knowledge this is not possible with Gaussian and of course the results will always be the same. I suggest you contact the Gaussian help desk for this one.
Have a nice day!
Dear Dr joaquin barroso
greetings
I am working in G09 .I want to study TD DFT for my molecule in different solvents. because it is very solvent sensitive molecule.
In G09 SCRF method shows, IEFPCM, SMD, CPCM, SCI-PCM model.
Which model is suitable for studying the solvatochrmoism effect?. and How it can be selected ?
thank you
I would choose SMD. The thing is that what you really want here is a solvation model that is suitable for getting the interaction right. I’m not aware about any issues on solvatochromic effects changing with the solvation model. I would use all of them with a simple single well reported molecule and then compare the results.
Hope this helps!
I am working with Gaussian 03 software. May request yo how to calculate fluorescence ? Please provide a simple input file so that I can check the data.
Hi there! I will post in January about how to calculate excited states, ok?
Stay tuned!
Dear Sir,
I couldnot find your post which helps in calculating fluorescence using Gaussian?
Is there anyway that the Gaussian 09 program can perform frequency calculations for a periodical boundary using PBC?
I think so but maybe only in a numerical (not analytical) way
Hola: ¿Existe alguna manera de que el Gaussian 03 o 09 impriman las matrices de recubrimiento? Gracias, saludos. Juan.
Hola Juan,
No lo sé pero me imagino que debe haber un iOP para ello. Intenta contactar directamente a Gaussian.
Saludos
Me refería al método de Hückel Extendido. Gracias.
Dear Sir,
Happy New year ,
Dear Sir,
I would like to optimize the molecule which contains Cl, Na,O,H, C,N Iodine atoms.
How to give the gaussain basis set, a split valence (SV) of 433321/43321/43 with two polarization functions with exponents of 0.105 and 0.334. for Iodine atom.
please help me in the input of Gaussain.
Bull. Korean Chem. Soc. 2010, Vol. 31, No. 8 page 2228
Chang Kon Kim et al.
DOI 10.5012/bkcs.2010.31.8.2228
or else please suggest me which basis set is more suitable for Iodine other that LANL2dZ.
already i used lanl2dz, there is a lot of difference in UV in the calculation and experimental.
Respected Sir
I am using AIMALL standard version. I have generated a wavefunction file for Ag-water complex using def2-TZVP basis set in G09 C-version. When I want to do AIMQB calculation it is showing the error that “Invalid traditional wfn file! Could be improperly formatted 2nd line or other line”. But wavefunction created for Al-water complex with the same basis set shows no error. What may be the problem for such an error?
Thank you
Dear Dr. Joaquin,
I am new in Gaussian and I want to optimize the icosahedral gold geometry by using Gaussian 03. My system consists of 144 gold atom. I’ve used Rhf/LANL2DZ basis set. When I try to run input file with the coordinates of 144 gold atom, it gives an error message as below;
Maximum number of bonds=100 exceeded for atom 1.
Error termination via Lnk1e in C:\G03W\l101.exe at Mon Jan 12 16:07:18 2015.
Job cpu time: 0 days 0 hours 0 minutes 0.0 seconds.
File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 1 Scr=
How can I solve this problem?
Thanks,
Ayse.
This means that somehow your atom Au1 is bonded to more than 100 other atoms. Check your coordinates. Make sure the units are angstroms because if you are using other kind of units then maybe when traslocated to A all atoms superpose.
Also, if you are using geom=connectivity get read of this keyword and delete the connectivity matrix at the end of your file.
I hope this helps
Hola que tal, esta vez con una consulta en español para explicarme mejor. Estoy tratando de reproducir un trabajo de deshidrogenación de MeOH catalizada con un cluster de 7 unidades de Pt, pero en el artículo mencionan que se eligió la estructura optimizada del cluster con multiplicidad quintuplete, por ser la mas estable (al correr la optimización del mismo cluster con multiplicidades 1,3,5,7 y 9, ésta última es la que me da una menor energía), además para los cálculos de adsorción ellos utilizan una multiplicidad de spin de septeto, en lugar de la de quintuplete utilizada anteriormente, este ultimo paso no lo entiendo, espero su respuesta, le envío el link del artículo por si quisiera checar la parte de la metodologia:
http://www.sciencedirect.com/science/article/pii/S2210271X14000103
De antemano muchas gracias
Por cierto se me pasó mencionar que utilizo Gaussian 09 para realizar los cálculos
Ya resolví esta duda, muchas gracias.
Whats up very nice blog!! Guy .. Beautiful .. Amazing
.. I’ll bookmark your web site and take the feeds
also? I’m satisfied to find numerous useful info here in the publish, we’d like work out extra
techniques in this regard, thanks for sharing. . . . . .
sir, I found the shape of molecular orbital in pop=regular calculation through edit=mo command. In this way I found by observing the MO diagram as that HOMO, HOMO- 1 are pi type, lumo, lumo+1 are pi* type and Lumo+4 as Rydberg orbital. But I cannot get any data by which I sanguine that the orbitals are pi, pi* and Rydberg type. Help is needed.
I also done pop=(nbo,regular) gfoldprint, for the same system but get no information.
How can I got data regarding the HOMO, LUMO and Rydberg orbital.
You can find it all in the summary of your NBO listing just the way its described in the NBO post of this blog.
Dear Sir,
Can you please help me to find reorganization energy using Gaussain 03 software for mobility calculation..??
Dear Dr. Joaquin,
greetings,
I’m performing a calculation of transition states for a free radical chain reaction (self accelerating reaction) . The chain reaction consists of 8 steps. i have calculated transition states for 6 steps using QST3 method in G09. But I’m not able to find the transition states for 1st and 8th steps. These two steps are of high activation energy, according to the literature. The first step (initialization reaction) is about breaking a peroxide bond of an aromatic hydro peroxide, thus forming a hydroxyl radical and aryloxy radical. Second step is release of methyl radical from the aryloxy radical so as to produce a stable closed shell product. Send step is a exothermic reaction with very less activation energy (6 kj/mol). The aromatic hydro peroxide has six rotamers, and this is creating problem in finding the transition state. whatever the initial guess I’m providing, most of the time output is a transition state regarding the conversion of one rotamer to another. I have also tried relaxed potential energy surface scan of peroxy bond and took initial guess from this scan for qst3. Then the resulting transition state is about release of a methyl radical along with hydroxyl radical. I tried freezing the bonds, but could not get the required transition state.
So my questions are:
1) Is the transition state for first step is very week, and that’s why im not able to find it?
2) Is low activation energy, and high exothermicity of second step reason for why I’m not able to find the transition state for first step?
Any help would be greatly appreciated.
Thanks in advance.
Hi there,
Finding TSs is an artform, this means there is no systematical recipe to find them. You said you froze the bonds but does this mean you froze bond lengths or torsion angles? If you did the former but not the latter then you might want to try it and avoid the rotamer interconversion.
1) what do you mean a weak TS?
2) Yes and no. More like probably.
Finding -easily- a TS depends on the topography (some say topology but i think its wrong) of the PES so a low Act.Barrier and high exothermicity would look like a cliff on your PES, not as a hill. Have you considered the possibility of having started from a metastable structure which is maybe not separated from 2 by a barrier at all?
Also, what is the level of theory you are using? large basis sets will sometimes tend to smooth your PES which is not entirely convenient if you don’t know where your TSs are.
If I were you I would use an indirect approach for the 1 -> 2 transformation: Oversimplify the system, remove all substituents and hinder if possible the rotation of your bonds of interest (maybe by defining a cyclic analogue, eg. cyclohexene wont spin around CC bond when EA occurs but ethylene will. This has the advantage of having less degrees of freedom messing with your PES.), find the TS for this analogue reaction and then use its structural features to define the proposed TS for your actual system.
Be patient. Finding TS’s is quite hard for it depends on too many variables.
Hope this helps!
Hi lam shatha , l need your help about quantum mechanic methods and the types of functions G.09 thank you.
Hi, I know that the keyword “charge” can be used in the Gaussian software to include background charge during calculation. I wish to know if there is a keyword which I can use to include background dipole moment during calculation?
Hello.
You can place as many ficticious charges as you want by providing their values and positions in cartesian coordinates. Thus you can define a dipole moment by defining its charges and separation. Now this dipole would be fix and it wouldn’t respond (with a torque) to the electrostatic field of the molecule under calculation.
Did I understand your question correctly?
Have a nice day
Hello,
I am trying to optimize a acetic acid-metal-complex by putting Au atom in place of H with O atom and i want to use B3LYP-6311G(d,p) for C,H,O atoms and B3LYP-LANL2DZ for Au but i am getting error “Error termination via Lnk1e in /app1/em64t/g09/l301.exe at ”
here is my input file
______________________________
%chk=ACT.chk
%mem=4GB
%nproc=1
# opt b3lyp/gen
Acetic-ion-gold
-1 2
C
C 1 B1
O 1 B2 2 122.45304405
O 1 B3 2 A1 3 D1
H 2 B4 1 A2 3 D2
H 2 B5 1 A3 3 D3
H 2 B6 1 A4 3 D4
Au 4 B7 1 A5 2 D5
B1 1.16058515
B2 1.23026900
B3 1.33426646
B4 1.36979191
B5 1.42432303
B6 1.61488560
B7 1.23726041
A1 120.98789433
A2 102.54676530
A3 176.32582829
A4 105.48227155
A5 97.17166115
D1 -179.35286866
D2 -0.07582274
D3 166.22268129
D4 178.81429785
D5 154.69881967
C O H 0
6-311G(d,p)
****
Au 0
LANL2DZ
****
_____________________________________
Please help me,Thanks
Shafqat
Hi,
It’s my first time generating a vibronic spectra in Gaussview8. I appreciate it if you can help me with a simple way to do it.
Thank you in advance for your help.
Sara
Dear Dr. Joaquin,
I have a small question about the frequency calculations for large molecules. I have noticed that when a molecule gets larger (has more and more functional groups) the frequencies can become very low. For example:
I optimised, Si(OC2H5)4 (TEOS) molecule using B971/6-311+G(d,p) level of theory with VeryTight Convergence criteria and Ultrafine Grid (I used Gaussian09). Subsequently, I performed the frequency calculations at the same level of theory. This what I found is that the first nine vibrational modes are within 18-62 cm^-1 range (this is apart from the six vibrational modes corresponding to the translations and rotations which are equal to:
Low frequencies — -4.3983 -0.0016 -0.0016 -0.0016 3.5600 4.2328).
I noticed similar thing in other large silica molecules. In some cases, the smallest frequencies were about 10 or 15 cm^-1.
May I ask you if it is correct to have frequencies which are so low? I know, that some of the vibrational modes correspond to internal rotations. Therefore, these nine low frequencies in TEOS case may be related to the C2H5 and OC2H5 hindered rotors. However, it could also be an effect of the accumulation of numerical errors in my calculations.
I am asking this question because I am trying to predict rate constants for some TEOS pathways and correct values of low vibrational modes is essential.
I would be very grateful for your help,
Daniel
Dear sir
I am Vidhya.I trying to calculate the PCM Analysis for molecular structure using basis set (HF/6-311++G(d,p)).Few solvents are run properly(Water) But some solvents are not run. What is the problem. Many time I try do it.Lower basis set HF(6-311G) solvents are run but free energy few values are positive.Can you give some information.
Hi Vidhya,
What solvents are you having troubles with? you don’t have to lower the level of theory but rather to increase it. About the sign for DG do you mean it happens only when the level of theory is decreased? I think I need more information.
Have a nice day
Dear Sir,
Could you please advise me how to customize a basis set, such as add a f-type, a p-type function to a certain basis set.
I often find in paper the description like: “LANL2DZ was used for Au. To presicely describe the……., one additional f-type function was implemented alfa(f)=0.2”
Could you please show me how to do so, by modifying the basis set. The LANL2DZ for Au from EMSL is as below:
Thank you Sir!
****
Au 0
S 3 1.00
2.8090000 -1.2021556
……
S 4 1.00
2.8090000 1.1608481
……
S 1 1.00
0.0598000 1.0000000
P 3 1.00
3.6840000 -0.2802681
……
P 2 1.00
0.6838000 -0.0952078
0.0977000 1.0299147
P 1 1.00
0.0279000 1.0000000
D 2 1.00
1.2870000 0.5844273
0.4335000 0.5298161
D 1 1.00
0.1396000 1.0000000
****
AU 0
AU-ECP 4 60
g-ul potential
5
1 622.6287956 -60.0000000
….
2 3.0481312 -4.2516681
s-ul potential
6
0 194.7374304 3.0000000
….
2 4.4916223 -152.4532773
p-ul potential
4
0 420.6158801 2.0000000
….
2 5.9879750 126.5814591
d-ul potential
5
0 219.2666158 3.0000000
….
f-ul potential
5
0 108.5506037 4.0000000
1 56.4795527 51.8065335
2 29.2069159 231.2183113
2 9.5440543 119.0047386
2 2.8965118 15.3424188
Hi there,
I think the easiest way to do so is by using the ExtraBasis keyword. You type your basis set normally, you add the aforementioned keyword and add the definition of the extra funtion you want to add.
Take a look at the following link. I hope it helps
http://gaussian.com/g_tech/g_ur/k_extrabasis.htm
Dear sir
could you help me about scan calculation .i need detail description with example about scan calculation with G09
Hello. Please google rigid scan joaquinbarroso so you get the proper post within this blog.
I hope this helps
dear sir,
i am doing research in polymer electrolyte using Gaussian theoretical work. I have a problem in running my compound with cationic and anionic geometry.
Thanks in advance
with regards
Maheswari
Hello Maheswari,
I’m afraid you need to be way more specific.
Have a nice day
Hola Joaquin
tengo una estructura que le esta costando optimizar y todos los parámetros lo hacen exepto el Maximun displacement que se que da muy cerca del valor
que opcion puedo utilizar para disminuir tantito la tolerancia de la optimizacion para que la estructura optimice
el defaut es de 3×10-4 digamos que quisiera 2×10-4
Agradezco tu ayuda
Atte
Javier
Cinvestav
Hola Javier.
Puedes utilizar la opción Opt=Loose para hacer una primera aproximación, pero es preferible que luego de hacerla optimices la estructura resultante, ya que el ‘grid’ para calcular la densidad (asumo que usas DFT) también se ve afectado. No sé si puedas modificar los criterios de convergencia a conveniencia, no tiene mucho sentido, ya que simplemente podrías decir en este punto “este es mi criterio y por lo tanto ya convergió”.
Saludos hasta el CINVESTAV
Perdon se me olvido decir que estaba trabajando en Gaussian 09 vC.01
gracias
Muchas gracias por la recomendación y en efecto utilizo DFT
Hi,
I am following your blog for few years and I really appreciate your efforts to help others.
I have a question related to AIM2000, I am running AIM2000 for my molecule however as it takes long time, sometimes because of limited memory or power problem I have to kill the job, is there any way to continue calculations from the last point?
Usually the step of calculating the maximum triples took very long time and I have to repeat the calculations again.
Kindly help
I need to make some theoretical calculations on some novel synthesized zinc- phthalocyanine complexes.
I have a problem in my calculations as the HOMO is always delocalized over zinc atom which is not logic. I try to make the same calculation for un-substituted ZnPc and obtain the same results (as shown in the attached photo).
Could you help me to explore the error.
Regards,
basma
What level of theory are you using? Probably you have a very large basis set on the Zn atom. I’m not familiar with these systems but are you sure this is an error? Try changing the level of theory first for a smaller basis set (and then for a larger one) and see what happens.
I hope this helps!
Thanks so much for your reply, I found the problem in the charge in the centeral metal and I can fix it now.
Can I ask you another question? I wonder How can I draw the MO energy diagram, and how can I extract the number of sub-symmetry number from gaussview or chemcraft, (i.e. (HOMO, —–2—-A1u)), as I can take the symmetry from chemcraft without this number (2) also the figure can be exported from chemcraft but it is not clear at all for publication and I can’t zoom it enough.
Regards,
Basma
dear sir,
how to run cationic geometry and anionic geometry of a polymer molecule using Gaussian 09 software. kindly help me sir.
Hi Maheswari, you can do it by varying the charge and multiplicity in the input file.
For instance,
neutral 0 1
cationic 1 2
anionic -1 2
– Uma
Hi,
I appreciate if you could help me with resources, as i am a beginner in using Gaussian09 with pharmacy background. I need tutorials for gaussian generally, and for energy optimization, bond freezing, excited state, fluorescence and absorption, specifically.
Thanks in advance,
Muhammad
Dear Muhammad,
Try finding a book called “Exploring Chemistry with Electronic Structure Methods” by Frisch and Frisch. I don’t have it available so I cannot share it with you. This is a great resource for beginners in Gaussian, although it was written for G98, most of it is still valid for G09.
I hope this helps!
Dear Sir,
Subject : Negative values for LUMO
I am doing DFT GO with 6-311 G++pd basis set and B31YP using Gaussian09 the molecular formula is (C15H11Cl2NO) with (150 electrons). I get (75) occupied orbitals However there are (82) orbitals with negative Energy . This mean the LUMO has negative energy. There is no imaginary frequency
Full mass-weighted force constant matrix:
Low frequencies — -7.1911 -0.0134 -0.0078 -0.0047 1.9631 3.9558
Low frequencies — 13.1999 28.5837 36.9769
Diagonal vibrational polarizability:
94.4862631 70.1500090 116.8961789
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A A A
Frequencies — 12.6214 28.5009 36.9430
Red. masses — 7.0918 4.2317 8.2861
Frc consts — 0.0007 0.0020 0.0067
IR Inten — 0.6342 0.2104 0.4398
I request your advice on the negative value of energy for the LUMO and how to tackle this problem. With my best regards.
This isn’t necessarily a problem. It depends on what your molecule is. Can you see it as a powerful electron acceptor? I would change the functional from B3LYP to PBEPBE. Give it a try and let me know what happened.
I hope this helps!
Hi,
I appreciate helping me in these matters!
a) should i freeze the bond length only? or freezing the bond angel and dihedral angel as well?
b) After having output log file for optimization and frequency; what should I do? i mean how to extract results?
c) Where i can find examples for the most common jobs (input files), coz i am a beginner and it may take weeks to know where is the error in my input files.
Hi Muhammad,
I’m not sure what are you talking about 🙂
a) Depending on what you want to calculate.
b) Search in the output for the phrase “Optimized parameters” this will take you to a long table with all the bond lengths and angles of the optimized molecule. This is very boring so try using a visualizer program instead. Also search for the word “Frequencies” this will display a long list of vibrational frequencies, the first one should be positive for you to know this is a stable state, a minimum on a surface and not another kind of state.
c) This blog has some examples but I suggest you look for that book I told you: Exploring Chemistry with Electronic Structure Methods
I hope this helps
How to use the output of low level of theory calculation, as input for a higher level of theory, in details please? i read that i can use the checkpoint file of low level method to save time and getting a better accuracy
In your new input include the chk line making a reference to your old calculation, then in the input specify that the wavefunction and the geometry have to be read from it. No need to add coordinates but you still have to specify charge and multiplicity. Example:
%chk=oldfile.chk
# guess=read geom=check all-other-keywords
comment
0 1
-blank line-
I hope this helps
Hi,
if the time was not enough for completeness of submitted job, should I repeat the calculation from the beginning or there is a way to resume the job?
Sir
I am from India.
I have been trying optimize the structure of cyclopropenyl carbene(triplet) using MP2/6-31G(d), I am sending the input file. But it says that there is a #2070 error after the optimization. Can you please check whether my level of theory and basis set is sufficient for this system, or suggest a better alternative.
%mem=6MW
%nproc=1
%chk=CPTRIP2.chk
# opt ump2/6-31g(d) nosymm geom=connectivity
Title Card Required
0 3
C
C 1 1.299101
C 2 1.463395 1 63.649311
H 1 1.079741 2 149.639600 3 -170.548274
H 2 1.079777 1 149.623659 3 170.566591
1 2 2.0 3 1.0 4 1.0
2 3 1.0 5 1.0
3
4
5
Dear Prof. Joaquin,
Thanks so much for recommending “Exploring Chemistry with Electronic Structure Methods” to read. it’s very helpful for beginners.
Do you recommend another resource showing how one could extract results from output file and how to present it in a table form. My study will be concerned with IR, UV-Vis, optimization and single point Energy.
I’m glad you liked it. Extracting numbers can be easily done by writing your own shell scripts. I think I will write a post on how to do it. Thanks
Hi,
I am wondering about the difference between single point Energy and energy after optimization. Also, how i use my optimized structure with its single point energy for IR, UV-Vis, excited state and solvatochromism studies.
Since both geometries are different energies will be different. You should always first optimize a molecule before drawing any conclusions, except in very specific cases like when you are trying to explore the crystal effects on a molecule’s specific conformation.
If you need the optimized structure for further calculations you can do one of two things:
1) The easy way. Open the optimized file with a visualizer and save it as an input file with new parameters and keywords as to set your new calculation.
2) The elegant way. Set a new calculation from scratch with %chk=oldfile.chk where ‘oldfile’ stands for the chk file from the optimization calculation. Then, in the route section, use guess=read geom=check This keywords will retrieve the wavefunction and geometry from the last point of the calculation stored in oldfile.chk. Don’t forget to still write the charge and multiplicity line, after which a blank space is needed (the coordinates should not be there since you are asking gaussian to read them from the oldfile.chk)
I hope this helps
Hello,
First, Happy Easter!
Please, can you help me find how to assign and scale vibrational frequencies from output file of gaussian09? I mean how to know of this vibration is scissoring or wagging or twisting, …….. and what is meant by scaling and how to do it.
The easiest way to do the assignment is to open the log file or the .fchk file with a suitable visualizer (GaussView, Molden, VMD, Chimera, etc.) and ask for it to animate each vibration. The scaling part needs you to find a suitable set of scaling factors from the literature. You can also scale them by hand by looking at the vibration of interest and relating them to the experimental values. Due this at your own risk and try to justify your conclusions properly.
I hope this helps
Hello
I am trying to do optimisation caluclation & also some other calculations using DFT in solvent for Co, Ni, Cu complexes. created an input file for the linux version. but whenever i am submitting the job it is showing the following error.
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff
rdx 0000000000002b44, rsp 00007fffea3ae6c8, rbp 00007fffea3aeca0
rsi 000000000000000b, rdi 0000000000002b44, r8 00002b2ebdea8160
r9 0000000000000000, r10 00007fffea3ae450, r11 0000000000000202
r12 0000000000000000, r13 0000000000000000, r14 00007fffea3aece8
r15 0000000000000000
— traceback not available
Can you tell me what is this error means and also please help me running my job.
ThanQ
vani
Sorry forgot to mention I m using gaussian09 software for the calculations.
Hello Vani,
This message is provided by the shell, not by gaussian. In other words this is your computer telling you the calculation was aborted but it doesn’t tell you why. What you need to do is to open your output file (probably with the .out or .log extension) and read (or send me) the last few lines. If you are getting this message almost instantaneously after submitting your job it most probably relates to a simple syntax error in your input.
I’m sorry for the lateness of my response. I hope it helps!
Awesome site you have here but I was wanting to know if you knew of any discussion boards that cover the same topics talked about in this article?
I’d really like to be a part of community where I can get feedback from other knowledgeable people that share the
same interest. If you have any suggestions,
please let me know. Thanks!
Hello,
I would be grateful if you could help me solving the problem i got on optimization:
The command I used is #opt b3lyp/6-31+g(d,p) scrf=(solvent=dichloromethane,smd)scf=xqc
the error message was as below:
CPHF failed to converge in LinEq1.
Error termination via Lnk1e in /center/local/apl/cx/g09/l508.exe at Sat Apr 18 09:03:20 2015.
Job cpu time: 34 days 5 hours 51 minutes 17.0 seconds.
File lengths (MBytes): RWF= 21126 Int= 0 D2E= 0 Chk= 69 Scr= 1
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff
rdx 0000000000002244, rsp 00007fff90a5b088, rbp 00007fff90a5b600
rsi 000000000000000b, rdi 0000000000002244, r8 00007f1754931700
r9 0000000000000000, r10 00007fff90a5ae10, r11 0000000000000206
r12 0000000000000000, r13 0000000000000000, r14 00007fff90a5b648
r15 00000000000003e6
— traceback not available
Thanks in advance.
Hi,
Try either one of two things: Remove the keyword scf=xqc and/or include a read flag on the scrf command, while using the OFac and RMin values that I wrote about in a previous post on PCM here in this blog.
I hope this helps.
Many Thanks..
Good Day..
Excuse me
I spent a lot of time on using materials studio software to studying adsorption on Fe(110) surface,
the problem is no reproducibility results by molecular dynamics!! where is the problem?
is materials studio an accurate software??
Recently I was trying to calculate the effect of ligand field on the acetylenic C-H stretching frequency. But I am unable to understand how to calculate projection of electric field onto the corresponding bond generated by different ligands. I am using MP2 method under Gaussian09 for my calculation. It would have been very helpful if you guide me how to make input to specifically calculate the electric field potential at the coordinates of C and H atoms originated from ligand field.
#fukuiindices
Hi Dr. Barroso,
Your blog is such a great reference– thanks for all the great posts! I was referring to your blog post from awhile back on calculation on the Fukui function (in this case I’m computing the minus function). Everything looks good from the visualization (in Gaussian), however, the area visualized is covering over more than my molecule– it’s covering a lot of the empty space. The empty space is zero as indicated by the visualization of the function, which is good, but I don’t know why it’s doing that. Overall, what I’m doing is mapping the Fukui function (my pop(neutral) – pop(cation) in cube form for Gaussian) with the ESP of the neutral molecule and the total density of the neutral molecule. Is this okay?
Thanks for your time and any assistance you can offer. It is greatly appreciated!
-Mike
Dear Mike,
Thanks a lot for your kind words about my blog; I’m glad you’ve found it useful.
Your problem is quite curious and I don’t think I’ve ever heard something like that! I imagine you have double and triple checked if you have loaded the correct fchk file. Maybe one cube is calculated or plotted on a different orientation to the standard or input orientation. I’ll try to find a solution but quite frankly I’m as surprised as you are.
Have a nice day
Respected Dr. Joaquin Barroso,
I want to estimate aqueous stabilization of some drug molecules. For this purpose I have to calculate the Delta G of solvation (aqueous solvation free energy) with a self-consistent reaction field method in Gaussian09. I have seen your blog, and I am quite impressed. I have following your suggestion I have calculated delta G solvation, but as a new user of Gaussian, I cannot interpret the results from .log file.
The syntax used for calculation is as follow.
%nprocshared=8
%mem=2000MB
%chk=CDK2_lig_11B_energy.chk
#p b3lyp/6-31+g(d,p) scrf=(smd,solvent=water,DoVacuum) geom=connectivity
Kindly guide me if something is missing in my input file.
Hi Dr. Barroso,
I am doing geometry optimizations with TD-DFT in Gaussian (CAM-B3LYP/cc-pVDZ level of theory) and get the following, seemingly after every SCF iteration:
“the largest alpha MO coefficient is ***”
or less commonly:
“the smallest alpha/beta delta epsilon is ***”
I notice you’ve responded to this before. Regardless of basis set, it seems to come up for my dimer system. The order for the alpha coefficient is around 0.1-0.2D+02. As far as I can see from digging around, since I don’t plan on using the computed orbitals for post-HF calculations, the warning can largely be ignored. (I hope this is true?) I did notice one response:
“For HF and DFT calculations the code which checks this [the calculation of MO coefficients] is run but seldom is it an issue, it is actually just after the SCF completes.”
I’m concerned about the wording of this sentence. Does it mean: “if the warning is printed as an SCF calculation completes, it is a problem?” or “the calculation is always performed as SCF completes.”
Thanks so much for your time and help, any and all you can/have time to offer!
-Kate
Hola.
Buena tarde, soy luis alumno de la Dra. Rubicelia Vargas de la UAM-I.
Pasa que estoy realizando unos calculos MP2 en NwChem, los sietmas sonde capa abierta, pero me arroja el siguiente error: cphd did not converge.
Eh aumentado el numero de pasos y e incluido la bandera set cphf:maxsub 45, pero sigue el mismos error. Espero me pueda ayudar.
Hola Luis,
No estoy familiarizado con NWChem pero intentaré ayudarte. ¿Has revisado tu estructura? ¿Se encuentra optimizada o tiene oportunidad de mejora? ¿Hay forma de seleccionar el algoritmo en NWChem para realizar el MP2? Estas son las tres primeras cosas que revisaría en tu lugar. Si me mandas más información podría ayudarte mejor.
Saludos a ti y a la Dra. Rubicelia
Si, la estructura de la que parto para el cálculo MP2 la obtengo de un cálculo a nivel M06-2X/aug-cc-pVDZ y el input que utilizo es el siguiente:
echo
title “_guan_VCl2OH2_N7”
start guan_VCl2OH2_N7
scratch_dir /tmp
permanent_dir .
memory total 3000 Mb
geometry units angstrom
symmetry c1
N 0.39260155 -0.56634869 0.43563084
C 1.09584544 -1.62021003 0.76274813
N 0.34884148 -2.76372259 0.69603046
C -0.91107146 -2.41494570 0.29582384
C -0.87283743 -1.03687591 0.13891439
N -1.94481839 -3.26604430 0.09698180
C -3.03636606 -2.65013844 -0.27631213
C -2.08239546 -0.36184169 -0.23507029
N -3.12134731 -1.29095165 -0.44060246
O -2.31868219 0.83152126 -0.36831821
N -4.18527687 -3.36139962 -0.47184555
H 2.14049413 -1.59585397 1.04758838
H 0.66356474 -3.70164659 0.90157671
H -4.01420820 -0.86473404 -0.66389265
H -4.05755392 -4.36374897 -0.48776633
H -4.88624913 -2.99639732 -1.10018020
O -0.19261385 2.12309436 0.67575857
V 1.20969819 1.46223979 -0.05583087
Cl 2.20723107 3.33196511 -0.86127258
Cl 2.95736789 0.88289946 1.26262476
O 1.08005838 0.75810801 -1.68683210
H -1.07137676 1.85902481 0.31498822
H 1.48130496 1.32861280 -2.35706209
end
basis “ao basis” cartesian
V library “aug-cc-pVDZ”
Cl library “aug-cc-pVDZ”
C library “aug-cc-pVDZ”
N library “aug-cc-pVDZ”
O library “aug-cc-pVDZ”
H library “aug-cc-pVDZ”
end
set lindep:tol 1.0e-06
set tolguess 1.0d-8
set cphf:thresh 2e-5
set cphf:maxsub 45
set int:acc_std double 1d-15
set cphf:maxiter 400
scf
uhf
semidirect
vectors input atomic output guan_VCl2OH2_N7.movecs
doublet
maxiter 200
tol2e 1.0e-14
end
mp2
freeze atomic
end
driver
maxiter 200
end
task mp2 optimize
task mp2 freq
hello, do you know if I can get a .com file from a .log file? I lost the .com file but the .log generated file I have in my computer. I want to know the exact parameters for the computer so I can try to submit a new job on a different structure.
I also ran a new calculation on a supercomputer remotely and it generated a .log file but I cannot view mulliken atomic charges on gauss view under Results–>Charge Distribution. The “Show numbers” option cannot be checked off.
Please let me know if you know the answers to these questions. It would be a huge help!
There is an echo at the beginning of every output file in which the route section is repeated. Try searching for it just a few screens down the beginning. Also try using the NewZmat utility if you still have the checkpoint file available.
Hope this helps!
Thank you.
I can access for those numbers under “Mulliken charges” when I open the .log file as a textfile. Is there a way to make this viewable on gauss view? It doesn’t show up as it normally would if I run my calculation on my own computer.
The .log file says # opt freq=noraman b3lyp/6-31+g(d,p). Is this the parameter that was used to run the calculation?
Thank you so much for your reply!
Hi Steve
Try editing your output file and change ‘Mulliken charges” for “Total Atomic charges” – not sure about the capitalization though.
I imagine you are using different versions of Gaussian between computers. Try comparing a test calculation between them with say water and look for differences of the header since they have changed but older versions of the visualizer are still looking for older headers.
I hope this helps
Hola Dr. Joaquin Barroso.
Muchas gracias! por su tiempo para responder a todas estas inquietudes de la gente.
Aprovecho para hacer una pregunta: Qué es lo que realmente se calcula cuando nos arroja un valor de -834 ha de energía libre de Gibbs. Ya que, al convertirlo en kcal/mol (multiplicar por 627.5095) queda del orden de los Mega kcal/mol (-523342 kcal/mol). La molécula es C3H5O5P y el nivel de teoría es B3LYP/6-311++G(d,p). Antes del cálculo de frecuencia, la molécula se optimizó a su estructura más estable (para esto se hizo una SCAN a nivel B3LYP 3-21G).
La verdad, es que no le encontramos sentido a ese valor ta enorme.
Muchas gracias!
Respected sir
While computing the anharmonicities xij coefficients by VPT2 using gaussian, if we detect the fermi resonance between modes depurtubation is applied. How depurturbation is being applied what are the key words for it? kindly solve the problem
Cordial Saludo Dr Joaquin Barroso
Quería comentarte que yo estoy trabajando con un sistema C–H–G en donde tiene lugar una transferencia proton, por lo que quería saber si hay alguna forma de calcular las frecuencias en el Gaussian 09 para cada paso a lo largo del IRC, una vez obtenido el estado de transición (alguna Keyword), o es necesario crear una tarjeta de entrada (input) para cada paso.
De antemano muchas gracias
Cordialmente,
Andres Felipe Cruz Ortiz
Hola Andrés,
Creo que lo que necesitas es usar el keyword FREQ=CalcAll o FREQ=CalcFC pero no estoy seguro si te imprime todas en la salida, a lo mejor usando el nivel de impresión #P al inicio del route section.
Saludos
Dear Sir,
I want to simulate the band structure of Boron Nitride in Gaussian software but didn’t found any fruitful resources yet. Can you please give me some suggestions regarding this? Thank you in advance.
Hello,
I have two issues. Can you please provide some useful tips for those two issues.
What is the suitable way for characterize CH-pi and SH-pi interaction using DFT method. Could you please provide some references for this.
How can I get the name of the MO’s from gaussian calculation. It is showing only the serial numbers according to their energy values if I load it on gaussview.
Best
shankar
Hello Sir,
Is there any software that can extract the emission spectra (fluorescence) from gaussian output file.? Like Gabedit which you can use directly to create a UV-vis spectra?
I’m using G09.
Rushie.
Dear Sir,
Kindly write a note on the calculation of Emission wavelength.
a very much awaited and requested topic.
Thank you in advance
Noted! I’m working on it 😉
Dear sir,
I am trying to calculate the transition density of a molecule. Using Gaussian I am trying to generate the .cube file which could be used for further calculations in qchem. I have input the co-ordinates of the molecule from the crystal structure of the molecule and am using the following command to generate the .cube file.
%chk=NI-absorption_cube.chk
%mem=1GB
# td=(singlets,nstates=12) b3lyp/6-311++g(2d,2p) scrf=
(solvent=acetonitrile,pcm) geom=connectivity
scf=(convergence=6,maxcycle=512)
As I am new to this type of calculation I am not much aware of the commands to use. Actually I want to calculate the transition density from the solid-state crystal co-ordinates and don’t want to use the solvent model (PCM). So what command should I be using in order to calculate the transition density in the solid state? Should I leave the scrf= (solvent= ) blank?
Thank and regards,
Abbey
Hello Sir,
I am trying to calculate the contribution of energies using NBO with help of Gaussian’09 in ionic state. But after getting the occupancies and energies for every bonds, I found the error.
___________________________________________________________________
Keyword ALPHA (or A) not found to start alpha NBO deletion input.
Error
Error termination via Lnk1e in /home/laserlab/ankit_g09/g09/l607.exe at Sat Jan 24 14:17:52 2015.
————————————————————————————————————-
Can you suggest something so that I can do that.
Thanking you
Ankit
Hello Ankit,
I imagine you have an open shell calculation, i.e. Your multiplicity is different than one. The NBO procedure handles the alpha spin wavefunction and orbitals separately to those with beta spin, and so the program asks explicitly on which spin do you want to perform your deletion.
On your input file you must specify ALPHA after the $DEL instruction. You should then repeat the instruction with BETA if you want the deletion to be performed on both spins.
Hope this helps
Thank You Sir, I did the same and got the result. But I also want to do NBO for excited states. Can you help me in this ?
Thanking You
Ankit
Dear Joaquin!
Espero poder escribir en castellano.
Tengo una pregunta para Ud., que es especialista en química teórica y computacional.
Revisor de Spectrochimica Acta me solicita atribuir números de onda con PED. Gaussian programas no fornece PED. Tengo una via alternativa para hacerlo, la que consiste en ver los desvíos infinitesimales de las coordenadas internas en cada modo vibracional, y así hago mis atribuiciones.
No he conseguido hacer funcionar el programa VEDA4; tal vcez mi error está en el comando de entrada en Gaussian.
Coloco, por ejemplo: # p B3LYP/3-21G Opt Freq=Raman Test
Preciso de agregar algo más en la línea de forma el resultado de salida sea compatible con la lectura del programa VEDA4?
Agradecería unas luces al respecto!
Quién es el nuevo director del Instituto? Antges era Ceo Olivares.
Un abrazo, Claudio
cayotellez@gmail.com
#Gaussian #QST2 #Transition State #Optimization
Dear Dr. Joaquin, I am trying to optimize nafthalene radical anion and TFO (as a preliminary step to QST2 for TS of protenation). in the first step when two molecules are far from each other, they optimization to single dot and i get “Problem with the distance matrix’ (i check it with the final cordination and it right…). what i do wrong?
#p M062X/6-31+g(d,p) opt=(maxstep=100)
[in gaussview i confirmes the z-matrix is fine)
Many Thanks for any Reply!!
Worked out. the molecule was needed to come a sharper angle
thank
Hi Joaquin,
I want to plot ACID map to visualize aromaticity. For that, I already have AICD-1.5.7.1 program from Prof. Herges and I have already done NMR computation by NMR=CSGT IOp(10/93=1) keywords by gaussian 09 D.01 (binary). So, gaussian generated one .log file and one data file. As far I know, from gaussian 09 help, that the data file can be processed by stand alone AICD program. My question is that how to do so? I could not find any detail manual for the program. Whatever I understood from the AICD script, in the root directory of the program, that gaussian should be patched with AICD program and for that I should have the source code. Unfortunately I dont have it; I have only binary. So, how to get ACID plot by using AICD and g09 binary?
I understand that this question may not be suitable for this blog but I tried to get my answer from somewhere else also and unfortunately I did not get. At this point, if possible, please help me to sort out the issue.
Thank you in advance.
Cheers,
Anup Rana
Hi Anup.
I’m very sorry but I have no experience with AICD. Perhaps you could contact the developers directly. If you get an answer please share it here!
Have a nice day
Hi, I want to know which one is more significant comparing “D95** and maug-cc-pvtz” OR comparing “6-311++G(2d,2p) and maug-cc-pvtz”. Thank you very much in anticipation.
Hi,
How can i calculate electrostatic interaction energy, dispersive energy, repulsive energy, cavitation energy and free energy using Gaussian?
Hi,
Please help me. In my calculation, I am using Cl and S atoms. There are other atoms like H,O, C,N etc. If I use 6-31G(d) for all atoms including Cl and S, the calculated energies are less negative than that if I use pseudo potential for Cl and S atoms using the following manner:
H N C O
6-31+G*
****
S 0
S 3 1.00
6.8335180 -0.0438750
2.0777380 0.3198940
0.4191210 -0.6612330
S 1 1.00
0.1532370 1.0000000
P 3 1.00
1.8171390 -0.0792270
0.8550700 0.2636710
0.3120530 0.5806820
P 1 1.00
0.1016870 1.0000000
P 1 1.00
0.0298100 1.0000000
D 1 1.0
0.49810406 1.00
****
Cl
S 3 1.0
14.073076000 0.020345000
2.331565000 -0.289223000
0.507100000 0.630367000
S 1 1.0
0.182433000 1.000000000
S 1 1.0
0.0912000 1.00
P 3 1.0
3.353129000 -0.041552000
0.785686000 0.399748000
0.267454000 0.591829000
P 1 1.0
0.078275000 1.000000000
P 1 1.0
0.015477000 1.000000000
P 1 1.0
0.0075000 1.00
D 1 1.0
0.61834526 1.00
****
As I know, for pseudopotential the results are more correct. So, what wrong I am doing, I have expected more negative energy (more stability) for pseudopotential. Please help me me in this regard.
Thanking you
#RydbergContamination
Hello Dr. Joaquin,
A lot many of paper mention that, TD-DFT calculation of singlet excited states some times produce one electron configuration that is severely contaminated by spurious Rydberg state. None of these paper mention how to detect presence of these type of contribution by inspecting the involved molecular orbitals (MO) of the molecule. If you can explain a little about this topic, it would be helpful.
Thanks
Sayan
when i run a particular programme it give link died error how it can we resolve
#gaussian #oxygen #energy #singlet #triplet
Hello Sir,
I attempted to calculate the energy difference between singlet and triplet molecular oxygen.
What I did, is I optimized O2(t) and O2(s) and calculated their single point energies at different levels of theories, B3LYP, MP2, CCSD(T), and CASSCF, but my results were far away from the reported value of 22.5 kcal/mol. of course I took the ZPE difference into consideration
Could you direct me in calculating the difference in a better way using G09
hi
when i launch the DFT calculation sometimes, after several days that runs, if i check the file start to give me this lines.
Estimated number of processors is: 3
CoulSu: requested number of processors reduced to: 5 ShMem 1 Linda.
CalDSu: requested number of processors reduced to: 6 ShMem 1 Linda.
LinEq1: Iter= 31 NonCon= 1 RMS=1.78D-02 Max=1.31D+00
what is your opinion?
thanks in advance
Hi
I try to do ONIOM calculations by gaussian, my system have a mtal (iron), when I wan to run, I have an error:
Read MM parameter file:
Define FE 1
End of file in RdPar.
Error termination via Lnk1e in /share/apps/g09/l101.exe
I run by #p oniom(b3lyp/6-31g:amber=hardfirst) geom=connectivity
Can you suggest something so that I can do that.thanks a lot
Great Article. Thanks for the info. Does anyone know where I can find a blank 6-J Form to fill out?
Dear sir,
I am having an error while optimizing structure in Gaussian 03. the error is as follows
.
Error termination via Lnk1e in /home/gauss/gaussian/g03/l101.exe
Your suggestion is needed.
Thank you
Manoj
Hello,
This is a general error that might mean many things, you need to look in the lines above for a specific error, in order to know what happened.
hello,
i need to find TS protenation of naphthalene radical anion by MeOH in the gas phase and in solvent. i tried with qst3, qst2, opt=(ts), but up till it found only different TS.
i guess the reaction occurs when the MeOH get closer to naphthalene from the upper side.after it didn’t work i tried the option the MeOH comes from the side and this also didn’t work well.
i have used m062x and opt=(calcfc).
thank you very much for helping me
Gil
Hello Gil
Try to obtain an MO picture for the naphthalene radical anion in order to study the HOMO and LUMO, since it is an attack on an anion, you might need to look at the LUMO, or the the LUMO+M (+1, 2 etc); This will give you a better idea where the MeOH should attack .
Another thing that might help, is to perform a relaxed scan on the MeOH-naphthalene system, and see how MeOH is approaching it from different angles, prior to attempt a TS
Hope that will help
Dr. Ismail Badran
#gaussian #TS #PES
thanks!
i didn’t think about SOMO+1. do you think the methanol get closer from the side?
i attach here image of MO. all these orbitals on the naphthalene radical anion are SOMO, the sidewalls orbitals is SOMO+1.
https://drive.google.com/file/d/0B7eNnfWTlbGLWnhXWkxUNHlhUWM/view?usp=sharing
i will try the scan.
Dear Dr. Barrose,
Kindly comment on the followings,
1. How to compute EPR J- values (coupling constant) for a particular metal complex?
2. We have modeled some AFC (anti-ferromagnetic coupling) calculations. What is the significance of followings appeared in output file..
(a) Isotropic Fermi Contact Couplings
Atom a.u. MegaHertz Gauss 10(-4) cm-1
1 O(17) 0.10558 -32.00032 -11.41851 -10.67416
2 N(14) 0.17788 28.73700 10.25408 9.58563
…………………………..
…………………………………
(b) Center —- Spin Dipole Couplings —-
3XX-RR 3YY-RR 3ZZ-RR
——————————————————–
1 Atom -0.439118 -0.090913 0.530032
2 Atom -0.137311 -0.338289 0.475599
3 Atom -0.041455 -0.049995 0.091450
……………………………………
……………………………………….
(c) Anisotropic Spin Dipole Couplings in Principal Axis System
———————————————————————————
Atom a.u. MegaHertz Gauss 10(-4) cm-1 Axes
Baa -0.5629 40.733 14.535 13.587 0.8994 0.4180 0.1280
1 O(17) Bbb 0.0072 -0.524 -0.187 -0.175 -0.4051 0.9069 -0.1156
Bcc 0.5557 -40.209 -14.348 -13.412 -0.1644 0.0521 0.9850
………………………. what is the meaning of Baa, Bbb and Bccc
…………………………….
From the above data can we say something regarding the electronic coupling (ferromagnetic or anti-ferromagnetic)
(3) How can we model the ferromagnetic coupling pattern in a particular system?
Thank you in advance,
Best
Dear Sir,
I have two questions and it would be great if you’d answer them!
1. I tried to compute a guess TS with Gaussian, but every time I get errors, some times it is Error in internal coordinate system, sometimes Error termination request processed by link 9999
and this is my input file http://pastebin.com/8ubZJtGV can you tell me what am I doing wrong? Ex. my colleague did very similar thing, and he hasn’t any errors.
2. Can you reccomend any CPMD tutorial? Something for newbie?
Sincerely,
F.
for your first question;
Explanation of Error
This means that the Gaussian job terminated abnormally in some fashion. Typically, it means that a geometry optimization has not converged.
Fixing the Error
Geometry optimizations usually fail to converge for one of a few reasons:
If your initial starting structure is not good, then you should ask if you can provide a better starting structure, for example, one optimized at a lower level of theory. However, if it looks as if the structure is converging to what you want, as seen in your visualizer of choice, then one should restart the optimization from the last step, for example by using geom=allcheck in the route line, and it generally is a good idea to also use opt=CalcFC in these situations if it is not too expensive (say HF or DFT).
If your starting force constants matrix (Hessian) is poor, use a better one. This typically manifests itself when they vary a lot between levels, or if there is a large geometry change during the optimization. One can carry out a series of linked jobs (–Link1–). If you have a previous job, then usually Opt=ReadFC works well, but occasionally Opt=CalcFC, or rarely Opt=CalcAll are needed. In these cases, the forces are often converged, but the steps are not, and the final output will look like
Item Value Threshold Converged?
Maximum Force 0.000401 0.000450 YES
RMS Force 0.000178 0.000300 YES
Maximum Displacement 0.010503 0.001800 NO
RMS Displacement 0.003163 0.001200 NO
Rarely, the coordinate system itself may be at fault. If z-matrix coordinates are being used, then in some cases, poor choices can be made, which result in angles, or three consecutive atoms of the four atoms used to define a torsion angle (dihedral angle) may be collinear (the angle is close to 0 or 180 degrees), which can give problems. In this case one can either formulate a better z-matrix or use the default redundant internal coordinates.
If these methods fail, another option would be to change the optimization method from the default to another type, such as opt=ef (if the number of variables is less than 50) or opt=gdiis (for floppy molecules).
(google)
and in this page
Dear Dr Joaquin Barroso-Flores,
I am a postgraduate chemistry student working on an electronic structure calculation project and I am having a really weird problem with Gaussian. I hope you don’t mind if I ask for your help.
The environment: The Gaussian (version: 09) I am using is installed in a remote Unix server. My workstation is PC Win7. I use Putty to get access to the Unix server and run Gaussian calculations.
Things I am doing: I wrote a Matlab program to
1) Compose a Gaussian input file (in ASCII plain format) and save it in my local PC
2) Compose a dos batch file (using pscp command) aiming to copy the Gaussian input file to the Unix server (i.e. pscp myinputfile.com myunixaccount@theserverpath).
3) In the Matlab environment, execute this dos batch file to get the Gaussian input file copied to the Unix server (i.e. using the dos() function).
4) Still in the Matlab environment, compose a dos batch file that contains plink command (i.e. plink myunixaccount@theserverpath g09sub CHBrClF) to execute the Gaussian input file (now located in Unix server) remotely and also contains a pscp command to copy the resulting log file back to PC local directory (pscp myuixaccount@theserverpath/gaussianjob.log C:\myfolder).
5) Then I will do some text/information extraction from the log file, and use this information to determine an updated geometry and compose an updated Gaussian input file.
One important feature of this Matlab program is that it iteratively executes the above 5 steps, i.e. the new Gaussian input file composed in step 5 will in fact be step 1 in the next loop. It is expected that the geometry of molecule will change gradually and reach some equilibrium state.
Problem: The first time I ran my Matlab program, it stopped at some point (say n=40, n is the loop number). I checked the log file and found out that the Gaussian calculation didn’t succeed because ‘No lower point found — run aborted’. OK I thought it was a matter of choosing the right basis set and method, so I tried countless number of basis sets/methods. But I never resolve the issue. Instead I just got my program stopped at different loop numbers with the same ‘no lower point found’ message. Then one day, by chance, I found out that, when my Matlab program stopped at a loop number because Gaussian calculation failed to find a lower point, if I log into the Unix server manually, and manually (command line) execute the Gaussian input file that was previously failing to achieve a lower point (g09sub mygaussianjob), it will magically terminate successfully. I then tried a number of times and confirm that the stops in my Matlab is irrelevant to the choice of basis sets/methods (it will stop at random loop numbers) and whenever it stopped and told me it couldn’t achieve lower point, I just need to go into Unix server and run the input file manually, I will then get the Gaussian program run successfully. It is really bizarre and I struggled to find an explanation. i.e. How could a single input file fails to terminate successfully when it was running remotely in an automated Matlab program, but successfully terminates when running manually by command line in Unix server.
I need to get around this issue because I know roughly when the molecular geometry achieves equilibrium, and at the moment it stopped way earlier than it should be.
I compared the ‘failed’ log file and the ‘succeed’ log file line by line. The discrepancies always start from a line like this:
>>>>>>>>>> Convergence criterion not met.
SCF Done: E(RHF) = -3167.38898285 A.U. after 65 cycles
Convg = 0.4913D-05 -V/T = 2.0001
i.e. either the E(RHF) starts to become different, or the Convg starts to become different in the two log file, although they started from exactly the same input file specification!
Sorry for writing such a long story, but the question I want to ask is, why does this problem happen? Does it have something to do with the server responding time, or the use of plink command, or the use of g09sub command? How can I solve it, to get my program run without stopping when it shouldn’t stop (because as I mentioned above I confirmed that the input specification is working)?
A few days ago I found out another thing, that is when my Matlab program stopped at some loop number, for the latest composed Gaussian input file, no matter I run it manually in command line in Unix server, or remotely via plink, it will terminate successfully of course, but it will also generate log files with slightly different results (charges, forces etc.), again starts from the SCF Done E(RHF) line. The difference is so small but what I couldn’t understand is, why starting from the same input file, Gaussian will reach different results?
Thank you so much for reading my question and I will be grateful if you could help.
Kind regards,
Kei
Dear sir
How to vary/create new partition function for a molecule. I am working with a molecule having 3 methyle substtutions. I feel, there is a need to chose/design a new/different partition function…?. The effect of these substitutions while calculating trans, vib, rot components may effect mutually?
Please suggest a working example to understand partition functions.
Thank you very much in advance
with best regards
Vasanth
Sir ,
I want to know how to do the geometry optimization and Potential surface scanning at the same time using GAMESS ..?
I’m sorry Iresh but I haven’t used GAMESS in about 15 years! I don’t think I remember anymore how to do it.
Sorry I can’t help. Have a nice day!
Hello,
Is there any way to compute the overlap integral between two Natural Bond Orbitals (NBOs) using Gaussian09?
Thanks in advance
ss
Hello,
There is a number of overlap integrals that can be calculated with NBO 3.1 which is the version included in Gaussian. If you use pop=NBORead in your route section and then in the last and separate line you type $NBO BOAO $END the BOAO keyword will give you the Bond Overlap in the Natural Atomic Orbital basis. Please refer to the official NBO site for further information on all the available keywords.
Have a nice day
Hello how are you? my name is Mohammed H. Rida , from Gaza stripe ,yes i studied chemistry, now i’m preparing my Ms.c thesis, it’s about theoretical chemistry especially about studying corrosion inhibitor on Fe(110)surface in different mediums and substituents effect by some software , Gaussian( DFT and calculation local and global reactivity) and material studio (to calculate molecular dynamics and Ebinding) . according to your experience in theoretical chemistry i’m looking forward to cooperate with you. I have some results but i need to some explanations.
thanx Date: Tue, 22 Sep 2015 21:45:33 +0000 To: brkaa2002@hotmail.com
Dear Joaquin,
I wonder if I can trust the value given by gaussian for the eigenvalue of the s**2 operator after the annihilation, and then on the energy and geometries I got after the optimization. I’m analyzing the saddle points of a termolecular reaction on a triplet PES and one of them as a
value before annihilation of 2.74, which is highly contaminated, but this value is reduced to 2.05 after the annihilation, which is acceptable.Then, Can I trust the geometry, energy and vibrational frequencies I got after the optimization and characterization of that stationary point as a saddle point with one imaginary frequency?
Hello Manuel,
A very interesting question! At first glance I would think you cannot trust the geometry because it pertains to a contaminated wavefunction, however upon annihilation you get an acceptable value indeed.
Also, finding a TS on a triplet state is hard enough.
I would keep the geometry and state the issue during the peer reviewing process.
I have to write something about spin contamination, I just haven’t had the chance.
I hope this helps! Have a nice day!
#Convergence failure high spin multiplicity rare earth metal ions#
Can you suggest the ways to optimise rare earth metal complexes (e.g. containing Dy3+ with f9 configuration, where spin multiplicity is usually high), either using Gaussian 09 or Turbomole 6.5.
I am finding it difficult to optimise these high spin multiplicity complexes.
I am using ECP-28 (for rare earth metal ion) along with 6-31G* for low ‘Z’ elements.
Dear Ritesh
I can suggest a few tricks.
1) Try optimizing a low multiplicity state first, then change the multiplicity and optimize again. Your calculation is demanding too many computational resources on the SCF alone, imagine how much it needs to fully optimize the molecule.
2) Use a larger ECP. Those by Almlof have always worked for me but make sure to use the corresponding basis set (double zeta quality) and keep the same ‘zeta’ for the low-Z elements.
3) Try a combination of 1 and 2 🙂
I hope this helps!
hellow sir,
can i create .wfn file from the output or .chk file of gaussian. If than please help me sir. and how can we calculate the electric potential surface in window…….i am waiting for the result. and sugget me the best way to make the graphene sheet.
Hello Dhaniram:
If you want the .wfn file to perform a wavefunction analysis using the QTAIM Bader theory, you can do two things:
1) Recalculate the system adding the keywords to generate the file .wfn
This is an example of a DFT optimization and frequency job for methane that also produces the .wfn file
%chk=methane.chk
# opt freq b3lyp/6-311+g(d,p) geom=connectivity density=all out=wfn
Calculation that produces methane.wfn
0 1
C -1.44716690 0.55895866 0.00000000
H -1.09051248 -0.44985135 0.00000000
H -1.09049406 1.06335685 0.87365150
H -1.09049406 1.06335685 -0.87365150
H -2.51716690 0.55897184 0.00000000
1 2 1.0 3 1.0 4 1.0 5 1.0
2
3
4
5
methane.wfn
2) You can also use the utility gaussian formchk (http://www.gaussian.com/g_tech/g_ur/u_formchk.htm) to format the checkpoint file and get the .fchk file. Using this, you can make the QTAIM analysis using for example the free software MultiWfn (https://multiwfn.codeplex.com)
I hope it helps you
Ángel is right, you can generate a wfn or wfx file from his instructions but you can also use the instruction guess=only to do it from the chk file, e.g.
%chk=oldfile.chk
#p method/basis-set geom=check guess=(read,only) output=wfn
Title card
0 1
-blank line-
filename.wfx
-blank line-
I hope this helps
#Born-Oppenheimer molecular dynamics (BOMD)
# Input in G09
Dear Dr Joaquin Barroso-Flores,
I am a postgraduate chemistry student working on electronic structure calculations focusing my efforts on non-covalent interactions and QTAIM analysis.
Nowadays I’m trying to expand my knowledge on my systems by using Born-Oppenheimer molecular dynamics. I now that at least the G09 version is able to perform this kind of calculations, but I found the information on Gaussian page very brief and confusing. The page contains only one example of the dissociation path of formaldehyde starting at the transition state and in the book Exploring chemistry with electronic structure methods there is not information.
Do you know any place, reference page, book, or by your own experience how to make an input for a BOMD for more complex cases than the one shown in the Gaussian page?
I want to simulate by BOMD the replacement of one molecule of a cluster by other which is similar (Imagine for example the replacement on a (HF)n molecular cluster of one HF molecule by an HCl), any idea of how to write the imput? could be the phase (n,m)keyword where n,m are the number labels of atoms a suitable way to do it?
Is it possible to use an specific thermostat or barostat insted of using the RTemp=300 keyword or the readisotopes option?
I hope you or somebody who have experience on that issue could help me
Thanks in advance
Dear Angel
at the time we are also trying to work with BOMD but as you said Gaussian is not very clear as how to use it. I usually perform my MD with AMBER. We are gathering some of the issues we found so we post them here. As soon as I find some more information I will share it with you all. Have you tried looking for some info at ccl.net? that is always a good place to start.
Have a nice day!
Hi Dr. Barroso!
I am trying to look at orbital interactions between some planar heterocycles and DNA base pairs with M06/6-31+g(d,p) and I’ve done some single points where I varied the XY position of the heterocycle and now I want do optimizations for some points of interest. Every job crashes at the same point, with:
Lowest energy guess from the checkpoint file: “stauranthine_GC_dimer_xyz_175_2
25_opt.chk”
B after Tr= 0.000000 0.000000 0.000000
Rot= 0.997707 -0.022077 -0.028339 0.057361 Ang= -7.76 deg.
Guess basis will be translated and rotated to current coordinates.
B after Tr= 0.000000 0.000000 0.000000
Rot= 0.999521 0.019024 0.024065 -0.004028 Ang= 3.55 deg.
Guess basis will be translated and rotated to current coordinates.
CkInt1: FT= 4.71D-01
Max alpha theta= 33.634 degrees.
Operation on file out of range.
FileIO: IOper= 1 IFilNo(1)= -526 Len= 882648 IPos= 0 Q= 47036
532319560
…then a dump. I tried SCF=QC. I even tried HF and got this:
Using GEDIIS/GDIIS optimizer.
Bend failed for angle 3 – 68 – 55
Tors failed for dihedral 2 – 3 – 68 – 55
Tors failed for dihedral 30 – 3 – 68 – 55
Tors failed for dihedral 53 – 55 – 68 – 3
Tors failed for dihedral 69 – 55 – 68 – 3
Tors failed for dihedral 70 – 55 – 68 – 3
FormBX had a problem.
These are angles between atoms in the heterocycle and the base pair. Do I have to connect all the atoms in my input file in some way for the optimizer not to crash?
Thanks!
Hello Ken,
This is a very common problem when dealing with supramolecular fragments. What I usually do is taking the last geometry and modify a little the torsion angles in the list; in your case I would try tempering around bond 55-68 (if it is indeed a bond). You don’t want to connect all those atoms!
If the problem persists, I have succeeded by exchanging the numbering scheme in two of those atoms (one from each molecular fragment). This is done by switching their corresponding two lines in the input (handle with care).
I hope this helps!
Dear Dr. Barroso,
indeedly, i could not understand the fluorescence example under gaussian SCRF keywords.
so, i appreciate if you could explain the job steps required to simulate fluorescence spectrum and route sections required for each step.
Sincere regards,
Muhammad
Dear Sir,
I am Gaya3 using Gaussian09 software for computing organic molecules.Can you help me to calculate molecular susceptibility and curie temperature from gaussian output. i read most of the links but till i can’t get clear. I feel good if you could explain the route section and model output for getting susceptibility..
Thanks in advance
Hola,
Estoy presentado este error para la molecula MgH:
the calculation has been terminated with the following error, “The
combination of Multiplicity 2 and 12 electrons are impossible”
agradezco la ayuda para resolver este error.
Hola, si tienes una molécula de capa cerrada, i.e., con todos los electrones apareados entonces la multiplicidad es de singulete. Solo si tienes un electrón desapareado entonces puedes tener un doblete (ese electrón tendrá espin alfa o beta, de ahí el doblete). Como tienes un número par de electrones o están todos apareados (singulete) o si tienes uno desapareado por fuerza tienes otro también, lo que da origen a un quintuplete, por ello es que dice que la combinación es imposible.
La carga también debe estar mal. Si tienes 12 electrones esto debe ser MgH+, no es cierto? Checa que todo sea consistente, primero define la carga que tiene tu molécula y en base a ello toma la decisión de la multiplicidad.
si tu molécula es neutra entonces la combinación es de 13 electrones y debe especificarse como 0 2 antes de las coordenadas. si es positiva entonces va como 1 1 para que sea singulete.
Saludos
Hi,
I’m trying to calculate NBO calculations in log file second order perturbation section was not printing but it gives Normal terminations, Could you suggest me to resolve this issue..
Hello Babu
You should use pop=NBORead in your route section. Then, in the last line of your file include the following line with one blank line before and another one after:
$NBO E2PERT $END
The E2PERT keyword will print the second order perturbation theory delocalization energies.
I hope this helps!
Dear,
Thank you for your reply. I tried with what you suggested previously, but the problem was not resolved.. and I also tried with different IOP numbers it doesn’t helped…
Dear joaquinbarroso,
I’m doing NBO calculations on Cu(II)-Gd(III) ions for dimer and trimer model, this case in second order perturbation section the intramolecular threshold energy is 0.25kcal/mol. But it is necessary for me to print below to that energy(i.e 0.25kcal/mol). So could you please suggest me the keyword which I have to use in input.
thanks in advance.
Dear Babu
The threshold in G09 for printing the E2PERT energies cannot be modified through a keyword, I guess it can only be modified from the source code but I don’t know how to.
Have a nice day
Dear Dr
can you help me
how can i calculate fukui function using gaussain09 ?
i try to found it in the blog put i cant found it
Here you go:
Dear DR:
By using DFTB ,How can i to try out calculating the
”polarization effect” which causes the molecular IP to be different from that in solids. Can we get the shifts of around 2 eV seen in practice.
Can you help me please
Dear Dr. Joaquin Barroso
I wrote you an email inquiring about the possible opening for post doctorate in your group.
Kindly have a look over it at your convinience.
I would be happy to receive a reply from you.
sincerely
jayshree
Dear Jayshree
I have read your email and will reply to you soon.
Thank you very much for your interest.
Dr. Barroso,
Is it possible to alter the default value of a nuclear charge in Gaussian? For example, could one change the nuclear charge of an oxygen nucleus from +8 to +9? Is it possible to request a non-integer charge? Thank you.
Dear Sean,
As a matter of fact it is possible to specify some nuclear parameters. You need to include them within the atom type field using parenthesized keywords and values. In your case, if you only wish to change the nuclear charge of a single oxygen atom you have to do it in the coordinates section:
O(ZNuc=9) x.xxx y.yyy z.zzz
I’m not sure this works with a non-integer nuclear charge but if it doesn’t then you can try changing Znuc for Zeff (effective charge); I seem to remember this actually worked when calculating nuclear shielding tensors, I don’t think I’ve never used it in any other context. Try them both and let me know if it works.
Have a nice day!
Hi! First of all thanks for the blog. Some posts really helped me out. I have a transition metal complex, the crystal structure of it and DFT calculations already done. I would like to do a calculation to see what happens if I reduce the complex by 1 or 2 electrons. What would you suggest that I should do?
Thanks.
Well, it depends on what do you want to analyze. If you only want to know ‘what happens’ to the overall geometry, then change the charge in -1 or -2 and adjust the multiplicity accordingly. The thing is that if you are working with TM’s then you must have some previous knowledge on the spin-field of the ligands in order to make an educated guess on what that multiplicity will be. If you were working with a neutral closed shell non-TM molecule you would have to change the charge from 0 to -1 and the multiplicity from 1 to 2. A second electron would be paired with the first and now the charge would go from -1 to -2 but the multiplicity would go back from 2 to 1. If you are certain that your two added electrons will be unpaired (and that these are the only two electrons unpaired) then your multiplicity would change -from the hypothetical singlet initial state- t0 a quintet!
I hope this helps. Thanks a lot for your kind words about this blog, I’m glad to know its useful.
I am trying to reduce it chemically, but it would be also nice if I can have some computational insight before isolating the reduced species. So, basically, I want to see if the reduced compound is stable enough to isolate etc. and see how the orbitals will be arranged after reduced. So, do I keep the x, y,z coordinates same from the crystal structure and just change the charge and/or multiplicity?
I would add the OPT option. The structure will most likely change upon reduction.
Dear DR Joaqiuinbarroso:
Est ce qu’on peut déterminer le spectre des Analyse Thermogravimétrique ATG en utilisant la DFT?
Not that I know. I don’t know but I don’t think it’s possible since TGA is a macroscopic-collective property. It would be like trying to calculate a boiling or a melting point from a single molecules density.
Sorry I couldn’t help
Dear Joaqiuinbarroso,
I’m doing NBO calculation on Cu(II)-Gd(III) system, i need nbo calculation for dimer model for the same system. out of two Gd,Cu i replaced one Gd with La and one Cu with Zn, but in output I’m facing this error “Subroutine NAOANL could not find a f-type valence orbital on atom La 3 (3=fragment number in my input for La).” can you suggest me how to over come this problem.
thank you in advance.
This is clearly a basis set problem. See if you can change it for the La atoms as to include f functions. You can also try to use non polarized functions, I.e, change from 6-31G** to 6-31G
Let me know what basis sets you’re using to help you properly.
Have a nice day
Dear Joaqiuinbarroso,
Thank you for your reply. I’m using TZV basis set for Cu,Zn,C,H,O,N and for Gd,La it was CSDZ basis set.
thank you.
Try the augmented versions for La. Let me know if it helps
#bondlengthissues
#optimization
Hello, Dr. Barroso,
I enjoy your blog so much and have found it to be an amazing reference over the past few months. Thank you for all this great information!
I am doing some DFT energy calculations for a set of catalysts in Group 4. Overall, there is a tetradentate ligand, and also attached to the metal is an olefin, specified as a pi complex. The olefin is what I’m having issues with– it seems to stay coordinated to the metal in the Zr and Hf catalysts, but using the exact same structure, just with Ti, I am getting ridiculously long bond lengths (3.7 A). I’m wondering what’s going on here and maybe if there’s some issue with the level of theory I’m using for Ti? I want to compare the energies of all three of the metal complexes, so I figured that changing the level of theory for Ti wouldn’t allow for a fair comparison.
The level of theory is: functional- B3LYP; LANL2DZ for Ti, Hf or Zr, depending on the structure and 6-31G* for all non-metal atoms (N, O, C and H, in this case). Additionally, I’m using the ECP for all cases, LANL2.
Thanks so much for your time and assistance in this matter. Any help you can offer would be greatly appreciated!
-Mike
Dear Sir,
I am calculating the optical rotation of a chiral ketone using Gaussian09 using density functional theory and the hybrid B3LYP. I am also studying the temperature effect on the optical rotation.
Many papers (e.g. 1-2) indicate the importance of the zero-point and the temperature-dependent vibrational correction to the optical rotation. I have observed a significant discrepancy between the theoretical and experimental results and, therefore,vibrational corrections might indeed be significant.
How can I calculate the vibrational correction to the optical rotation using Gaussian09 if possible?
Thanks for your help.
1 http://scitation.aip.org/content/aip/journal/jcp/136/11/10.1063/1.3693270
2 http://onlinelibrary.wiley.com/doi/10.1002/ange.200500642/abstract
Dear Sir
I am working on radical cations. In the output file of NBO analysis, I found that “Second Order Perturbation Theory Analysis of Fock Matrix in NBO Basis” is computed twice in the output file (for alpha orbitals and beta orbitals separately), unlike the corresponding neutral molecule. I am not sure which one to consider for interpretation of the results.
Kindly, guide me. Please reply asap.
Actually you need both. These calculations on radicals are of the open shell variety, meaning you have separate densities for alpha electrons and for beta electrons. In fact, you will see there’s one more orbital for one of this kind, that is your SOMO. You can then take all the perturbative delocalizations within a certain class of electrons but not between them. Analyze both densities separately and you will get the full picture of your molecule.
I hope this helps!
Dear sir
b3lyp/6-31g(d,p) opt freq = raman||mefnamic acid||0,1|C,-2.1197585985,
1.7187440385,-3.0027517595|
i got output like this for my compound how can i write explanation for this this frequencies
Hello Dr. Barroso,
I am trying to optimize the geometry of Eu(NO3)3(H20)3 in Gaussian 09 by b3lyp/genecp keyword. Its not working. Can you help me out. If possible, can you send me similar script?
Dear Sir
Thank you so much for your kind reply. I analysed my output files. There is no data for SOMOs. The file only has data for alpha and beta orbitals. I am looking for interactions between donor-acceptor NBOs. Say, if I analyze interactions for both the types separately to get the full picture of my molecule. Then the occupancies will also be different for the alpha and the beta orbitals. Sir, how to interpret that?
Can you give me examples from some publications of such kind.
Dear Sir,
I have calculated the anharmonic force constants for small molecule. I see the CUBIC
as follows: How these indices are preinted they are printed as method1 or method 2
method 1 :i,j,k are decreasing order of frequency
method 2 :i,j,k are increasing order of frequency
for example:
Method1 Method 2
i=1=j=k 1353.04526 i=9=j=k
i=2=j=k 1334.87209 i=8=j=k
i=3=j=k 1312.53560 i=7=j=k
i=4=j=k 1265.45003 i=6=j=k
i=5=j=k 1242.26563 i=5=j=k
i=6=j=k 1221.31627 i=4=j=k
i=7=j=k 1216.82920 i=3=j=k
i=8=j=k 1201.08947 i=2=j=k
i=9=j=k 1186.75790 i=1=j=k
frequencies are:
1265.45003
1242.26563
1221.31627
1216.82920
1201.08947
1186.75790
1173.82457
1171.33255
1154.12879
1150.94678
1108.55709
1097.01957
……………………………………………….
: CUBIC FORCE CONSTANTS IN NORMAL MODES :
: :
: FI = Reduced values [cm-1] (default input) :
: k = Cubic Force Const.[AttoJ*amu(-3/2)*Ang(-3)] :
: K = Cubic Force Const.[Hartree*amu(-3/2)*Bohr(-3)]:
:……………………………………………..:
1 1 1 135.69513 0.68528 0.02329
2 2 1 115.84286 0.57717 0.01962
3 1 1 -37.19681 -0.18502 -0.00629
3 2 2 -75.07496 -0.36841 -0.01252
3 3 1 -66.55862 -0.32607 -0.01108
3 3 3 -96.52965 -0.46576 -0.01583
4 1 1 5.09816 0.02490 0.00085
4 2 2 -61.56273 -0.29663 -0.01008
4 3 1 58.80730 0.28288 0.00961
4 3 3 9.10174 0.04312 0.00147
4 4 1 66.85152 0.31575 0.01073
4 4 3 25.36369 0.11799 0.00401
4 4 4 83.68976 0.38228 0.01299
5 2 1 51.76968 0.24883 0.00846
5 3 2 54.01017 0.25568 0.00869
5 4 2 -44.92468 -0.20882 -0.00710
5 5 1 -66.89022 -0.31015 -0.01054
5 5 3 -33.60899 -0.15348 -0.00522
5 5 4 23.67966 0.10618 0.00361
6 1 1 3.64907 0.01751 0.00060
6 2 2 -3.72065 -0.01761 -0.00060
6 3 1 4.07792 0.01927 0.00066
6 3 3 -3.25677 -0.01516 -0.00052
6 4 1 7.78350 0.03612 0.00123
6 4 3 7.37547 0.03371 0.00115
6 4 4 -24.42150 -0.10959 -0.00372
6 5 2 17.62453 0.08048 0.00274
6 5 5 -2.26670 -0.00999 -0.00034
6 6 1 -62.40575 -0.28448 -0.00967
6 6 3 44.10182 0.19801 0.00673
6 6 4 1.63636 0.00721 0.00025
6 6 6 112.73472 0.48824 0.01660
7 2 1 15.18140 0.07222 0.00245
7 3 2 1.94025 0.00909 0.00031
7 4 2 -6.64179 -0.03055 -0.00104
7 5 1 -0.62290 -0.00286 -0.00010
7 5 3 -6.11414 -0.02763 -0.00094
7 5 4 -20.75480 -0.09211 -0.00313
7 6 2 -62.06928 -0.28052 -0.00953
7 6 5 -87.06888 -0.37961 -0.01290
7 7 1 -66.07957 -0.30012 -0.01020
7 7 3 44.31945 0.19825 0.00674
7 7 4 -15.09518 -0.06630 -0.00225
7 7 6 60.35947 0.26045 0.00885
8 2 1 -29.67015 -0.14022 -0.00477
8 3 2 -39.24938 -0.18270 -0.00621
8 4 2 -26.55740 -0.12138 -0.00413
8 5 1 14.59054 0.06652 0.00226
8 5 3 46.95819 0.21086 0.00717
8 8 4 41.14384 0.18141 0.0061
8 8 6 -60.15583 -0.25621 -0.00871
QUESTION 2::=>
What is the threshold for anharmonic force constant printout in gaussian. i.e what is the samllest value of force constant that gaussian print out.
Gaussian do not print all the couplings i,j,k but it omits many. How gaussian selects the frequency mode coupls to prontout the force constant. for example: Gaussian prints 8 8 4 but do not print 8 8 7, 8 8 5, 8 81, etc.
I appreciate your help
Thanks
Hi,
I am doing DFT calculation on MOF my molecule contains Zn atoms.
Input line is opt freq ub3lyp/gen scf=(qc,maxcyc=5000) geom=connectivity pseudo=read
But I am getting an error “CPHF failed to converge in LinEq1
Can some one suggest me how to solve this error?
Thanks in advance
Sir,
Firstly I want to congratulate you for this wonderful blog of yours.We have got a gaussian 09 windows version.I have managed to optimise my complex using LANL2DZ basis set and B3LYP method directly from the gaussian interface in chemdraw 3D. My question : Is it correct to assign a job directly.I don’t know the exact input commands I should give to use separate basis sets for the p block elements and the metal atom.Also I have done TDDFT analysis of the optimised structure using LANL2DZ. The calculated spectra is in accordance with the experimental spectra but the transition assignments are absurd like from HOMO-7 to LUMO+21.Please guide me to do the calculations properly.
Regards
just technical qustion..
Which software can be used to create energy profile of rection?
thnaks
Good afternoon, Dr. Joaquin Barroso
I’m student of pregrade and I turn to you to ask somethin;, I’m doing a geometry optimization of a complexes between cysteine and mercury (II), one of the structures that I’m doing, I have a presented me a error, it I could not solve it, my script is the following:
%chk=4b.chk
%nprocshared=8
%mem=2GB
# opt genecp scrf=(solvent=water,pcm) nosymm maxdisk=500GB geom=connectivity m062x test
CysHg_4b from original
-2 1
………..(coordenadas)
C S N O H 0
6-31g(d,p)
****
Hg 0
SDD
****
Hg 0
SDD
The calculation starts well, and is runs on average 16,5 hours, after get the following error:
Inv3 failed in PCMMkU.
Error termination via Lnk1e in /home/gifacuser/gaussiandir/g09/l502.exe at Sat Dec 12 02:03:25 2015.
Job cpu time: 2 days 7 hours 45 minutes 3.5 seconds.
File lengths (MBytes): RWF= 774 Int= 0 D2E= 0 Chk= 28 Scr=1
¿How to solve this error?
I appreciate your valuable assistance and care provided.
Ubeiden Cifuentes Samboni.
Funciones Fukui de aniones.
Buena tarde doctor Joaquin, quisiera hacerle una pregunta respecto al cálculo de funciones de fukui en aniones, resulta que tengo un complejo de mercurio que tiene carga de -2, ¿puedo realizar cálculos de energía, asumiendo que mi molécula neutra es -2, el anión sería -3 y el catión con -1?
Agradezco su colaboración y atención.
Atentamente,
Ubeiden Cifuentes Samboni
Estudiante de Química
Exactamente! Usualmente nos referimos al estado de referencia como neutro con lo que los siguientes estados a calcular son aniónico y catiónico pero esto solo es para tener una idea; en realidad el sistema de referencia tiene N electrones para después pasar a N+1 y N-1 electrones. N no tiene que ser igual al número de protones para que q = 0.
Así que no tienes que asumir nada, tu sistema de referencia tiene q = -2 para el estado N; q = -3 para N+1 y q = -1 para N-1
Saludos!
Muchas gracias doctor Joaquin ha sido muy valiosa su colaboración.
Hola. He tenido exactamente el mismo error, “Inv3 failed in PCMMkU”, para el cual estoy encontrando muy poca ayuda por Internet. ¿Conseguiste solucionar este problema?
Gracias
Dear Sir,
We use NBO analysis approach to understand bonding-antibonding interaction by means of second-order perturbation interaction energy E2, or, stabilization energy, say, of hydrogen bonded dimer. These numbers measures the relative strength of H-bonds. I did such calculation for O-H…O H-bonded dimer and it turns out to be 15.61 kcal/mol. Oftenly,We do compare our theoretical values with some experimental data. I wanted to know whether we have any experimental data with regard to my computed stabilization energy where i can compare or some references?
Many Thanks.
dear prof
I am studying weak interactions using crystallographic data therefore i want to generate a wfn/wfx file in gaussian/ or orca for this purpose. So Is it fine to use keyword output=wfx and perform a single point energy calculation using coordinates from cif file as i am afraid if i optimize the structure this weak interaction will no longer be there. Help me with your comments
Dear Kekule (cool nickname BTW)
Yes you can just get the wfx file from the CIF file. I sometimes just optimize the hydrogen atoms but if the are involved in the weak interactions you want to study then use it as it is. Just make sure the quality of the crystal is high enough to guarantee the presence of these interactions.
Happy new year!
thx for quick response
HNY all readers
Buenas Tardes llevo ya meses tratando de completar unos cálculos con G09 en Gaussian 09 en mi caso cada vez que relizo un calculo de frecuencia y a veces de optimización siempre obtengo el mismo resultado de error:
Internal consistency error detected in FileIO for unit 1 I= 6 J= 0 IFail= 1.
dumping /fiocom/, unit = 1 NFiles = 79 SizExt = 524288 WInBlk = 512
defal = T LstWrd = -1192802304 FType=2 FMxFil=10000
Number 0 0 0 0 0 0 22 23
Base 10355712 9707520 22378496 16677376 10345472-1193341952 510345728 1842683904
End 10975744 9709056 87616512 20478976 10347008-1192802304 1842683496-1193342400
End1 10975744 9709056 87616512 20478976 10347008-1192802304 1842683904-1193341952
Wr Pntr 10355712 9707520 22378496 16677376 10345472 88892416 1842683496 1842683904
Rd Pntr 10355712 9707520 22378496 16677376 10345472 88892416 510345728 1842683904
Length 620032 1536 65238016 3801600 1536 539648 1332337768 1258940992
Number 501 502 503 507 508 511 514 515
Base 23552 1314304 96256 101888 1322496 647168 5779968 3246080
End 24552 1318044 96979 102839 1322511 852289 6413343 5779580
End1 24576 1318400 97280 102912 1323008 852480 6413824 5779968
Wr Pntr 23552 1314304 96256 101888 1322496 647168 5779968 3246080
Rd Pntr 23552 1314304 96256 101888 1322496 647168 5779968 3246080
Length 1000 3740 723 951 15 205121 633375 2533500
Number 516 517 518 520 521 522 523 524
Base 1345536 9580032 7679488 1344000 1307136 10342912 9704960 10975744
End 3245661 9704907 9579613 1344005 1307171 10345162 9707210 12241369
End1 3246080 9704960 9580032 1344512 1307648 10345472 9707520 12241408
Wr Pntr 1345536 9580032 7679488 1344000 1307136 10342912 9704960 10975744
Rd Pntr 1345536 9580032 7679488 1344000 1307136 10342912 9704960 10975744
Length 1900125 124875 1900125 5 35 2250 2250 1265625
Number 526 528 530 532 534 536 538 545
Base 13510144 12241408 9709056 12876288 14775808 15409664 16043520 10349056
End 14775769 12874783 10342431 13509663 15409183 16043039 16676895 10349070
End1 14775808 12875264 10342912 13510144 15409664 16043520 16677376 10349568
Wr Pntr 13510144 12241408 9709056 12876288 14775808 15409664 16043520 10349056
Rd Pntr 13510144 12241408 9709056 12876288 14775808 15409664 16043520 10349070
Length 1265625 633375 633375 633375 633375 633375 633375 14
Number 547 548 551 552 559 561 562 563
Base 10350592 21112832 1304576 1303552 43008 1305088 1297408 12875264
End 10352842 22378457 1304601 1303570 43009 1305089 1303472 12875827
End1 10353152 22378496 1305088 1304064 43520 1305600 1303552 12876288
Wr Pntr 10350592 21112832 1304576 1303552 43008 1305088 1297408 12875264
Rd Pntr 10350592 21112832 1304601 1303552 43008 1305088 1303472 12875264
Length 2250 1265625 25 18 1 1 6064 563
Number 565 569 571 575 577 579 580 581
Base 1321984 10348544 20478976 105984 1320448 1304064 41472 1320960
End 1322179 10348545 21112351 646818 1320474 1304120 42598 1321555
End1 1322496 10349056 21112832 647168 1320960 1304576 43008 1321984
Wr Pntr 1321984 10348544 20478976 105984 1320448 1304064 41472 1320960
Rd Pntr 1322179 10348544 20478976 105984 1320474 1304064 42598 1321555
Length 195 1 633375 540834 26 56 1126 595
Number 582 583 584 598 603 605 606 607
Base 1318400 43520 1323008 44032 1344512 1345024 10347008 10349568
End 1320088 43576 1323674 44034 1344513 1345025 10348134 10350131
End1 1320448 44032 1324032 44544 1345024 1345536 10348544 10350592
Wr Pntr 1318400 43520 1323008 44032 1344512 1345024 10347008 10349568
Rd Pntr 1318400 43520 1323008 44032 1344512 1345024 10347008 10349568
Length 1688 56 666 2 1 1 1126 563
Number 619 634 658 665 670 672 674 685
Base 1324032 87616512 88892416 97280 1307648 22016 102912 6413824
End 1340069 88892275 510345541 101436 1313979 22185 103707 7679449
End1 1340416 88892416 510345728 101888 1314304 22528 103936 7679488
Wr Pntr 1324032 87616512 88892416 97280 1307648 22016 102912 6413824
Rd Pntr 1324032 87616512 88892416 97280 1313979 22016 102912 6413824
Length 16037 1275763 421453125 4156 6331 169 795 1265625
Number 694 695 698 701 761 989 991 992
Base 10353152 1340416 1306112 852480 1305600 24576 37888 37376
End 10355402 1343885 1306778 1297373 1305601 37076 41169 37381
End1 10355712 1344000 1307136 1297408 1306112 37376 41472 37888
Wr Pntr 10353152 1340416 1306112 852480 1305600 24576 37888 37376
Rd Pntr 10353152 1340416 1306112 852480 1305600 24576 41169 37381
Length 2250 3469 666 444893 1 12500 3281 5
Number 993 994 995 996 997 998 999
Base 23040 20480 22528 21504 103936 20992 44544
End 23140 20510 22538 21604 105485 21192 95796
End1 23552 20992 23040 22016 105984 21504 96256
Wr Pntr 23040 20480 22528 21504 103936 20992 44544
Rd Pntr 23140 20510 22538 21604 105428 21192 45796
Length 100 30 10 100 1549 200 51252
dumping /fiocom/, unit = 2 NFiles = 7 SizExt = 0 WInBlk = 512
defal = F LstWrd = 3683328 FType=2 FMxFil=10000
Number 0 508 522 536 538 634 998
Base 2565458 20480 20695 1298708 1932083 22945 20495
End 3683328 20495 22945 1932083 2565458 1298708 20695
End1 3683328 20495 22945 1932083 2565458 1298708 20695
Wr Pntr 2565458 20480 20695 1298708 1932083 22945 20495
Rd Pntr 2565458 20480 20695 1298708 1932083 22945 20495
Length 1117870 15 2250 633375 633375 1275763 200
dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512
defal = T LstWrd = 67072 FType=2 FMxFil=10000
Number 0
Base 20480
End 67072
End1 67072
Wr Pntr 20480
Rd Pntr 20480
Length 46592
Error termination in NtrErr:
NtrErr called from FIOCnC.
NO creo que sea un problema del equipo puesto que tengo un I5 con 4 Gb de RAM
el principio del imput es el siguiente:
# opt=calcfc freq mp2/6-31g(d,p) geom=connectivity
————————————————–
1/10=4,18=20,19=15,38=1,57=2/1,3;
2/9=110,12=2,17=6,18=5,40=1/2;
3/5=1,6=6,7=101,11=9,16=1,25=1,30=1,71=2/1,2,3;
4//1;
5/5=2,38=5/2;
8/6=3,8=1,10=2,19=11,30=-1/1;
9/15=3,16=-3/6;
11/6=1,8=1,15=11,17=12,24=-1,27=1,28=-2,29=300,32=6,42=3/1,2,10;
10/6=2,21=1/2;
8/6=4,8=1,10=2,19=11,30=-1/11,4;
10/5=1,20=4/2;
11/12=2,14=11,16=1,17=2,28=-2,42=3/2,10,12;
6/7=2,8=2,9=2,10=2/1;
7/10=1,12=2,25=1,44=2/1,2,3,16;
1/10=4,18=20,19=15/3(2);
2/9=110/2;
99//99;
2/9=110/2;
3/5=1,6=6,7=101,11=9,16=1,25=1,30=1,71=1/1,2,3;
4/5=5,16=3/1;
5/5=2,38=5/2;
8/6=4,10=2/1;
9/15=2,16=-3/6;
10/5=1/2;
7/12=2/1,2,3,16;
1/18=20,19=15/3(-8);
2/9=110/2;
6/7=2,8=2,9=2,10=2/1;
99//99;
——————-
Title Card Required
——————-
Charge = 0 Multiplicity = 1
Symbolic Z-Matrix:
Seria de enorme ayuda que me ayudara a resolver este problema, ya me ha retrasado casi dos meses, gracias de antemano
Dear Dr. Joaquin,
I have a small question : I want to simulate an OLED .
How can i simulate an OLED using an oligomer (like an active layer) ?
i am having an error while optimizing a molecule in gaussian 09. error msg is as follows
“error terminatio via Lnk1e in gausssian09/l1111.exe” when i have gone through the gaussian manual the error l1111 is written as “2 particle density matrix and post-SCF derivatives” please help me to overcome the same.
i am having an error while optimizing a N2 molecule in gaussian09 using CCSD method and ccpV6Z basis set. but i found an error msg is as follows
“error termination via Lnk1e in gausssian09/l1111.exe” when i have gone through the gaussian manual the error l1111 is written as “2 particle density matrix and post-SCF derivatives” please help me to overcome the same.
Dear joaquinbarroso,
I’m trying to calculate NBO calculations for Cu(II)-Gd(III) dimer systems (contain like this Cu(II)Gd(III)-La, Zn), but I was encountering with the following error.
******************************Gaussian NBO Version 3.1******************************
N A T U R A L A T O M I C O R B I T A L A N D
N A T U R A L B O N D O R B I T A L A N A L Y S I S
******************************Gaussian NBO Version 3.1******************************
/RESON / : Allow strongly delocalized NBO set
/PLOT / : Write information for the orbital plotter
Analyzing the SCF density
Job title: gd11-hs
Storage needed: 7053984 in NPA, 9350581 in NBO, 17038899 in NLMO (1048477192 available)
Subroutine NAOANL could not find a f-type valence orbital on atom La 3.
IVAL : 1 1 1 1 M : 1 LA : 1
This problem arises only with the dimer model, where as for full cluster [Cu(II)Gd(III)-Cu(II)Gd(III)] it works well. Is it possible to calculate NBO for dimer model (as I mentioned above). If so could you please suggest me how to solve this problem.
thank you in advance..
Dear Professor,
I am trying to calculate freq for a system of 85 atoms. Since the no of atoms are more while calculating freq it is using disk memory. In that situation I used int=acce2e=11 keyword so I came out of this problem.
But when I used the same keyword for the same system with a +ve and -ve charges, calculation is not moving at all not even like whenever I was not used that keyword.
Could you please suggest something in this regard?
Thank you so much in advance.
Dear all,
I am facing one problem. I am trying to perform excited calculation (TD-SCF) in gaussian 09 for some organic trimers. I am able to get results from some of trimers. However, calculation of some trimers by TD-SCF gives error:
“Gaussian job terminated without producing a log file”. I am unable to troubleshoot the error. Please help me in this regard.
Thanking you in advance.
Dear Dhruba, could you please share some more details about your input file? Have you checked if you still have disk space available either in your work or SCRATCH directories?
Have a nice day
Hi Dr. Joaquin,
I am trying to do the charge transfer length characterization as proposed by Carlo Adamo in JCTC 2011,7, 2498 (http://pubs.acs.org/doi/abs/10.1021/ct200308m).
In the process I learnt that, for ground state optimized geometry, I have to do SP TD-DFT calculation by including the keyword “density=all” at TD-DFT level of calculation. And then follow the script provided by Carlo Adamo to get the CT length.
But unfortunately for my molecules, I have done the TD-DFT calculation without density=all keyword. And therefore I am not able to run the script given by Carlo Adamo. I have the fchk files for all of my molecules. I have about 50 molecules.
Can you please tell me if there is anyway that I can get the CI density for the TD-DFT files that I an without using the keyword “density=all”. This will help me save a lot of time.
If I am not clear with my question, kindly let me know.
Thanks you,
Raghav
#gaussian error
Sir,
While working on the geometrical optimisation of AH2 structures , a Gaussian error came from the downloaded cif file as “Cannot cope up with ghost atoms or translational vectors” and “Atomic number out of range”
Hello!
If you are working with coordinates from a cif file then you probably have more atoms than you think. During refining of crystalline structures some disorder of the atoms in the crystal (due to either thermal motion or just plain poor quality of the crystal) is accounted for by ellipsoids that encapsule most of the electron density around that atom. When translated into an xyz coordinates file (or even a z-matrix one) you may have more than two atoms on a single position, i.e., instead of AH2 it may be AH3 but H2 and H3 may be located to close to each other.
My recomendation is that you open that file in a suitable program such as ‘mercury’ from the CCDC and delete all those atoms that you find bogus by hand.
After that you have a second problem: when gaussian says that the atomic number is out of range it means that you are trying to use a basis set that is not defined for a particular atom, e.g. 3-21G has no basis functions defined for Uranium.
Check the availability of the basis set in accordance with the atoms in your molecule, this can be done at the g09 website under the label ‘basis sets’.
Have a nice day!
Thanks Sir for a well said reply. You are an awesome scientist
Thank you for your kind words! I’m honored.
Hola Doctor, mi nombre es luis y soy estudiante de Doctorado de la UAM. Pasa que quiero realizar una optimziacion de geometria en gaussian pero con algunos átomos congelados, es decir que se mantengan fijas las coordenadas de algunos átomos. Podria usted ayudarme con esto?.
Gracias.
Hola Luis, hace poco escribí un post al respecto. Gaussian tiene una lógica un tanto rara, sin embargo creo que hay que revisar el post, tal vez no sirva tan bien como creí al principio. Me avisas.
Hola Luis!
Yo también soy estudiante de doctorado pero en España! y no tengo tanta experiencia como el Dr. Barroso, pero te puedo contar brevemente como hago yo para fijar los átomos que no quiero que cambien de posición durante las optimizaciones. Si empleas GaussView, en la barra de herramientas tienes el editor de Redundant coordinates, en el cual tu puedes hacer un scan, congelar, activar si tienes varias congeladas etc. Para ello, supongamos que quieres evitar que un átomo se mueva de sitio, abres el redundat coordinate y en add, clicas el átomo que no quieres desplazar en la optimización. En las opciones de las pestañas inferiores seleccionas cartesian coordinate y Freeze coordinate. Si deseas que no se optimice una distancia, en vez de cartesian, seleccionas en la pestaña bond, y clicas en tu sistema sobre los átomos que no quieres que se desplacen) similar con 3 átomos para ángulos y con 4 para diedros). Simplemente preparas tu entrada como lo realizas habitualmente, y el propio GaussView escribe las instrucciones de bloqueo de las corrdenadas que le especificaste.
Un ejemplo muy rápido para una molécula de etano. En ella quieres que el enlace entre los dos carbonos no se optimice, (son los átomos 1 y 5), el input quedaría así:
%chk=etano.chk
# opt=modredundant freq b3lyp/6-31+g(d,p) geom=connectivity
Etano bond_Freeze
0 1
C -0.73855241 0.34711964 0.00000000
H -0.38189799 -0.66169036 0.00000000
H -0.38187957 0.85151783 -0.87365150
H -1.80855241 0.34713282 0.00000000
C -0.22521019 1.07307591 1.25740497
H 0.84478981 1.07306259 1.25740471
H -0.58186483 2.08188584 1.25740510
H -0.58188289 0.56867726 2.13105626
1 2 1.0 3 1.0 4 1.0 5 1.0
2
3
4
5 6 1.0 7 1.0 8 1.0
6
7
8
B 1 5 F
En esta última línea, la B simboliza Bond, 1,5, los números de los átomos y F es Freeze.
Espero haberte ayudado!
#fireflyerror
Hello! I have very interesting fail. I have complex with Sm3+. Сoordinates of this complex were obtained X-ray analisys single crystal. Multiplicity of this complex=2. And Firefly terminated abnormally. To verify that my .inp file is normal I have replaced Sm3+ with Eu3+ (Multiplicity=1). And everything else is left remained unchanged. Firefly terminated normally and it showed excellent identity with experiment. I do not know what it may be due. What can I do to optimize the geometry with Sm3+? Grateful for any ideas.
I have zero experience with firefly, sorry. Maybe try changing to an unrestricted method although it will take more time to finish. I mean, if you are using, say, B3LYP change it to UB3LYP so it can work with the M=2.
I hope this helps!
Sorry, that my question is beyond the scope of your scientific interest. Necessarily I’ll try your advice. I did not say at once, I have complex of Yb3+, yet. Which has multiplicity=2. And it like Eu3+ have successful completion. All three complexes have analogous .inp file, one basis, one functional-B3LYP. But Sm3+ – did not want to be completion. I do not understand in this life)
Try changing your basis set to something smaller, you won’t get an accurate result but at least you could identify a problem with the basis set.
I hope this helps
Finished calculation with UB3LYP, but marched 1024 steps and energy changes 10^-3 and calcilation terminaled abnormally again
Hello Sir,
I am currently working on prediction of the crystal structure of ZnH2. Is there a procedure to follow for such a system in order to find the crystal system and lattice parameters? And since there are metals involved, can i use Gaussian for optimisation calculations? Also i would be grateful if i could know which basis set can be used as the pre calculation showed `”Atomic number out of range”.
Thank You sir
Dear Professor,
I´m trying to run a QM/MM simulation. However, when I try to run the simulation with gaussian, the program does not recognize the extra parameters not included in the FF. Do you know how can I solve this problem?
The .gjf file has the extra parameters after connectivity in this way:
VDW CX 1.91 0.01094
VDW 2C 1.91 0.10940
VDW NH 1.8240 0.1700
VDW C3 1.9080 0.1094
VDW CD 1.9080 0.08600
VDW ND 1.8240 0.17000
VDW CL 1.9480 0.26500
HrmStr1 N3 CX 318.7 1.4720
HrmStr1 CX HP 340.0 1.0900
HrmStr1 CX CT 310.00 1.5260
HrmStr1 CX C 350.8 1.4860
….
….
And i´m getting this output:
Read MM parameter file:
Define CX 1
Define 2C 2
Define NH 3
Define C3 4
Define CD 5
Define ND 6
Define CL 7
Include all MM classes
Bondstretch undefined between atoms 1 7 N3-CX [L,L]
Bondstretch undefined between atoms 7 8 CX-HP [L,L]
Bondstretch undefined between atoms 7 9 CX-CT [L,L]
Bondstretch undefined between atoms 7 15 CX-C [L,L]
Bondstretch undefined between atoms 1255 2587 SH-SH [L,L]
Bondstretch undefined between atoms 4837 4839 N-CX [L,L]
Bondstretch undefined between atoms 4839 4840 CX-H1 [L,L]
Bondstretch undefined between atoms 4839 4841 CX-2C [L,L]
Bondstretch undefined between atoms 4839 4846 CX-C [L,L]
Bondstretch undefined between atoms 4841 4842 2C-H1 [L,L]
Bondstretch undefined between atoms 4841 4843 2C-H1 [L,L]
Bondstretch undefined between atoms 4841 4844 2C-SH [L,L]
Bondstretch undefined between atoms 4918 4921 NH-C3 [H,H] *
Bondstretch undefined between atoms 4918 4925 NH-C3 [H,H] *
…..
…..
I hope you can help me.
Greetings,
Maria Belen
Hello Sir, I am running a frozen transition state Opt+Freq with the following input line:
opt=(calcfc,ts,modredundant,noeigen,loose) freq=noraman b3lyp/6-31g(
d) geom=connectivity
But I obtain this error:
Error parsing secondary structure:
QPErr — A syntax error was detected in the input line.
B 1 35 F
I have never seen this before, but I am guessing it has to do with the redundant coordinates which the atoms 1 and 35 seem to be in this structure B = bond F = frozen.
Would you be so kind as to, tell me what caused the error, and how could I fix it.
Thank you for your valuable input!
Dear Peter,
I’ve never seen that error before either but I guess you are right in your interpretation.
Why are you including the modredundant option? I suggest you try two things: either eliminate the modredundant option and launch it again or eliminate it and change the coordinates from internal to Cartesian. Let me know how it goes.
Have a nice day!
Dear Professor,
I opened chk file on GaussView, but it showed following error message:
CConnectionGFCHK::Parse_GFCHK()
Missing or bad data: Alpha Ortbial Energies
Line Number 1737
What is the problem? and what is the meaning of this error message? I will used G09 and I read a solution for this problem in your page but really i don’t understand the solution?
Any advise will be appreciated.
Dear Prof. Barroso,
I want to know something about the calculation of SAS (solvent accessible surface) calculation in Gaussian09. Kindly comment on the following..
1. What is the keyword for the SAS computation i.e., in the input line.
2. After calculation how to generate the surface structure using GaussView.
Your comment and help will be highly appreciated
Thank you in advance
Hi
prof.barroso,
i want to know list of software packages that can do basic function of geometry optimization, and out put the major physical properties of the molecules. such as bond length,bond angle, ir frequency polarity.
i know some packeges like avogadro, gabedit,luscus. can you please tell me how to search molecules in gabedit and luscus.
Dear Professor,
I am trying to calculate reorganization energie by Gaussian 09,
1) What is the meaning of the energy of the cation calculated with the optimized structure of the neural molecule ? Is that : we optimise the structure at the neutral molecule (0,1) and we re- optimise it at the cation structure(+1,2).
can you help me please to calculate reorganization energy ??
I am doing TDDFT calculation of curtain OLED molecules using Gaussian09
software. I would like to know how to calculate reorganization energy for
hole/electron transfer. I have read the following paper J. Phys. Org. Chem.
2009, 22 11041113. They have explained as follows
lamda hole = lamda 0 + lamda + = (E*0-E0)+(E*+-E+)
lamda electron = lamda 0 + lamda – = (E*0-E0)+(E*–E-)
E0 and E+ represent the energies of the neutral and cation species in their
lowest energy geometries, respectively, while E*0 and E*+ represent the energies
of the neutral and cation species with the geometries of the cation and neutral
species, respectively.
It is confusing for me. I have calculated E0 , E+ and E- but I dont know how to
calculate E*0 , E*+ and E*-. Please help me. Thanks in advance.
Thanks in advance
Dear Professor,
I’m trying to model a triruthenium complex containing two radical ligands. the experimental magnetic moment at room temp. give a value of 0.9 B.M. I woulder what spin multiplicity should I use in DFT geometry optimization.
Kind regards
Attia
Dear Prof. Barroso,
I am a beginner in computational chemistry.
I am trying to calculate the ZFS parameters of a single-ion-magnet(showing slow relaxation of magnetization below 5 Kelvin) using ORCA and Guassian09.
My concern here is: Should I try the zfs calculation after geometry optimization of the structure or we should directly use the coordinates from x-ray diffraction data of the single crystal collected at 140K?
Thanks in Advance
Hello,
I want to use explicit solvent model in gaussian 9. Please can you tell me how can I use this model
Hi Sarita
Simply place as many solvent molecules as you think you may need. Remember G09 is a quantum mechanics calculation program so you will get the electronic structure of the whole thing and that could be a bit hard to handle.
Have a nice day!
Dear Sir,
I kindly request your advice to solve the following problem:
I got unusual C-Cl bond length when trying to optimize the structure below, which is a chromene with two chlorine atoms(green color) and amine group(blue nitrogen) and the other atoms are carbons and hydrogens.
Route :# opt=tight freq b3lyp/6-311++g(d,p) scrf=(solvent=acetonitrile)
nosymm geom=connectivity
The following is the first part of frequency output:
Full mass-weighted force constant matrix:
Low frequencies — -5.5455 -4.2666 -0.0100 -0.0053 -0.0037 5.5907
Low frequencies — 7.0396 9.8289 11.1345
Diagonal vibrational polarizability:
13983.2563880 3843.2579338 9396.2565212
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A A A
Frequencies — 6.6897 9.4638 10.1817
Red. masses — 19.2383 23.1033 7.1491
Frc consts — 0.0005 0.0012 0.0004
IR Inten — 23.4833 32.6624 11.3293
The bridge C-Cl bond length is (5.3 Angstrom) , which is unusual, and the summary of the results are:
File Type = .chk
Calculation Type = FREQ
Calculation Method = RB3LYP
Basis Set = 6-311++G(D,P)
Charge = 0
Spin = Singlet
Total Energy = -1628.86211634 a.u.
RMS Gradient Norm = 0.00000378 a.u.
Imaginary Freq =
Dipole Moment = 25.6363 Debye
The question is: We do not trust this bridge C-Cl bond length (5.3 Angstrom). How can we solve this problem? I highly appreciate your guidance and assistance. With my best regards.
Ghazwan
Is there a way to vary the percentage of Hartree Fock exchange for a given functional?
Dear Prof. Barroso,
I am relatively new in computational chemistry. I ran a successful PBC-DFT job for a conjugated polymer, how can I find HOMO LUMO gap values and other important results from .out file?
Thank you very much for this learning portal.
Hi! I’m afraid of making a mistake in Gaussian software. Probably, I chose a wrong file to create a Gaussian input file. Is there a way to find out the name of “the wrong file” from the Gaussian input file (.gjf) or other related files (.log or .chk)? I must look for a lot of these wrong files in my calculation tree to make sure calculations are valid. Thank you in advance.
Dear Prof Barraso and other readers
I performed optimization on an organometallic compound containing heavy elements using B3PW91-GD3 level of theory but getting bonds distances like 2.600 Angs, after opt. But starting structure had 2.800 Angs.(as in crystallographic data). Is it usual to have such values after optimisation and if not What should be min difference one should consider.
Kindly help if someone faced this too
#checkpointwontReadFC
Hello everyone. I have been trying to optimize structures using # b3lyp/6-31+g(d). This ended with error termination request processed by link 9999.
Error termination via Lnk1e in /home/applications/gaussian/g09/l9999.exe
So I attempted to resume from the checkpoint file using
# b3lyp/6-31+g(d) fopt=(readfc) guess=read geom=check freq
But it seems that Gaussian isn’t reading the force constants from the checkpoint file now I get this error
FileIO operation on non-existent file.
FileIO: IOper= 2 IFilNo(1)=-20997 Len= 20 IPos= 0 Q= 140733598347328
dumping /fiocom/, unit = 1 NFiles = 14 SizExt = 524288 WInBlk = 131072
defal = T LstWrd = 2228224 FType=2 FMxFil=10000
I am installing Gaussian G09 and There’s a problem when I try to run any file.com, finishing to install G09 appears a error like this:
PGFIO-F-/OPEN/unit=11/error code returned by host stdio – 2.
File name = home/flavio/Gaussian/scratch/Gau-7058.inp
In source file ml0.f, at line number 195
May you tell me what about this?
Thanks a lot.
Please tell me some basic aspects of BOMD and ADMP simulations in gaussian
Hello Professor Barroso,
I am trying to locate transition state structure for C-C bond formation reaction. In which one carbon is aromatic carbon and another is carbonyl carbon (C-C). Catalyst is present in the reaction to activate nucleophile and electrophile by hydrogen bonding interaction. I got TS at HF/6-31G** level which I confirmed by frequency calculation. There is only one negative vibration corresponding to C-C bond (-374.85). When I tried to optimize the same TS structure for higher level B3LYP/6-31G** (ReadFC from previous checkpoint file) then it failed by an error message.
Error in internal coordinate system.
Error termination via Lnk1e in /share/apps/gaussian/g09/l103.exe at Wed Apr
I also tried different functional like M062X and PBE0 but no success.
When I visualized the out file in gaussview then it shows that reactive centres are going away from each other (C-C bond distance increases up to 3.210 angstrom) compared to provided input structure for TS which was obtained at lower level ( C-C distance 1.868 angstrom).
What does that mean?
Is the TS obtained at lower level does not exist at higher level !.
I tried following keywords to fix the problem.
1. opt=(calcfc,ts,redundant,noeigentest) b3lyp/6-31g** Int=grid=UltraFine nosymm scf=direct
2. opt=(calcall,ts,cartesian,noeigentest) b3lyp/6-31g Int=grid=UltraFine nosymm scf=direct
I also tried qst2 and qst3 method to find the TS at higher level. Job completes successfully but after visualization it shows that reactive centres are far away from each other.
How can I fix this problem? I appreciate your help in advance.
Thanks and best regards
Swarada
#gaussianerror #external basis set
Hello, Dr. Joaquin Barroso. Help me with adding an external basis set, please! I Have:
%chk=F:\g09w\UDISEF.chk
# opt b3lyp/Gen pseudo=read
Title Card Required
0 2
Sm 2.23980000 1.03110000 4.37760000
S 2.94980000 -1.49240000 3.30800000
etc.
1 2 1.0 9 1.0 14 1.0 26 1.0 38 1.0 49 1.0 60 1.0 71 1.0
etc.
H 0
S 3 1.00
18.7311370 0.03349460
2.8253937 0.23472695
0.6401217 0.81375733
S 1 1.00
0.1612778 1.0000000
****
Any atom basis
****
Sm 0
еtс.
****
SM 0
SM-ECP 5 28
h-ul potential
1
2 1.000000000 0.000000000
s-ul potential
1
2 22.344471000 572.985332000
p-ul potential
1
2 16.694590000 272.359145000
d-ul potential
1
2 13.727705000 115.293900000
f-ul potential
1
2 24.059092000 -51.108392000
g-ul potential
1
2 20.197249000 -25.421885000
But, in .out-file i have error:
Rotational constants (GHZ): 0.0645388 0.0277158 0.0268049
General basis read from cards: (5D, 7F)
WANTED AN INTEGER AS INPUT.
FOUND A FLOATING POINT NUMBER AS INPUT.
1 2 1.0 9 1.0 14 1.0 26 1.0 38 1.0 49 1.0 60 1.0 71 1.0
?
Error termination via Lnk1e in F:\g09w\l301.exe at Thu May 05 12:28:43 2016.
Job cpu time: 0 days 0 hours 0 minutes 2.0 seconds.
File lengths (MBytes): RWF= 42 Int= 0 D2E= 0 Chk= 1 Scr= 1
I don’t understand – have I done something wrong?’
Try deleting the connectivity matrix and the connectivity keyword as well. If the problem persists then exchange the positions of the basis set and ecp listed at the end of the file.
Let me know if it helps
Fantasy, but when I removed the connectivity matrix – my calculations began. I still don’t understand why this is so. But anyway – thank you so much! You are a great magician!
I’m glad it worked; I’m annoyed not to know why either!
Have a nice day!
dear Dr. Joaquin,
I found this “Anisotropic Spin Dipole Couplings in Principal Axis System” in gaussian09 .log file. What the meaning
Thanks
dear Dr. Joaquin,
I want to frequence calculation a crystal structure in gaussian 09. But programme always giving different error. Now I want to try different methode, if I would use only the elements and their bonding and coordinate, I mean like a molecule, it would be a correct methode?
Thanks.
I have a question, didnt know how to put it here on the blog.
What does a calculation run on HF or DFT or any other level of theory, in gaussian gives us? The energy that the software calculates, when we give the keywords “opt”, is that energy the solution of the electronic part of the total hamiltonian?
Or the energy calculated is the total energy of the system, including the nuclear part too?
I had nowhere to ask this question to. Kindly help. Its blowing my mind!
The best book to look for your answer is”Exploring Chemistry With Electronic Structure Methods” by J.B.Foresman and A. Frisch.
Also try to find (Kubelka, J. in 1–257 (2012).) in the net it is open access NOTE. Very useful.
Below is taken from the last reference.
Gaussian predicts various important thermodynamic quantities at the specified temperature and pressure, including the thermal energy correction, heat capacity and entropy. It also give the zero point energy (ZPE). These items are broken down into their source components in the output:
Zero-point correction= 0.029209 (Hartree/Particle)
Thermal correction to Energy= 0.032062 (Etherm = ZPE+Etrans+Erot+Evib)
Thermal correction to Enthalpy= 0.033007 (Htherm= Etherm+pV)
Thermal correction to Gibbs Fre1. Kubelka, J. in 1–257 (2012).e Energy= 0.008252 (Gtherm= Htherm?TS) Sum of electronic and zero-point Energies= -113.837121(E0=Eelect+ZPE) Sum of electronic and thermal Energies=
-113.834268 (E= E0+Etrans+Erot+Evib= Eelect +Etherm)
Sum of electronic and thermal Enthalpies= -113.833324 (H= E+pV= Eelect+Htherm) Sum of electronic and thermal Free Energies=-113.858079 (G= H?TS= Eelect+Gtherm)
Be careful here, because the description is little confusing. The thermal corrections and the sums all contain the zero-point energy, although it is not explicitly stated!
I am attempting to do a broken symmetry calculation in gaussian 09 for the first time. I have tried to follow the tutorial provided by gaussian (http://www.gaussian.com/g_tech/afc.htm) as closely as possible but am having problems with the input for the antiferromagnetically coupled solution.
I want to compare the antiferromagnetically coupled S=0 ground state to the closed shell singlet solution that I have already calculated. First I optimized the entire molecule as a triplet. Then I used Gaussian’s atom groups editor to generate two fragments both triplets and assigned one as alpha spin and one as beta spin. Then I am using the guess=(fragment=2,only) entry to attempt the single point broken symmetry calculation. Every time though I get the error of “Charge and multiplicity card seems defective”
My input is as follows
%nprocshared=16
%mem=16GB
%chk=/home/mchalkley/TPB/NO/TPBFeNOAnion_bssinglet2.chk
# ubp86/gen guess=(fragment=2,only) int=ultrafine
TPBFeNOAnion_bssinglet2
-1 1 0 3 -1 -3
Fe(Fragment=1) 0.10894900 -0.01257700 -1.03256300
P(Fragment=1) -2.27652500 -0.71041500 -0.67649800
P(Fragment=1) 0.28193300 2.17184600 -0.46968700
P(Fragment=1) 2.02171300 -1.12263200 -0.66242900
O(Fragment=2) 0.40474600 0.16106300 -3.91869800
N(Fragment=2) 0.05005800 0.02575500 -2.75068200
C(Fragment=1) 1.51630700 -0.42690500 1.92274000
…
C H 0
6-31G(d)
****
N P B O Fe 0
def2TZVPP
****
Thanks very much in advance for your help!
Hello Joaquin,
I am looking for a PES scan method where I can only change the bond angle of one particular molecule in a pool of multiple molecules by keeping all other degrees of freedom frozen. Could you please guide me if you know any such feature in Gaussian?
Your help will be appreciated.
Thanks.
With regards,
Tarak
scale factor B3LYP 6-31G(d,p) and B3PW91 6-31G(d,p)
#convergenceIssue
Hello,
I am facing troubles with optimising a transition state structure in water (PCM). I have found a a number of transition states of a reaction in gas phase then re-optimized them in water and calculated their frequencies. While I managed to obtain most of the transition states both in gas phase and in water, I am having big troubles in re-optimising a couple of TS structures in water. The troubles are two folds:
(1) Either they never converge at all and going on and on without an end. I see only one YES for RMS Force.
(2) Or ending up with different types of errors, when i tried to run with different options..
For, example, Step requested is out of bounds, Error Termination.. or sometimes due to geometry failures after running for several hours.
Technical details and what i tried until this date..
* I am using M062x/6-31+g(d) model.
*I have tried different combination of options from opt=calcfc/calcall (with different maxcyc values), SCF=QC/XQC, nosymm, tight, maxcyc=N, int=grid=ultrafine.
None of them really worked in the case of these two structures. Indeed using calcall option didn’t fail yet, but already running over 2 weeks without any sign of convergence..
*Indeed I also tried to first optimize with lower models and basis sets, for example, B3LYP/631+g(d), B3LYP/TZVP. This option was atleast useful in getting one of the two troublesome TS structures. However, When I restarted the job with the chk file from B3LYP opt and optimised it again with M062X/631+g(d), it never converged..
*I also chose skipping re-optimization of the gas phase TS structure in water and just perform freq. But again, as it is expected, the freq outputs ended up giving several imaginary frequencies. So I gave up this option..
I think i pretty much tried most options suggested in the literature, still facing trouble. I know it is tempting to come to conclusion that either these TS structures are in flat PES in water, or they don’t exist at al in water. But, from the experience I had with the gas phase structures and the chemical reaction I am trying to study, I am almost sure that this could not be the case.
It is a shame that I am working on this project, i mean identifying different reaction pathways and the TS and GS structures involved in these pathways both in gas and water, for almost 2 years now. But I am still struggling to complete this because of these two TS Structures..
I would really appreciate if you could suggest me some solution that you think could help. Or do you think I am doing anything not correctly..
Please let me know..
Thanks in advance.
PS: Sorry for a very long message.
Hello,
I hope you are doing well. I am attempting to run transition state searches for certain azobenzene derivatives. In reading up on the procedure, I noticed that the software I’m using (Schrodinger software) recommends keeping the number of canonical orbitals consistent for the cis/trans isomers I’m comparing. This makes sense, as only molecules run at the same theory/basis set can have their energies compared. However, I am wondering whether it is also essential for the transition state scan to be run using the same number of canonical orbitals (I intend to use the same basis set/theory, but of course that does not guarantee the same number of canonical orbitals). Thank you very much for your time.
Warm regards,
Unni Kurumbail
It would be desirable to keep the same number as to make a right comparison but as you say there is no guarantee. However if you keep the same level of theory and you use the QST3 method, there is a good chance of achieving the desired consistency.
I hope this helps
During potential energy surface scan, how to obtain zero minimum energy. We get negative energy values as the minimum energy. We perform the calculations for a neutral molecule. Most of the suggestions are to try with reactant and product. Can we get the zero minimum energy without including the reactant?
What do you mean by zero minimum energy? All electronic energies are lower than zero by definition, E = 0 would imply no interaction or stability by any physical principle. What you need is the minimum energy which is found as the lowest point in your scan. The methodology you mentioned is called QST2 but it is by no means the only one.
I have been working with gaussian for along time, but still i dont know the meaning of a lot of keywords and terminologies used in the output code. Can anyone help me and find out as to from where I can get to understand the meaning of each and every term in the output file?
Try the Gaussian site: http://www.gaussian.com
hello everyone,
Can anyone please tell me how to find the overlap integral value from the orbital overlap in chemcraft? I have made the orbital overlap diagram in chemcraft, also I want to know the overla integral of the overlap. cal anyone please help me
Hello Dr. Joaquin,
By using external iteration approach, my structure collapsed to the ground state giving incorrect emission energy. Therefore, I had to use SCF approach and it did worked. My question is, Is SCF approach for emission calculation accurate??? how i can determine transitions relative contributions?
Hi!
I performed a scan calculation, and I’d like to know how to calculate %population of isomers, can you help me?
n1 =(N*e^(−ε1/kT))/((e^(−ε1/kT)+(e^(−ε2/kT))
Thanks!
Hello..
I performed a optimization of a selenium complex using b3pw91/6-31G(d,p), and now I want to calculate the nmr so that i can corelate with the experimental data. My question is do I need to use a solvent for nmr calculations?
#gaussianerror
Hello..
I want to scan a bond length using CAM-B3LYP and compare the result with CCSD(T) method. The basis set used for both methods are the same(6-31+G(df)). Every thing was good in the case of CAM-B3LYP method while for CCSD(T) method I receive the below error:
NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-
NUMERICAL EIGENVECTOR FOLLOWING MINIMUM SEARCH
INITIALIZATION PASS
************************************************
** ERROR IN INITNF. NUMBER OF VARIABLES ( 0) **
** INCORRECT (SHOULD BE BETWEEN 1 AND 50) **
************************************************
I used the” # opt=modredundant iop(5/48=10000) ccsd(t)/6-31+g(df) maxdisk=5GB ” keywords. the “iop” was added for solving the error but it didn’t help.
can you please help me to run the CCSD(T) method???
any suggestion would be regarded.
Hi,
I’m having problems with DFT convergence in Gaussian 09. I’m studying nanotubes BN. First I optimized the geometry using these paremeters: opt=verytight scf=verytight pm6. After this, to have sure that my geometry is correct, I did a frequency calculations and the geometry didn’t show up any imaginary frequences. So I start the DFT calculations using this paremeter: sp b3lyp/6-31g scf=tight prop=(field, potential). But I’m having this error:
The value of 5 for MaxDer is out of range
Error termination via lnkie in /opt/gaussian/g09/l602/exe
Could you help me?
Igor, opt=verytight will not give you any imaginary freq by default. Why are you searching for imaginary freq, and how do you expect the structure to have imaginary freq?
I optimized the geometry fist and after it I did DFT calculation, but always the calculation gave me a error. So I though that geometry wasn’t correct, so is the reason a did frequence calculation. I was looking for the imaginary freq because I though the energy of geometry wasn’t in a global minimum. And if was the reason of my errors I could fixed the geometry e try do again the DFT calculation. But the freq calculation didn’t show up any freq imaginary, and I really don’t know what to do!
You can try to use the optimized structure from pm6 basis set and try a higher basis set with DFT/ROB3LYP, try opt=tight first. Is there a similar structure from the literature? BN has been around for sometime so I think you may find a similar structure in the literature, it’s better than trying to optimize the structure with other software or very low basis set because that can take you far away from the optimized structure and hence the error in your DFT calculation.
Hi,
I would like to save all the points from an IRC calculations into separate (individual) input files for Gaussian. Is it possible? How can I do it?
Of course, I can save one by one using Crtl+S but it is rather tedious!!
Thanks in advance
Pedro
Hi Pedro, I don’t know how to help you.
How can one expand a basis set in such a way as to have an s-type Gaussian on every point on a cubic grid?
I don’t think that’s possible with Gaussian since you need to associate every basis set to an atom and thus you also define a positive charge on that grid. Maybe with CRYSTAL or even VASP which deal with periodic systems.
Would associating a basis set to a ghost atom not be an acceptable method?
Also, is it possible to add confinement potential to a ground state energy calculation?
I think the first part could be interesting to try. About the second part I wouldn’t know how to do it with a constrained software such as gaussian. If you find out how to do it please let me know about the details!
Have a nice day!
Dear Doctor Barroso,
I have problems with the Fukui + and – indices for benzene. All of them are negative! but my calculations are correct. I obtain this functions using the Hirshfeld population analysis using Gaussian. Can you help me??
Mishka
Dear Mishka,
Sorry for the lateness of my response. It is very weird indeed that ALL are negative. Are you sure you are using the equations in the right order? Maybe you exchanged terms and that is what causes the sign change. You are using a good population analysis but is your wavefunction a good one too? what level of theory are you using?
If the problem persists, use the negative values then, or just multiply them by -1 until you figure where the error is.
I hope this helps!
Dear Mr. Barroso,
yes I’m pretty sure I’m using equations in the right order. Level theory B3LYP, and basis set aug-cc-pVTZ, seriously I’ve no idea what’s wrong.
Dear Dr.joaquin
I have used mp2 method for wfn file in gaussian.when I see wfn file I have some MO with non-integer occupation and zero energy.would you please guide me about this zero energy?and I have HF energy at the end of wfn file?
Best regards
Dear Mina,
Make sure to use density=current in the route section of your mp2 calculation and to use output=wfn in that very same input.
If you don’t take these steps then you will get the HF energy in your wfn and not the MP2 correction.
I hope this helps
Hello Dr.joaquin,
I want to know the difference between using counterpoise with generic basisset and ONIOM method.
There is a huge difference! as in they are not even close to what they do. Counterpoise will allow you to calculate the correction to the energy of a system where some electron density is shared to orbitals where it shouldn’t be; that is called Basis Set Superposition Error (BSSE). Whereas ONIOM allows you to calculate a large system with a mixed approach: A section uses a large level of theory, say DFT with large basis set and a second calculation of the entire molecule is run with a low level of theory say semiempirical PM6, then the energies are substracted and then you have a large system divided in two.
I would suggest you take a look at the Gaussian website for these two keywords.
Have a nice day!
Hi Dr. Joaquin
I am trying to understand the functional form of B3LYP from the Gaussian output file. I have tried to relate the details in the output file with the functional form of B3LYP. But I am not sure what certain terms correspond to. I have mentioned below the details. Can you pleaese help me.
In the output of TD-DFT calculation files, I see the following (this is an e.g. of B3LYP)
IExCor= 402 DFT=T Ex+Corr=B3LYP ExCW=0 ScaHFX= 0.200000
ScaDFX= 0.800000 0.720000 1.000000 0.810000 ScalE2= 1.000000 1.000000
And in this case, it is well known that the funcitonal B3LYP has 20% Hartree Fock Exchange and 80% Density Exchange, the terms ScaHFX= 0.200000
ScaDFX= 0.800000 which says the scaling factor for HFX is 20% and DFX is 80% respectively. And when summed up, they give the value ‘1’.
0.720000 corresponds to the coefficient for gradient of Ex(Becke88).
Can someone please tell me what do the last two terms (1.000000 & 0.810000) correspond to.
Please let me know if I am not clear.
Sir,I want to build a nanoparticle coated with other groups.Which software should I use?
It depends on what you have. For example, if you don’t have the coordinates for your nanoparticle but the composition is already reported you can download the structure from the CCDC or any other source as a .cif file and grow it as you need with Mercury. I don’t recommend doing it with GaussView unless you have an extremely good .cif file but the problem is that from time to time some residual density is left behind or some atoms look double or triple due to thermal motion or poor refining and GV will show them all! Mercury doesn’t have this problem because it averages the position of each atom. After using mercury you can save it as a .mol2 file and then open it with GV or you can use OpenBabel to translate it into any other file format.
If you need to draw each atom by hand then I suggest you find a crystal with similar properties and just change the atom labeling if possible.
I hope this helps.
Thanks for your reply.
Is there any other software which can be used to build a NP?
CRYSTAL but it is really expensive
Hi Dr. Barroso!
I am using Psi4 to look at interactions between DNA base pairs with SAPT (Symmetry-Adapted Perturbation Theory), which gives interaction energies by the components: Electrostatic, Induction, Exchange, and Dispersion. The dominant term, energetically, is the dispersion energy, which is supposed to be due to correlation between monomers. But I don’t have a good understanding of what the physical interpretation of exchange energy is, so I don’t know if I should be paying attention to it, as well. Do you have experience with this method, and if I’m looking for regions on the potential surface that correspond to maximum secondary overlap between monomer frontier orbitals, which term(s) are most important?
Thanks
I knew your name rang a bell! You’ve worked with my colleague Karina Martínez, right?
Anyway, so I have no experience whatsoever with Psi4, I will try to fix that soon if I get the time.
Now if I understand correctly this exchange term comes from the Hartree-Fock based exchange operator which has no precise physical interpretation; it is a consequence of the antisymmetric wavefunction required to satisfy Pauli’s exclusion principle. I would pay attention to it since it is a pure quantum effect arising from a pure quantum argument but I wouldn’t sweat trying to interpret it. In the case of frontier orbitals overlap I would pay close attention to it but be careful because if you are using a large basis set then some artificial overlaps may occur. Can you include a basis set superposition error correction? what is the full level of theory used with SAPT?
I hope this helps. Have a nice day!
Yes, indeed. Karina and I hit you up for some advice when we were back at Torrey Pines. Thanks for that, and thanks for this blog. There’s great advice here.
As far as the SAPT procedure in Psi, it looks like they are using HF in two basis sets – monomer and dimer – and getting the interaction energy from the difference. Each set uses different “tweaks” to the aug-cc-pvdz basis set. I was hoping I could use this method to look at the dominant forces between intercalators and the DNA base pairs without having to review all my quantum mechanics notes, but that was not to be! I mean, I have numbers for each energetic component, but there’s that exchange energy that I don’t know what to do with… Anyways, thank you for your continuing assistance. You’ll probably see Karina before I do, so say ‘hi’ for me!
Hello Dr. Barroso,
I am so glad that I stumbled across your blog – this site is incredibly useful for a beginner like myself. I am computing shielding tensors for a charged system using various charge models. My input script is the following –
%Chk=name
# B3LYP/6-311++G** pop=Hirshfeld
name
-1 1
coordinates
–Link1–
%Chk=name
# B3LYP/6-311++G** nmr charge=Check Geom=Check Guess=Read scrf=(solvent=water)
name
-1 1
For the script above, I am wondering if the atomic charges from the Hirshfeld pop analysis are the ones being used in link 1 for the scrf calculation and nmr calculations.
If you would be so kind as to give me some pointers about my approach, I would really appreciate it.
Thanks!
Dear Effy,
Thank you so much for your kind words about this little blog of mine. I’m glad you’ve found it helpful.
I don’t think you are achieving what you want to with the CHARGE keyword because it is used for imposing point background charges in an otherwise empty space. In other words, your Link1 will read background charges from the checkpoint file but since you didn’t define any in your first section then it will read zero charges and run the nmr calculation in the same empty space as the first calculation.
Pop=Hirshfeld is a population analysis, i.e., it is a way of “slicing” the electron density and distributing it between atoms (charges arise just as the difference between the “electron density slice” for each atom and its nuclear charge).
So long story short, you could try this input, compare to a single job input in which you combine both route sections (lines beginning with #) and get the exact same result. I think.
The shielding tensor is, as far as I know, independent from the population analysis therefore I think you will get the same result if you use Hirshfeld, Mulliken, NBO or any other. But in the end you don’t loose anything by trying and that is what science is about, right?
I hope this helps. Have a nice day!
Dr. Barroso,
You were right – the calculated shielding tensors were the same for all of the pop analysis models that I tried. My thinking was that if these analyses would provide different electron densities, then the point charges and therefore the shielding tensors would also be slightly different – but I misunderstood how charge is taken into account when calculating the tensors.
I’m now wondering if there is a way to add a single point charge to my DFT calculation at an x distance from my molecule. I tried using the charge keyword and added a line at the end of my script with the coordinates (x,y,z) and charge – however the Gaussian job crashed as it was expecting a field of background charges instead of just one.
Do you possibly have any suggestions on this?
Best,
Effy
copy the last few lines of the log file so I can take a better look at the error, but I think if you define a vector for the field instead of coordinates for the charge it should work. Let me know.
Dr. Baroso,
Thanks for your speedy reply! I am not sure how to add a vector – but I will look into it and let you know what I come up with.
My input script looks like this:
%NProcShared=2
%Chk=checkpoint.chk
#n B3LYP/6-311++G** nmr(printeigenvectors) Charge NoSymm
molec_sparkle
0 1
H 1.37495 0.31583 -0.88477
C 0.59092 -0.40156 -0.52962
N 1.29755 -1.62823 -0.08888
…..
O -1.26659 -1.66984 -1.50246
H -1.71906 -1.86019 -2.31854
5.60350 5.68149 6.75474 -1.0000
My log file error is below:
Self energy of the charges = 0.0000000000 a.u.
MM energy of the charges = 0.0000000000 a.u.
Nuclei-charges interaction = 0.0000000000 a.u.
Nuclear repulsion after external point charges = 405.0824450874 Hartrees.
One-electron integrals computed using PRISM.
Illegal input to OneElI: NGrid= 1 NMatD= 1 NAtoms= 0.
Error termination via Lnk1e in /export/apps/Gaussian/g09/l302.exe at Tue Sep 13 18:00:23 2016.
Job cpu time: 0 days 0 hours 0 minutes 0.6 seconds.
File lengths (MBytes): RWF= 42 Int= 0 D2E= 0 Chk= 2 Scr= 2
Thanks Again!
If this were an optimization you would need to use Opt=z-matrix
Try changing your coordinate system to Z matrix just to rule that variable out. I hope it works belt me know if it did.
Unfortunately not, I used newzmat to convert from Cartesian to Z-matrix and used these keywords #n B3LYP/6-311++G** Opt=Z-Matrix Charge NoSymm Geom=Connect, keeping the point charge on the bottom (like my previous script) and got the same exact error.
I changed the case on the keywords charge and nosymm to all lower case and got my script to run (and terminate normally) – I have to check and make sure that the point charge is being considered – but I just wanted to update you. Sorry to bother you with such a dumb mistake!
It isn’t dumb at all! I was certain that Gaussian wasn’t case sensitive! I’m glad you worked it out. Launch the same calculation with a 0.0 or 0.001 charge just to make sure the influence of this charge is being considered.
Have a nice day!
Dear Joaquin,
I wish to know is there is a way to count the kind of bonds between elements on gaussian or gaussview. For example: B-C bonds, C-C bonds…..
Hello Igor,
There isn’t such a feature in either GaussView or G09. I imagine you have a very large and complicated molecule to just go and count them! I think this could be a very interesting feature that we could write as a standalone script, I hope I can get the time to do it and if I make it I will let you know.
Have a nice day!
Thanks for your answer! Yes, I have a very large and complicated molecule, and I really don’t know how I can start write this script. I have some knowledge in Fortran and if you could help me I will be so gratefull!
i am in trouble kindly help me….
my (GaussView 5.0) calculation feature are disable …i am a new user how can i enable it
gave me solution…..thanks ….me waiting for your positive response
check this link
https://drive.google.com/file/d/0B77aw9RUp_0iMlFiSWlKcGx4U01FZW14SDFOQThpeDd1Ukpn/view?usp=sharing
Those options will be active, only if you have gaussian 03 or 09 or any gaussian version. You can get gaussian setup from your institute if your institute have license.
I suggest you try editing your input files by hand. It is not that hard and it will make you more proficient with the use of Gaussian. So, in short it may be a good thing that the calculation feature got disabled.
Sir,I want to make a monolayer protected nanoparticle.I have the xyz file of both the nano particle and the ligand.How to do that?
You can use GaussView to open one then open the second one but make sure to select the option “append molecule” to active group (or something like that, but it has to say append). Now you can manipulate them both together.
Maybe you will need to first run them by openBabel to translate them from xyz to gjf.
I hope this helps
if you were to randomly pick an iridium atom from a large collection of iridium atom .which isotope are you more likely to selce
193 according to:
https://www.webelements.com/iridium/isotopes.html
Dear Dr. Joaquin,
I want to receive .wfx-file after gaussian calculations. But I had “Error termination”.
My inp:
%chk=C:\g09w\32.chk
# b3lyp/Gen opt output=wfx
Table with coordinates
Basis
***
32.wfx
My Out:
A syntax error was detected in the input line.
# b3lyp/Gen opt output=wfx
‘
As I understand, the problem is in the symbol “w” after the “=”
Thank you for your ideas!
Without “output=wfx” gaussian run calculations normal
It looks ok to me I’m. It sure why isn’t working. Try running a separate calculation after the optimization is finished by reading the geometry and the guess from the checkpoint file.
I hope it helps
It normal run with “output=wfn”. But I all the same do not understand, why gaussian does not want to work with “output=wfx”
As a result, the problem was solved by using a higher version of the Gaussian. Starting with “output=wfx” is not possible using ECP and Gaussian 09 A.02, but it works for Gaussian 09 B.01. It can be useful to someone)
Dear sir,
I am having a problem when i optimized cluster 4, i.e.
Error in internal coordinate system.
Error termination via Lnk1e in /usr/chem//g09/l103.exe
Please suggest me a solution
Thank you.
You need to open it with a visualizer such as GaussView and define it again; your starting geometry is clearly wrong.
Dear sir,
I want to calculate ELF topological by Multiwfn combined with Gaussian 09, but i don’t know how to do for entering path input in Multiwfn to have wfn file
thank you
You need to use the following keyword in your input:
output=wfn
And then, at the end of the input file leave a blank line and then write:
filename.wfn
And leave another blank line after that. Replace filename for any name you want to give your file. This should create the file you need to work with MultiWfn
I hope it helps
Thanks for your help, I tried to practice your advice but i failed
IN HARD disk D, I created a file name ELF
and in Gaussian for CH4 energy I have put:
%chk=C:\G09W\NED\CH4.chk
# b3lyp/6-31g(d,p) output=wfn
0 1
C 0.82644489 0.51775076 -0.02437770
H 1.18309931 -0.49105924 -0.02437770
H 1.18311773 1.02214895 0.84927381
H 1.18311773 1.02214895 -0.89802920
H -0.24355511 0.51776395 -0.02437770
ELF.wfn
ELF
then in multiwfn, I’m entering this INPUT PATH:
D:\ELF\CH4.wfn
but in vain, Multiwfn does not work
You need to leave a blank line between the coordinates and the file name. Also another blank line after the file name and delete the second ELF.
Hi Abdo,
No need to create wfn file. Multiwfn accepts .fchk file itself as input and you can get ELF. You just drag your .fchk file into the multiwfn. It will take the path automatically. Hope this helps.
Thanks for your help,
%chk=ap21c_0.chk
%nprocshared=4
%mem=6000MB
#p mp2/6-311+G(d) POP=CHELPG density=current NoSymm
Cristal Acetamida p21c
0 1
C 5.697564 1.964000 2.628051
O 5.712034 2.229068 1.432646
N 4.576077 1.979592 3.358167
error: Symmetry turned off by external request.
Stoichiometry C14H11ClINO
Framework group C1[X(C14H11ClINO)]
Deg. of freedom 81
Full point group C1 NOp 1
Rotational constants (GHZ): 0.6262353 0.0945558 0.0840652
Leave Link 202 at Sun Sep 25 10:47:33 2016, MaxMem= 786432000 cpu: 0.0
(Enter /usr/local/g09/l301.exe)
Standard basis: 6-311+G(d) (5D, 7F)
Atomic number out of range for 6-311G basis.
Error termination via Lnk1e in /usr/local/g09/l301.exe at Sun Sep 25 10:47:33 2016.
Job cpu time: 0 days 0 hours 2 minutes 48.1 seconds.
File lengths (MBytes): RWF= 5 Int=
I assume there is a question there somewhere. The error you’re getting is due to iodine not having a standard 6-311+G(d) basis set in gaussian. You have to input it manually using the Gen keyword. There’s a post about it in this blog.
I hope this helps
excited state optimisation and frequency calculation using TD-DFT is not proceeding.. There is no termination at all. The calculation has stopped in between for days. Kindly provide some ideas to troubleshoot this.
It probably ran out of space on your disk or just the queue time expired if you’re using a queue system.
Have a nice day
Thank you Sir for your reply. But I have tried increasing the memory as well there is no queue issue. It seems something else is creating a problem. Can there be any other reason for the same?
Dear Sir,
Is it possible to have two photon absorption calculation by using G09? If it is possible then what is the method for the same?
Unfortunately it isn’t possible.
okk thx
Cordial saludo doctor Joaquin
Podría usted decirme si hay una forma de determinar cuántos estados sigletes y tripletes estudiar en una molécula orgánica de 40-50 átomos para obtener un “buen espectro de absorción”
Yo estoy tratando de hacer un UV con TD-DFT, rb3lyp/6-311++g(d,p) usando gaussian 09.
Muchas gracias por su atención y colaboración.
Atentamente,
Ubeiden Cifuentes Samboni
Estudiante de Química
.
Dear Joaquin,
I have a small question for you.
how can we performed a scan of total energy of a systeme as a function of an angle (o) using the frozen geometries of the molecules. (o) is formed by one bond that link the functionals group to the hemisphere structure of the pcbm and a plan parallel to the central thiophene ring of the oligomer.???
how to define (o) in gaussian ?? is it a scan redundant ??
thank you
Dear Joaquin,
Do you know the estimative of error for PM6 and DFT calculation on Gaussian 09?
Hello Igor,
No, I’m afraid I’m not aware if there is such a thing. I would imagine it varies from case to case specially from property to property but it raises an important point though: Validation of our calculations is always important, contrasting our results to previously published ones or to experiments is always a good idea if the data is available of course.
Have a nice day!
Thank you!
Dear Dr. Barroso,
is there any software except cosmologic to perform COSMORS calculation?
Mishka
Not that I know of but you should try to contact the Computational Chemistry List (ccl.net) for a better answer.
Have a nice day
Thanks!
Please help 😦
I am struggling with Gaussian 09W,
I am trying to optimize the structure of polymer dithienosilole difuorobenzothiadiazole
Tellurophene,
Here is my input file:
%chk=PDFDTemodifynew.chk
%nprocshared=16
%mem=10GB
# opt b3lyp/6-311g(d) geom=connectivity symmetry=none
Title Card Required
0 1
C 13.48351686 7.02586306 -8.74982925
C 12.53045532 6.01310392 -8.26039842
C 11.26837425 6.65119408 -7.95994522
C 11.40615440 8.11624463 -8.26226387
H 14.52520581 7.07763760 -9.09954034
H 12.50453022 4.93143638 -8.06191003
C 8.97308433 8.93696659 -7.61136124
C 8.30632410 10.21979805 -7.61871494
C 9.24062655 11.25113326 -8.10551296
C 10.37675956 9.14135379 -8.10598411
H 7.26219973 10.19714623 -7.27321297
S 12.71589159 8.19795983 -8.70472516
S 10.40047783 10.50379020 -8.35317442
Si 9.42551189 7.04115178 -7.42620821
C 8.25982023 12.43304350 -7.99278700
C 6.97289079 12.25430775 -7.52692699
C 8.66304716 13.72602504 -8.36615515
C 6.06758717 13.37730538 -7.42905673
C 7.79273130 14.80568871 -8.27195438
C 6.47967695 14.64135788 -7.80008995
N 6.24567767 11.07814548 -7.06585385
N 4.80572351 12.86454822 -6.91031180
S 4.94671267 11.47940394 -6.70278493
F 9.83275582 14.19868214 -8.84665170
F 8.20973188 16.03623828 -8.63850357
C 5.56212260 15.87545963 -7.71831664
C 4.25301942 15.72661756 -7.23623768
C 3.44061063 16.84227232 -7.16854686
H 3.88790649 14.73939878 -6.92065121
C 3.92848200 18.12008436 -7.58234254
C 1.50273950 18.79524504 -6.87147990
C 2.86024541 19.10018723 -7.40014784
C 1.63519026 21.15941585 -7.37007920
Si 2.01695481 16.96149119 -6.69829414
C 2.46456001 16.19395673 -4.97372451
H 2.44153811 15.12636438 -5.04166985
H 3.44468109 16.51194069 -4.68536907
H 1.75433574 16.52023448 -4.24295485
C 0.36181784 16.18163852 -7.34323712
H -0.43346462 16.42574253 -6.67030396
H 0.13902791 16.57069454 -8.31478231
H 0.46700580 15.11835368 -7.40034089
S 5.28430412 17.47710693 -7.92864643
S 2.81946261 20.46229154 -7.64686522
C 8.08696030 7.31868274 -6.04967045
H 8.40304808 8.10671543 -5.39852301
H 7.15621076 7.58451944 -6.50567063
H 7.96334907 6.41788446 -5.48559358
C 9.33005151 5.21054700 -8.06132507
H 9.98804745 4.59721626 -7.48187121
H 8.32731265 4.85051948 -7.96235555
H 9.62214364 5.17424219 -9.09004473
C 0.73462797 20.12997170 -6.86101657
H -0.18587855 20.23938589 -6.56304345
C 0.93744124 22.53211283 -7.39127594
C 1.55609000 23.74463146 -7.60040348
C 0.61904219 24.82681506 -7.55818609
H 2.62364751 23.88672907 -7.77784180
C -0.66072277 24.37794357 -7.31846233
H 0.90613585 25.87016539 -7.70077596
C -2.17692751 24.53462108 -7.09897350
C -3.34017794 23.65547454 -7.03685694
H -3.30105119 22.56288925 -7.15854061
C -4.07682202 25.93804784 -6.69553573
C -4.57527942 24.53801288 -6.77753016
C -4.91269971 27.11285830 -6.45877674
C -6.38803630 27.08583911 -6.26395948
C -5.62217639 29.37691327 -6.12294244
C -6.82125737 28.54814234 -6.05044418
H -7.90789934 28.62367146 -5.89688966
C -6.49351344 30.62199582 -5.87366111
C -7.85733338 30.51687149 -5.68899001
C -5.90847196 31.89854904 -5.82966868
C -8.65745057 31.69841708 -5.45652626
C -6.67768240 33.03446873 -5.60606426
C -8.06686206 32.94537281 -5.41629028
F -4.57560747 32.01658447 -6.00866551
F -6.08624405 34.24746262 -5.56936947
Si -6.34853174 25.18516791 -6.47120876
C -7.14852148 24.50692913 -4.83915221
H -8.16986506 24.82132253 -4.78516994
H -7.10386298 23.43786265 -4.83757340
H -6.61306765 24.88752222 -3.99455877
C -7.36194589 24.55231520 -7.99963581
H -7.27750512 23.48781797 -8.06757248
H -8.39074928 24.82169260 -7.88174009
H -6.97652794 24.99838759 -8.89259293
S -2.71152066 25.81379606 -6.89152613
S -4.59169972 28.45630619 -6.35893869
N -8.76511916 29.37649676 -5.67300337
N -10.03772398 31.25604754 -5.30332522
S -10.06748557 29.85522654 -5.43891587
C -9.51248664 33.41176137 -5.16281188
C -10.82590829 32.78800143 -5.03728995
H -11.45388170 31.88482399 -5.03789591
C -11.07714261 35.18180832 -4.76187129
C -11.84916287 33.90941300 -4.77847315
C -11.65157499 36.50800455 -4.54702964
C -13.09491686 36.78555048 -4.31243555
C -11.88011484 38.87802674 -4.27712019
C -13.21814892 38.31113858 -4.14215693
H -14.27242643 38.57049502 -3.96521743
S -9.77195995 34.77836651 -4.98909695
S -11.06406595 37.76139783 -4.50580751
Si -13.44501051 34.91054408 -4.44972846
C -14.60366452 34.42189591 -5.92700429
H -14.83217506 33.37808805 -5.87089647
H -15.50952640 34.98875893 -5.87240974
H -14.10834323 34.62932874 -6.85249251
C -14.32169405 34.48517046 -2.77220550
H -15.17380742 35.11953328 -2.64419524
H -14.63675582 33.46267118 -2.78366345
H -13.63805029 34.63869377 -1.96352645
C -12.48743661 40.27489554 -4.05014482
C -11.77733154 41.43063808 -3.81208599
C -12.64657401 42.55654505 -3.64561292
H -10.68982045 41.50300935 -3.75345901
C -13.97010944 42.19508623 -3.76541660
H -12.28299484 43.56666977 -3.44865399
C -15.44994239 42.62104811 -3.74957590
C -16.73298097 42.02626448 -4.11006596
H -16.44558948 41.02699912 -4.46916942
C -17.12587180 44.26796543 -3.27958464
C -17.82693811 43.06936006 -3.81543160
C -17.78084013 45.50653359 -2.86498683
C -19.24737770 45.75542817 -2.91618173
C -18.14956123 47.72608620 -2.04053688
C -19.46072072 47.18435546 -2.38302926
H -20.55578238 47.20518109 -2.48540439
S -15.79080651 43.89995278 -3.28770214
S -17.26407256 46.68587047 -2.35510779
Si -19.48914975 43.99528514 -3.62364672
C -20.71520304 43.14958689 -2.38059089
H -21.60415738 43.73955576 -2.29936931
H -20.96687844 42.17254933 -2.73690126
H -20.25079829 43.07021399 -1.41989940
C -20.25454882 43.96844082 -5.40607305
H -20.40844382 42.95500127 -5.71292251
H -21.19137785 44.48536597 -5.39976768
H -19.58597768 44.45014938 -6.08861939
C -19.01113776 48.94286065 -1.65486106
C -20.38473300 48.91948966 -1.78846236
C -18.40688212 50.10876282 -1.15551726
C -21.17536180 50.07276157 -1.42083903
C -19.16699685 51.21747027 -0.80197726
C -20.56588533 51.21057684 -0.93173052
F -17.06426701 50.14597363 -1.01950256
F -18.55707473 52.32336662 -0.32501996
S -22.61670984 48.42049420 -2.18135767
N -21.31211790 47.89918694 -2.26145786
N -22.56960827 49.73377303 -1.67672892
C -22.07809668 51.50057451 -0.95852947
C -23.29332643 50.78318994 -1.33066483
H -23.86663581 49.92006145 -1.69999662
C -23.90650855 52.99921001 -0.56741627
C -24.48364673 51.72934464 -1.08667945
C -24.68023583 54.18273938 -0.19927194
C -26.16164013 54.29605199 -0.28817309
C -25.26721152 56.37876041 0.55904061
C -26.51565444 55.71207095 0.20291159
H -27.61193180 55.74429160 0.11798700
Si -26.22673569 52.50474586 -0.95454300
S -24.28423972 55.41605249 0.29061245
S -22.54384785 52.75393677 -0.53749295
C -27.21190822 52.76505081 -2.60538411
H -27.44590334 51.81340501 -3.03493803
H -28.11781839 53.29618847 -2.40015367
H -26.61537101 53.32912916 -3.29157576
C -27.13281529 51.18186479 0.13752178
H -28.11073155 51.53604538 0.38879032
H -27.21477752 50.26485517 -0.40770803
H -26.57268146 51.01506385 1.03380719
C -25.64725668 57.78941930 1.04607981
C -24.80487591 58.67359985 1.68269699
C -25.47331483 59.89939931 2.00139331
H -23.75715145 58.48545206 1.92400377
C -26.78762479 59.87983884 1.59034807
H -24.98221199 60.73226485 2.50783931
H -27.50429082 60.68889280 1.71686681
Te -0.70790707 22.71447071 -7.15482341
Te -14.13530942 40.55871779 -4.06733269
Te -27.17881467 58.43182190 0.85118403
1 2 2.0 5 1.0 12 1.0
2 6 1.0 3 1.0
3 4 2.0 14 1.0
4 10 1.0 12 1.0
5
6
7 10 2.0 8 1.0 14 1.0
8 9 2.0 11 1.0
9 13 1.0 15 1.0
10 13 1.0
11
12
13
14 45 1.0 49 1.0
15 16 1.0 17 2.0
16 18 1.0 21 2.0
17 19 1.0 24 1.0
18 20 1.0 22 2.0
19 20 2.0 25 1.0
20 26 1.0
21 23 1.0
22 23 1.0
23
24
25
26 27 2.0 43 1.0
27 28 1.0 29 1.0
28 30 2.0 34 1.0
29
30 32 1.0 43 1.0
31 32 2.0 34 1.0 53 1.0
32 44 1.0
33 44 1.0 53 2.0 55 1.0
34 35 1.0 39 1.0
35 36 1.0 37 1.0 38 1.0
36
37
38
39 40 1.0 41 1.0 42 1.0
40
41
42
43
44
45 46 1.0 47 1.0 48 1.0
46
47
48
49 50 1.0 51 1.0 52 1.0
50
51
52
53 54 1.0
54
55 56 2.0 180 1.0
56 57 1.0 58 1.0
57 59 2.0 60 1.0
58
59 61 1.0 180 1.0
60
61 62 2.0 88 1.0
62 63 1.0 65 1.0
63
64 66 1.0 65 2.0 88 1.0
65 79 1.0
66 67 2.0 89 1.0
67 69 1.0 79 1.0
68 69 2.0 71 1.0 89 1.0
69 70 1.0
70
71 72 1.0 73 2.0
72 74 1.0 90 2.0
73 75 1.0 77 1.0
74 76 1.0 91 2.0
75 76 2.0 78 1.0
76 93 1.0
77
78
79 80 1.0 84 1.0
80 81 1.0 82 1.0 83 1.0
81
82
83
84 85 1.0 86 1.0 87 1.0
85
86
87
88
89
90 92 1.0
91 92 1.0
92
93 94 2.0 103 1.0
94 95 1.0 97 1.0
95
96 98 1.0 97 2.0 103 1.0
97 105 1.0
98 99 2.0 104 1.0
99 101 1.0 105 1.0
100 101 2.0 104 1.0 114 1.0
101 102 1.0
102
103
104
105 106 1.0 110 1.0
106 107 1.0 108 1.0 109 1.0
107
108
109
110 111 1.0 112 1.0 113 1.0
111
112
113
114 115 2.0 181 1.0
115 116 1.0 117 1.0
116 118 2.0 119 1.0
117
118 120 1.0 181 1.0
119
120 121 2.0 130 1.0
121 122 1.0 124 1.0
122
123 125 1.0 124 2.0 130 1.0
124 132 1.0
125 126 2.0 131 1.0
126 128 1.0 132 1.0
127 128 2.0 131 1.0 141 1.0
128 129 1.0
129
130
131
132 133 1.0 137 1.0
133 134 1.0 135 1.0 136 1.0
134
135
136
137 138 1.0 139 1.0 140 1.0
138
139
140
141 142 1.0 143 2.0
142 144 1.0 150 2.0
143 145 1.0 147 1.0
144 146 1.0 151 2.0
145 146 2.0 148 1.0
146 152 1.0
147
148
149 150 1.0 151 1.0
150
151
152 153 2.0 164 1.0
153 154 1.0 156 1.0
154
155 157 1.0 156 2.0 164 1.0
156 162 1.0
157 158 2.0 163 1.0
158 160 1.0 162 1.0
159 160 2.0 163 1.0 173 1.0
160 161 1.0
161
162 165 1.0 169 1.0
163
164
165 166 1.0 167 1.0 168 1.0
166
167
168
169 170 1.0 171 1.0 172 1.0
170
171
172
173 174 2.0 182 1.0
174 175 1.0 176 1.0
175 177 2.0 178 1.0
176
177 179 1.0 182 1.0
178
179
180
181
182
And here is the error:
Rotational constants (GHZ): 0.0558210 0.0005390 0.0005361
Standard basis: 6-311G(d) (5D, 7F)
Atomic number out of range for 6-311G basis.
Error termination via Lnk1e in /opt/gaussian/g09/l301.exe at Sun Oct 23 22:15:13 2016.
Job cpu time: 0 days 0 hours 0 minutes 15.3 seconds.
File lengths (MBytes): RWF= 32 Int= 0 D2E= 0 Chk= 1 Scr= 1
As you see, the atomic no is out of range, which is like an unsolvable
mystery to me.
For the Sulfur and Selenium in the same period, I can perform calculation well but not with the Tellerium.
Please help me to choose a suitable basis set, is there any way to use basis set 6-311G(d) combine with ECP.
please help me.
Thank you.
The 6-311G(d) basis set is not defined for Te in gaussian but you can add it using the GEN keyword as described here:
In that same post there is a link to the Basis Set Exchange list, in which you can select Tellurium from a clickable periodic table and then select the basis set you want and save it in gaussian format to add at the end of your input file.
I hope this works
Have a nice day
Thank you so much 🙂
Dear Mr Joaquin,
Please help me to clarify these issues:
I chose ECP for my structure already, and apply 6-311(d) for S,C,N,H,Si, F and apply ECD (SDD) for Tellirium (heavy metal).
And the calculation ran perfectly,
But I do not understand about this below input I made, could you help me to clarify it:
#p rb3lyp/genecp 5d 7f Pseudo=read opt geom=connectivity symmetry=none
1. Why they put the character “p” after symbol “#” ?
2. Why they use “restricted” in rb3lyp but not b3lyp?
3. what is the meaning of 5d and 7f ?
Pleae help me to answer all of this question.
Thank you so much.
Here is my input file:
%chk=PDFDTescan.chk
%nprocshared=16
%mem=10GB
#p rb3lyp/genecp 5d 7f Pseudo=read opt geom=connectivity symmetry=none
Title Card Required
0 1
C -37.17364536 4.93495069 9.77318208
C -38.59197240 4.88180402 9.75494754
C -36.62322723 6.12173230 10.13860658
C -39.39860485 6.04129435 10.11060361
C -37.40187666 7.26160876 10.48819817
C -38.78238221 7.29793177 10.49783568
N -39.31175097 3.81054136 9.42413948
N -40.70490453 5.79811616 10.03358236
S -40.88773537 4.23929537 9.55344140
F -35.29286606 6.27651477 10.18789402
F -36.68985644 8.35373124 10.82489167
C -39.55503027 8.47518049 10.85964339
C -40.93598102 8.60450897 10.91100359
C -41.39020386 9.88143797 11.29944623
H -41.58356030 7.77616315 10.66715166
C -40.33308558 10.74845115 11.55025724
C -42.03297310 12.39064282 12.06416820
C -40.68055413 12.09604603 11.96034493
C -42.24355714 13.73721642 12.47244838
C -41.07984837 14.43102151 12.66859134
H -40.95329333 15.45868506 12.97690267
S -38.79120299 10.01233339 11.31533159
S -39.67446138 13.45407177 12.35841473
Si -42.99763320 10.82910961 11.60508915
C -44.01701547 10.13497841 13.02751106
H -44.43559647 9.15649172 12.77284703
H -43.41153582 10.01358763 13.92880748
H -44.85480393 10.79441579 13.27417099
C -44.05808158 11.03195498 10.06281608
H -44.47741899 10.07336918 9.74228720
H -44.89683117 11.71064926 10.24577835
H -43.47727665 11.43631671 9.23044897
H -43.21823170 14.18799254 12.61926090
C -36.35859935 3.78393130 9.42012330
C -36.76569817 2.53890387 9.02428730
S -34.62342065 3.91494575 9.47989185
C -35.68547157 1.65159441 8.75634078
H -37.81287853 2.27520280 8.92990878
C -34.45854536 2.26586523 8.96296427
Si -35.34555860 -0.12357888 8.20406851
C -33.27352621 1.46245355 8.72240039
C -33.47751042 0.15410961 8.30841861
C -35.94861294 -0.50047962 6.46023254
C -35.97681599 -1.41857790 9.41708972
S -31.59090027 1.85798071 8.86647450
C -32.25274667 -0.52339744 8.09459075
H -37.04182786 -0.50426351 6.41005151
H -35.58456670 0.24048506 5.74460876
H -35.60358457 -1.48403061 6.12658910
H -37.07075140 -1.44797621 9.43151204
H -35.62734350 -2.41975610 9.14658427
H -35.63595878 -1.21004472 10.43396728
C -31.12540006 0.23769248 8.33438557
H -32.18273459 -1.54699396 7.74192684
C -29.73365693 -0.12139006 8.20678063
C -28.66176778 0.71425708 8.04355283
Te -29.07103337 -2.11879685 8.29466189
C -27.35144622 0.14582311 7.94609911
H -28.80455563 1.78802175 7.96056479
C -27.23122258 -1.20396031 8.02110757
H -26.48152572 0.77999411 7.80181510
C -26.00457573 -1.95708561 7.91960780
C -25.73413758 -3.21318653 8.39197351
S -24.63684850 -1.25449519 7.10631704
C -24.40870860 -3.64648417 8.10950229
H -26.47098496 -3.80218384 8.92571653
C -23.69519315 -2.68066513 7.41330341
Si -23.26359606 -5.12994479 8.36982997
C -22.32442923 -3.00327584 7.06423769
C -21.85777451 -4.25118689 7.46055634
C -22.88437988 -5.47260744 10.18174051
C -23.85827715 -6.69380342 7.50669394
S -21.13712820 -2.07974660 6.22051300
C -20.51831382 -4.45466309 7.07043297
H -22.10522499 -6.23401027 10.28510105
H -22.53878203 -4.57119262 10.69329699
H -23.77018676 -5.83792637 10.71039591
H -23.10068291 -7.48221741 7.55055378
H -24.76502002 -7.08542916 7.97791432
H -24.08355969 -6.50667772 6.45412112
C -19.94972874 -3.39006220 6.38506837
H -19.95498367 -5.35279534 7.27291035
C -18.60008453 -3.29022155 5.85375232
C -17.62726717 -4.36193063 5.97157686
C -18.11795240 -2.17752217 5.19295239
C -16.28313891 -4.22595158 5.42715615
N -17.82445953 -5.54058230 6.55756508
C -16.80121426 -2.05553883 4.66460754
F -18.90611548 -1.10180215 5.00669397
C -15.87222242 -3.04174725 4.76111080
N -15.51698448 -5.29885023 5.61954824
S -16.42889693 -6.39455329 6.42709162
F -16.51372611 -0.89742142 4.05439254
C -14.53326953 -2.89506865 4.21385704
C -13.50386141 -3.79659021 4.22316761
S -14.09149882 -1.40806642 3.42313257
C -12.32480392 -3.31206884 3.58987037
H -13.59819773 -4.77815123 4.67335745
C -12.49915454 -2.02305121 3.10675003
Si -10.55781387 -3.83925923 3.17562147
C -11.36432381 -1.41420148 2.43662100
C -10.20982820 -2.17765772 2.34160094
C -10.46377751 -5.30259457 1.99388570
C -9.49270483 -4.14821663 4.69779651
S -11.18638777 0.15078946 1.71028001
C -9.18006562 -1.48533839 1.65964245
H -10.81701612 -6.22193478 2.47105168
H -11.07309848 -5.13408151 1.10281499
H -9.43494277 -5.48020534 1.66572630
H -9.81951061 -5.04409020 5.23480255
H -8.44336487 -4.29645903 4.42471805
H -9.54041617 -3.30711456 5.39348368
C -9.52423565 -0.21727823 1.23391928
H -8.20339118 -1.90911879 1.45097865
C -8.73791564 0.74961063 0.50659611
C -9.18589355 1.79665500 -0.25294959
Te -6.63176436 0.73404489 0.52424568
C -8.22700686 2.64888997 -0.88839343
H -10.25019088 1.96189569 -0.39512084
C -6.90948147 2.37832191 -0.70696830
H -8.54942218 3.47960976 -1.50944528
C -5.80336690 3.10466446 -1.28238074
C -4.51048549 3.18034448 -0.83877525
S -6.05430165 4.03399438 -2.73121841
C -3.68145082 3.99460367 -1.65973951
H -4.17273538 2.66339987 0.05197536
C -4.38908284 4.52588672 -2.72913132
Si -1.89781356 4.61263759 -1.78772723
C -3.65247255 5.37773617 -3.64383131
C -2.30652578 5.57887577 -3.36083445
C -1.38188794 5.71020218 -0.34779142
C -0.64577388 3.23227413 -2.05474144
S -4.17194263 6.21104296 -5.06165075
C -1.69423132 6.42076656 -4.31165995
H -0.40542698 6.16899467 -0.53091286
H -2.10211860 6.51505707 -0.18300983
H -1.30408193 5.13623557 0.58070028
H 0.34694995 3.63607907 -2.27589820
H -0.55208924 2.60505759 -1.16287565
H -0.93582636 2.58701392 -2.88731973
C -2.54185730 6.86860700 -5.31533213
H -0.65484424 6.71077736 -4.28825672
C -2.21828749 7.74058829 -6.43280946
C -0.88514357 8.27151190 -6.65566369
C -3.13850112 8.14429766 -7.38013910
C -0.59801666 9.14340545 -7.78655924
N 0.18705535 8.04410235 -5.90057352
C -2.84642732 8.99749904 -8.48221345
F -4.41809411 7.73186928 -7.30522969
C -1.60912683 9.50782065 -8.71374124
N 0.67199847 9.54170799 -7.84601912
S 1.44221051 8.86395554 -6.56863865
F -3.87082830 9.28063161 -9.29872205
C -1.33389975 10.37730754 -9.84601273
C -0.14735410 10.95230066 -10.21207453
S -2.62590489 10.79666931 -10.93525128
C -0.24659658 11.75034913 -11.38649886
H 0.76680222 10.80145063 -9.64940699
C -1.53980189 11.75781360 -11.88942446
Si 0.80950646 12.83252389 -12.52022273
C -1.77230340 12.53897861 -13.09081364
C -0.67960209 13.20642827 -13.62491955
C 2.17800335 11.88869566 -13.40515051
C 1.50521885 14.35841928 -11.66316011
S -3.22121445 12.79778276 -14.00847715
C -1.02554819 13.92098975 -14.79731351
H 2.95033278 11.55819337 -12.70377557
H 1.78701384 11.00333082 -13.91203513
H 2.66736949 12.51492822 -14.15753914
H 2.26622987 14.08598826 -10.92531832
H 1.97558352 15.03731280 -12.38115919
H 0.72131243 14.91418100 -11.14322807
C -2.35189288 13.81156582 -15.16678063
H -0.31591896 14.48933403 -15.38928859
C -3.03808531 14.38737862 -16.29804178
C -4.20196293 13.96259386 -16.88014365
Te -2.33895583 16.11283473 -17.28315406
C -4.72027919 14.69015384 -17.99887585
H -4.70905564 13.07247691 -16.51848808
C -4.02994173 15.77488273 -18.43337868
H -5.63367971 14.37105096 -18.49245993
H -4.29156406 16.40378518 -19.27265574
1 2 1.0 3 2.0 34 1.0
2 4 1.0 7 2.0
3 5 1.0 10 1.0
4 6 1.0 8 2.0
5 6 2.0 11 1.0
6 12 1.0
7 9 1.0
8 9 1.0
9
10
11
12 13 2.0 22 1.0
13 14 1.0 15 1.0
14 16 2.0 24 1.0
15
16 18 1.0 22 1.0
17 18 2.0 19 1.0 24 1.0
18 23 1.0
19 20 2.0 33 1.0
20 21 1.0 23 1.0
21
22
23
24 25 1.0 29 1.0
25 26 1.0 27 1.0 28 1.0
26
27
28
29 30 1.0 31 1.0 32 1.0
30
31
32
33
34 35 2.0 36 1.0
35 37 1.0 38 1.0
36 39 1.0
37 39 2.0 40 1.0
38
39 41 1.0
40 42 1.0 43 1.0 44 1.0
41 42 2.0 45 1.0
42 46 1.0
43 47 1.0 48 1.0 49 1.0
44 50 1.0 51 1.0 52 1.0
45 53 1.0
46 53 2.0 54 1.0
47
48
49
50
51
52
53 55 1.0
54
55 56 2.0 57 1.0
56 58 1.0 59 1.0
57 60 1.0
58 60 2.0 61 1.0
59
60 62 1.0
61
62 63 2.0 64 1.0
63 65 1.0 66 1.0
64 67 1.0
65 67 2.0 68 1.0
66
67 69 1.0
68 70 1.0 71 1.0 72 1.0
69 70 2.0 73 1.0
70 74 1.0
71 75 1.0 76 1.0 77 1.0
72 78 1.0 79 1.0 80 1.0
73 81 1.0
74 81 2.0 82 1.0
75
76
77
78
79
80
81 83 1.0
82
83 84 1.0 85 2.0
84 86 1.0 87 2.0
85 88 1.0 89 1.0
86 90 1.0 91 2.0
87 92 1.0
88 90 2.0 93 1.0
89
90 94 1.0
91 92 1.0
92
93
94 95 2.0 96 1.0
95 97 1.0 98 1.0
96 99 1.0
97 99 2.0 100 1.0
98
99 101 1.0
100 102 1.0 103 1.0 104 1.0
101 102 2.0 105 1.0
102 106 1.0
103 107 1.0 108 1.0 109 1.0
104 110 1.0 111 1.0 112 1.0
105 113 1.0
106 113 2.0 114 1.0
107
108
109
110
111
112
113 115 1.0
114
115 116 2.0 117 1.0
116 118 1.0 119 1.0
117 120 1.0
118 120 2.0 121 1.0
119
120 122 1.0
121
122 123 2.0 124 1.0
123 125 1.0 126 1.0
124 127 1.0
125 127 2.0 128 1.0
126
127 129 1.0
128 130 1.0 131 1.0 132 1.0
129 130 2.0 133 1.0
130 134 1.0
131 135 1.0 136 1.0 137 1.0
132 138 1.0 139 1.0 140 1.0
133 141 1.0
134 141 2.0 142 1.0
135
136
137
138
139
140
141 143 1.0
142
143 144 1.0 145 2.0
144 146 1.0 147 2.0
145 148 1.0 149 1.0
146 150 1.0 151 2.0
147 152 1.0
148 150 2.0 153 1.0
149
150 154 1.0
151 152 1.0
152
153
154 155 2.0 156 1.0
155 157 1.0 158 1.0
156 159 1.0
157 159 2.0 160 1.0
158
159 161 1.0
160 162 1.0 163 1.0 164 1.0
161 162 2.0 165 1.0
162 166 1.0
163 167 1.0 168 1.0 169 1.0
164 170 1.0 171 1.0 172 1.0
165 173 1.0
166 173 2.0 174 1.0
167
168
169
170
171
172
173 175 1.0
174
175 176 2.0 177 1.0
176 178 1.0 179 1.0
177 180 1.0
178 180 2.0 181 1.0
179
180 182 1.0
181
182
H F N Si C S 0
6-311G(d)
****
Te 0
SDD
****
Te 0
SDD
Hello Hieu,
1. Why they put the character “p” after symbol “#” ?
The letter after # controls the printing level into the log file. Not all the information is printed out if you use no letter or if you type “t”. P will print a lot of stuff into your log file. Useful for post-processing. I suggest to always keep it.
2. Why they use “restricted” in rb3lyp but not b3lyp?
For a closed shell system there is no difference. G09 would have used a restricted wavefunction unless you have stated otherwise.
3. what is the meaning of 5d and 7f ?
These are used to specify use of Cartesian or pure d and f functions.
I hope this helps
Hi again 🙂
Could you please explain when one should use density functional dispersion correction, let say e.g. D3?
Best,
Mishka
Basically always but it becomes more important when you are dealing with intermolecular interactions. If you are using an empirical correction like Grimme’s then always find the suitable one for your problem in the literature.
I hope this helps!
Yes! Thank you a lot!
Have a nice day!
Dear Sir,
please help me with this: I’m preparing MD simulation which is organic molecule in methanol solution, but I don’t know how many methanol molecules should I put into my computational box, can I get any guidance?
It depends on the size of your box. Take a look at our publications in JCTC and JCC as guidance for organic Supramolecular species in water. That should give you a rough idea.
Have a nice day
Hello Dr. Barroso,
I want to do TD calculation even I never did.
Cam-b3lyp and wb97xd are readily found in td calculation paper. However fitting sets are always omitted.
What I want to know is proper fitting set for each method and how faster is computing speed than nofit keyword. Basis se tis 6-31G** due to organic molecules.
Regards,
Junho
Dear,Dr Barroso
Please help me with this::
Can a transition state have two negative frequencies? because this transition state with two negative frequencies connected reagents and products in IRC. what do you recomend?
I ask because I could find a state of transition with a single imaginary but very low sequence of -143.9 but being a small frequency the irc does not allow me to advance to reagents and products.
In the strictest sense it can only have two negative frequencies, however if one of them is pretty small, say, around -100 cm-1 or higher (i.e. closer to zero) then it can be ascribed to noise in your calculation. If the aforementioned pesky vibration is preventing you to get from A to B in your IRC then maybe try to eliminate it by modifying your geometry in the direction suggested by it. It usually helps. Now, some computational chemists rely a lot on the IRC, and some others just calculate it as a way to validate the observed TS. In my opinion is a matter of case to case (which I know its ambiguous but bear with me) because if you have found without ambiguity your TS with a single significant negative vibration in the direction you want it then the IRC will only confirm what you already know. On the other hand, if you have some doubts on the TS obtained (as you describe) the IRC can help you discern if its right or not and even can help you modifying your initial guess to better reach the desired structure.
I hope this helps!
Dear Sir,
I would like to calculate adsorptions of compounds on surfaces (MgO, graphene)? Is it possible? If yes would you be so kind and provide me any guidance? (software, how to prepare input)?
Hello!
Being such a general question giving a single answer is hard. We have used G09 to do some atomistic calculations on the interactions between a small section of a surface and organic molecules; these are rather lengthy calculations and only useful to some degree due to their complexity. We’ve also used the NBO methodology described in this blog to calculate the interaction energy between arsenic acid and graphene oxide. Please search the NBO and NBODel posts within this blog for more details about the input format.
I think you could best benefit from Materials Studio but the license is rather expensive. Maybe the best freeware available for this kind of calculations in RASPA by the group of Randy Snurr at Nortwestern, I think I’d start from there, the only downsize is that there is no available help desk or forum so you are pretty much on your own with it.
I hope this helps.
Thanks for your comprehensive answer!
Dear sir,
Can u please explain how to give input for hybrid functional such as PBEg/CBSB2** for fre calculation and CBSB4 for optimization for hetrocyclic compounds
Dear Sir
I’m trying to optimize geometry of complex with hydrogen bonds, if I use B3LYP/cc-pvtz everything is ok, but if I use B3LYP/aug-cc-pvtz with empirical dispersion I get convergence failure, can you help me?
Change the functional to B97D or M06 or basically anything that is not B3LYP
Is there any other way? Beacuse all of my other calculations are done using B3LYP, and I’d like to be consistent..
What have you tried so far? I would start with SCF=QC in the route section. It will require some work with the SCF algorithm to make it converge and even some manipulation of the initial geometry. With more details I can help you better.
Have a nice day
Hello!
This is probably a silly question, but could you possibly show me how to run a stability calculation (stable=opt) using Gaussian?
Thank you for your assistance!
Hi Patrick!
Not a silly question at all. Just so we’re on the same page (and I apologize in advanced if I sound pedantic), the STABLE keyword in gaussian has nothing to do with the concept of chemical stability but with the robustness of a given/found wavefunction.
If you optimize the geometry of a molecule at a given level of theory the associated wavefunction can be tested for its stability with the STABLE keyword, this will try to sort of ‘knock it’ out of its configuration by allowing certain perturbations to happen (e.g. complex orbitals, unrestricted v restricted selection of orbitals, etc.); if the wavefunction is stable negligible changes in energy will occur, otherwise the program will let you know.
If you run stable=opt the opt acts not on the geometry but on the optimization of the wavefunction as to make it robust enough in case it wasn’t already.
This calculation is mostly used as a test and not for obtaining chemically relevant information therefrom.
If you have a successful calculation already in file.chk you can test the robustness of the wavefunction like this:
%chk=file.chk
#p stable=opt geom=check guess=read
Title
charge multiplicity
–blank line–
I hope this helps! Have a nice day
#transitionstate
Hi Dr. Barroso,
Greetings.
Can you please clarify my query.
I have performed geometry optimization and frequency calculations for the structures of transition states with DFT/B3LYP/6-311++G(d,p)/IEFPCM in water. The transition state involved the formation of Hydrogen bonds between water and the reactants.
But, I have been told that DFT/B3LYP/6-311++G(2d,2p)/IEFPCM is more accurate for solvent correction. Is it more accurate to use 2p orbital than just 1p orbital? or is it ok to use 1p?
Hello Dr. Barroso,
I had a quick question about adding restraints to my Gaussian optimization. I’m not sure if this is possible, but I’d like to fix the dihedral angles – without fixing the bond lengths. I’ve tried a few different methods but do not seem to get differing results between no restraints and restrained optimization. Could you please take a look at my script(s) and show me where I’m doing something wrong?
Attempt 1: Restraining the C/N coordinates
%mem=2GB
%nproc=10
%Chk=pep2
# b3lyp/6-31+G* Opt=ReadFreeze
pep
-1 1
C 68.38000 143.77300 -25.35000
H 68.74500 143.35100 -26.31100
H 67.30500 144.04600 -25.40700
….
H 68.35300 153.14100 -19.90200
H 66.99100 152.69700 -18.94800
atoms=1-35 noatoms=C,N
Attempt 2: Restraining the Dihedrals %mem=2GB
%mem=2GB
%nproc=10
%Chk=pep2
# b3lyp/6-31+G* Opt=modredundant nosymm
pep
-1 1
C 68.38000 143.77300 -25.35000
H 68.74500 143.35100 -26.31100
H 67.30500 144.04600 -25.40700
….
H 68.35300 153.14100 -19.90200
H 66.99100 152.69700 -18.94800
N5 N7 N9 N12 F
N7 N9 N12 N14 F
N12 N14 N16 N24 F
N14 N16 N24 N26 F
N24 N26 N28 N31 F
N26 N28 N31 N33 F
Thank you very much for the time you put into this blog.
Good day! I have small question again) I read your Flash lesson “Atoms in Molecules”. It was very interesting and informative. I used “output=wfx”, because i have ECP-basis. After gaussian finish I started AIMQB. He found CP (3, -1), bonded with atom ytterbium (I used ECP for him), but he didn’t found CP (3, -3), appropriate for atom ytterbium. May be have you any idea? I do not know how to “get” to find CP (3, -3) for atom with ECP-basis
Well, either it’s not present at all or you should try to increase the basis set while also decrease the size of the core in the ECP. Try a mid core one.
Hope this helps
is it possible to do frank condon analysis with g09 under PBC?
No I don’t think so. You should try using CRYSTAL.
I hope this helps
Is it possible to control and restrict the NBO anslysis to detect the charge transfer within the specific atoms of the molecules?
You can use the E2PERT flag in your NBORead section to request a second order perturbation theory analysis of charge transfer between NLOs.
I hope this helps
I am beginner and I want to calculate NLO properties of a molecule, I am using this line in rout section:
#n B3LYP/6-31G(d) Opt Polar=(DCSHG,Cubic) CPHF=RdFreq
but the calculation is aborted saying
CPHF=RdFreq but no frequencies in input.
Error termination …………..
I don’t understand where to put the frequency, either in the route section and with which keyword and units? and also which values ?
Thank you.
Please add frequency range at last line with section. ex) (empty line) 300nm 400nm (empty line)
Hey, Recently I have started using MD simulations in double precision, which obviously offers a more precise data than single precision. I want to know whether any data calculated in double precision md simulations can be analyzed using single precision md simulation and what are the differences I will be experiencing in my analysis.
Dr. Barroso,
I have a matter I hope you can help me with. I have a set of compounds on which I wish to perform relaxed potential energy scans after elongating a specific bond by a certain length repeatedly (potential energy scan to be performed after each elongation). the Gaussian manual says this could be performed using the opt keyword and the “S” action code.
Could you possibly offer me assistance on how to perform such a calculation?
Thank you!
#P b3lyp/6-31G opt=modRed
tiltle
0 1
H
O 1 OH
H 2 OH 1 HOH
OH = 1.08
HOH = 107.5
1 2 3 103.0 S 10 +1.0
this is scan the angle HOH from 103 to 112 degrees
Dear Dr. Joaquin Barroso’s
I am trying to calculate the radiative and non-radiative rates of molecule alone and when near to metal nanoparticle. I can calculate the excited state lifetime from ZINDO out put but not getting how to calculate the radiative and non-radiative rates. Plz help me.
Hello Wari,
What level of theory and software are you using? Please search for a paper of mine published in JPC-A in 2013 or 14. It’s even available on my ResearchGate profile. You can find there the corresponding equations.
Have a nice day
Dear Dr. Joaquin Barroso’s
I need to compare series of calculations, Which of the following keyword affects on energy, so if I use it for one calculationI have to apply it to the entire series?
Tight, maxstep, integral=grid=ultrafine, SCF=QC
thanks!
dear sir,
I have synthesized a crystal where i get the proton transfer, however, I have found no proton transfer after optimization. I am not understanding what I should do at this stage. Use different functional in g09 software but theoretical prediction (no proton transfer) different from experimental result.
It is very hard to understand what you got from so few sentences. I believe you need to do an optimization of a transition state in which the proton is transfered from atom A to B if that’s the case in your crystal.
Have a nice day
Dear Dr. Joaquin Barroso
I am a Petroleum Engineer working on a Project that relates to molecular modelling of a component of Crude Oil: Asphaltenes. Asphaltenes after some time, come out of the crude oil solution forming aggregates that later plug the crude oil flowlines and hinder safe production. Inhibitors stop Asphaltenes from forming aggregates and coming out of solution.
My challenge is developing an Inhibitor Model that would portray the Inhibition Process. I tried using the Schrodinger Equation to start the modelling process or at least, characterize the system in its molecular state.
Please I would be glad if you could help or maybe give me some pointers.
I appreciate your work here. You are far too kind.
Thank you.
Best regards
IMHO the best way to elucidate inhibition mechanism is an initio molecular dynamics simulation, but you must have huge computational power for your system (since asphaltene is big molecule and you didn’t wrote what’s inhibitor, not mentioning solvent, but even for isolated system costs will be rather high, but it depends on your supercomputer)
Dear Uzoma,
Your question cannot be answered in this short space. If I understand correctly, you should start by studying the interactions between asphaltene molecules which lead to their macroscopic aggregation. I would start with simple DFT approaches such as B3LYP/6-31G(d,p) and then move forward depending on what you found.
I hope this helps!
In Gaussian 09 periodic boundary condition vibrational frequency calculation, I always face the error, ”
——————– ATTENTION——————–
Total charge is not ZERO — -0.000000002397
——————– ATTENTION——————–
”
. I changed the basis sets such as 3-21g, 6-31g, 6-311g, ccpVTZ, LANL2DZ etc and functions such as B3LYP, CAM-B3LYP, B3PW91 and PBEPBE as well as HF and DFT. However, I don’t get the convergence.
Can you help me regarding this?
Hello
Is your calculation finished correctly? I mean, does it get aborted? if not, I think you can safely disregard this so called error, which is more like a warning. This amount of charge gets left out of the box defined by your PBC specifications, therefore it is independent from the level of theory. As you can see is pretty minimal, in the billionths of electrons (10⁻⁹ e) so unless your calculation ends with an abnormal termination I think you can proceed with what you’ve got.
I hope this helps!
How can I calculate the “Tv” values (vectors) of a molecule (monomer), because I want to calculate it as a polymer? Summaryzing,I need give PCB to a monomer. Thanks a lot.
Hello Silvia,
If I remember my PBC correctly you should only give Gaussian the length in angstroms from the head to the tail of the monomer. So, if you have say polypropylene -CH2CH(Me)- you want to measure the length from the first methylene to the binding point on the methyne group plus half the expected bond length for the bond between monomers or your C atoms will clash.
I hope this helps. Thanks for reading
dear doctor
i make graphene sheet with vmd.and then i opened it with gaussview and do optimization with 3-21 .and gaussian run without error.then in gaussview i change some atoms and optimize it again….now i want to put pd hollow the graphene.but gaussian show “erorr 2070
the processing of the last link ended abnormally.All processing has aborted”
what is the problem here?memory limit or basis set or………..?
thenk you
Dear fatemeh,
It is hard to give a diagnostic with such short information. I would imagine the problem is the basis set if you are trying to use 3-21G on Pd for which it is not defined in gaussian. The error you mention is just the code for how the program is exiting but not the reason why. Try sending me the previous lines for better help.
Thanks for reading.
I have two questions
1. Opt+freq keyword in g09 calculates optimization and frequency. For excited state optimization, is it analytically done?
2. For tddft excited state optimization, selecting root=2 gives same energy and geometry as root=1. However vertical excited States are 0.213 eV apart (S1-S2) I mean.
Any suggestion will be appreciated….
Is it possible to do DFT-D3 calculations in Gaussian 09? How can I do it?
Hi,
Use the keyword EmpiricalDispersion=GD3 in your route section (only available in revisions Dx). Also, depending on the functional you are using, there are overlay options to turn on Grimme’s D3 dispersion.
I hope this helps but I think I’ll write a post about it.
Hello,
Could you tell which model is the cpu-cheapest and most accurate for calculating fluorescence spectrum? TD-DFT or ZINDO or CIS or ….
Cheapest: ZINDO. Most accurate: CIS. You cannot have both 🙂
I hope this helps
Thanks! what about TD-DFT? is it too expensive or it can’t be used for emission calculations.
It becomes expensive depending on the functional and basis set employed but the accuracy is pretty variable. Try finding a proper benchmark for similar systems in the literature.
Have a nice day
Hi Joaquin,
Great blog, its very useful and informative!
I have a question regarding generating density cube files – do you have any experience in doing this for ONIOM calculations? I have a central molecule at TDDFT/wb97xd/6-31G* surrounded by frozen atoms at amber level of theory. I would like to generate the difference density plot between s0 and s1 electron densities.
I have done this routinely for vacuum calculations (no oniom), however for the oniom calculation the cubegen utility throws an error saying there is no density saved on the checkpoint file.
My input line in the .com file is:
#p ONIOM(wB97XD/6-31G* td=(nstates=1,root=1):amber=(hardfirst))=(EmbedCharge) geom=connectivity density=all nosymm
And I use :
cubegen 2 density=SCF checkpoint.fchk s0.cub h
to generate the cube file from the formatted fchk file. When I do that, it gives the error:
“Could not find Total SCF Density on formatted checkpoint file.”
Any help is much appreciated!
Best wishes
Michael
Hello Michael!
Thanks for your kind words about this little blog of mine.
I’ve never tried to use the cubegen utility with ONIOM calculations, let alone excited state ONIOM calculations.
I would either try removing the density keyword from the route section or using density=fdensity in the cubegen utility.
It could also have to do with the options used during the formchk, did you use the defaults for that?
Let me know if any of this helped.
I’m having the same problem. I’ve tried using density=fdensity in cubegen utility and it only resulted in another error:
Could not find ” “,”Total FDENSITY Density” on formatted checkpoint file.
I’ve used all default options for formchk.
Hi Joaquin,
I really appreciate this blog. The questions and answer are very informative and helpful.
I have come across a problem while carrying out the OVGF calcualtion for ICN orbitals in gaussian. It works fine for FCN, ClCN, BrCN . When it comes to ICN , the results are very erroneous. No matter whether the basis for I is with or without ECP , the polestrenth of the HOMO are less than 0.8 . SO the corresponding energies are not acceptable. I have tried lots of basis sets from EMSL basis but could not get an acceptable value of binding energy and every time it compains ‘****WARNING**** : Pole strengh too small – OVGF does not work!!!’.
Also could you please give an idea about what controls the number of orbitals its printing in the output. My input(.com) is as follows-
%chk=ref-q1_ovgf.chk
%mem=10gb
%nprocshared=4
#p hf nosymm scf=xqc scf=tight ept=ovgf tran=iabc
ATZP for I,C,N
0 1
I 0.00000000 -0.89783310 0.00000000
C 0.00000000 2.95720966 0.00000000
N 0.00000000 5.17302297 0.00000000
C 0
S 5 1.00
7615.05999113 0.0017784
1145.08684615 0.0136680
261.91952431 0.0692908
74.66834196 0.2631529
24.40551202 0.7344482
S 2 1.00
8.68679013 0.5885314
3.23657623 0.4536170
S 1 1.00
1.30179999 1.0000000
S 1 1.00
0.52768873 1.0000000
S 1 1.00
0.15694534 1.0000000
S 1 1.00
0.0457300 1.0000000
P 4 1.00
34.50767936 0.0114038
7.91304441 0.0765963
2.36615458 0.3029741
0.81172425 0.7264544
P 1 1.00
0.31228882 1.0000000
P 1 1.00
0.11400266 1.0000000
P 1 1.00
0.0344390 1.0000000
D 1 1.00
1.1540490 1.0000000
D 1 1.00
0.3511286 1.0000000
D 1 1.00
0.1167520 1.0000000
F 1 1.00
0.8193120 1.0000000
F 1 1.00
0.2922100 1.0000000
****
N 0
S 5 1.00
10259.65669438 0.0017931
1542.36864597 0.0137833
352.92239285 0.0698018
100.80632697 0.2641269
33.10725394 0.7328001
S 2 1.00
11.88253928 0.5913763
4.46790829 0.4499684
S 1 1.00
1.19676433 1.0000000
S 1 1.00
0.63915992 1.0000000
S 1 1.00
0.19744232 1.0000000
S 1 1.00
0.0529500 1.0000000
P 4 1.00
49.11376009 0.0114857
11.32541037 0.0786357
3.42249686 0.3087282
1.1785157 0.7194875
P 1 1.00
0.43449114 1.0000000
P 1 1.00
0.15193747 1.0000000
P 1 1.00
0.0411900 1.0000000
D 1 1.00
1.7291770 1.0000000
D 1 1.00
0.5083460 1.0000000
D 1 1.00
0.1611360 1.0000000
F 1 1.00
1.1635804 1.0000000
F 1 1.00
0.3864030 1.0000000
****
I 0
S 8 1.00
5464702.08060097 0.0001093
849942.52168504 0.0007913
207458.86762606 0.0036900
64929.86485391 0.0131833
23909.80880875 0.0395406
9850.71275593 0.1040723
4222.34623514 0.2741166
1781.76403452 0.6488818
S 2 1.00
749.21394356 -0.5595941
318.75246448 -0.4728234
S 2 1.00
59.88344918 -0.7200351
29.50227605 -0.2987074
S 2 1.00
12.24593624 -0.5061450
6.20345391 -0.5148945
S 2 1.00
2.43764323 0.5412411
1.14985168 0.4841938
S 1 1.00
118.02205930 1.0000000
S 1 1.00
0.30638210 1.0000000
S 1 1.00
0.11926836 1.0000000
S 1 1.00
0.05963418 1.0000000
S 1 1.00
0.02381709 1.0000000
P 7 1.00
20182.20166081 0.0004988
4999.21100888 0.0038641
1768.53795847 0.0174910
734.77528080 0.0632147
317.51165410 0.1951982
139.60118455 0.4117047
63.12833732 0.4496355
P 2 1.00
13.45203045 -0.6861431
6.52579989 -0.3486363
P 3 1.00
3.02467901 0.5601269
1.38040546 0.4313665
0.52669045 0.0821826
P 1 1.00
28.34086632 1.0000000
P 1 1.00
0.22217820 1.0000000
P 1 1.00
0.08328104 1.0000000
P 1 1.00
0.04164052 1.0000000
D 6 1.00
565.98837950 0.0067496
168.69681731 0.0529920
63.14306896 0.2071444
26.10306850 0.4270744
11.24530421 0.4189456
4.63907320 0.1167256
D 1 1.00
1.91572411 1.0000000
D 1 1.00
0.72024616 1.0000000
D 1 1.00
0.36012308 1.0000000
D 1 1.00
0.06666136 1.0000000
F 1 1.00
3.85297909 1.0000000
F 1 1.00
1.265860195 1.0000000
F 1 1.00
0.37945225 1.0000000
G 1 1.00
2.97888999 1.0000000
G 1 1.00
0.56073086 1.0000000
****
Also the HOMO and HOMO-1 are degenerate and have same energy (from molpro calculation). But in the above output the HOMO is not degenerate .
Any help will be appreciated.
Regards
Soumitra
Dr.barroso
I want to running togehter two basis set in GO9 to Te added to the fullerene molcule
6-31G d,p and NAL2LD to compute electronic properties
any helped please
Hello sir, I am trying to explore the mechanism of an organic reaction using gaussian 09. Some of the intermediate structures I wish to optimize are zwitterionic species (molecular massed around 400-500g/mol). When i upload my input files with B3LYP/6-31G (d,p) set to gaussian it gives an error : “Unrecognized atomic symbol: ?d.” What does it mean, how could I correct it?
Thank you..
It means there are dummy or ghost atoms labeled as “?”. Go to your input file and delete those lines. If you’re using the geom=connectivity keyword you have to be careful to delete also those lines in the connectivity matrix which reference the atom numbers of those you just deleted. It’s easier to just delete the connectivity matrix and the geom=connectivity keyword all together.
I hope this helps!
I have a similar issue:
#p b3lyp/gen pseudo=read opt scf
0 1
(Atoms coordinates)
RU 0
S 1 1.00
2.5650000 1.0000000
S 1 1.00
1.5080000 1.0000000
S 1 1.00
0.5129000 1.0000000
S 1 1.00
0.1362000 1.0000000
S 1 1.00
0.0417000 1.0000000
P 1 1.00
4.8590000 1.0000000
P 1 1.00
1.2190000 1.0000000
P 1 1.00
0.4413000 1.0000000
P 1 1.00
0.0830000 1.0000000
P 1 1.00
0.0250000 1.0000000
D 1 1.00
4.1950000 1.0000000
D 1 1.00
1.3770000 1.0000000
D 1 1.00
0.4828000 1.0000000
D 1 1.00
0.1501000 1.0000000
****
RU 0
RU-ECP 3 28
f-ul potential
5
0 554.3796303 -0.0515270
1 155.1066871 -20.1816536
2 48.4976263 -105.9966915
2 14.7701594 -42.2166788
2 5.2077363 -3.7675024
s-ul potential
5
0 66.7118060 2.9578344
1 77.3503632 25.3748707
2 18.3571445 536.1262372
2 11.8404727 -651.2057221
2 8.1179479 381.3816943
p-ul potential
5
0 54.9937915 4.9651557
1 13.9399212 23.8861501
2 15.2118246 464.4631344
2 10.5460691 -714.4451788
2 7.5539486 377.5503594
d-ul potential
4
0 60.3444595 3.0352988
1 45.2100305 23.2901723
2 19.1190074 146.0926620
2 4.2712090 28.9129770
****
CL C H P S 0
6-31G(d)
———————————————————————————————————–
This produces the error:
Unrecognized atomic symbol ****
————————————————————————————————————
Switching the order:
…
(Atom coordinates)
CL C H P S 0
6-31G(d)
****
…
Produces the error:
Wanted an integer as input.
Found a string as input.
S 1 1.00
Any idea why this is happening?
(Using G09).
#excitedstateoptimization
Hi sir,
To interpret emission spectrum, i will perform an excited state optimization for a neutral mononuclear Pd(II) complex ( with S=1 multiplicity) containing chloride and picoline ligands. The following input is sound for the program to avoid giving error during calculation?
b3lyp/3-21g** opt TD=(Nstates=10, root=1,singlets)
the complex consists of about 70 atoms in total. In this case does it take too long time for the calculation to be completed in personel computer with 8 gb ram, intel core i5
Thanks for advanced..
The input seems right although the level of theory might be inadequate (too bad a functional and too small a basis set), also the 3-21G basis set isn’t defined for Pd unless you download it from the EMSL basis set exchange site and then defining it through the GEN keyword. Consider changing the basis set to LANL2DZ. In the processor you mention and for the amount of atoms it might take a while (days).
I hope this helps!
Estimado Joaquin, su blog está excelente… Quisiera dejarle una pregunta que hasta el momento no logro entender… Cuando reproduzco un artículo, aplicando el mismo software y la misma técnica usada ¿cuál es el motivo por el cual cual no logro obtener los mismos resultados que fueron publicados (los resultados que obtengo varían muy poco, como en diezmilésimas, pero siempre varían)?… Tiene algo que ver los parámetros computacionales (%mem, %nprocshared), la estructura del Hardaware, plataforma o la version del software?… Se supondría que los valores deberían reproducirse exactamente, ya que los algoritmos de la solución de las funciones no se ven afectadas…
Gracias, Jackeline!
En varias ocasiones puede deberse a la arquitectura (la precisión de los dígitos en 32 o 64 bits) pero frecuentemente se debe a ligeras variaciones en la geometría. Estás partiendo de las mismas coordenadas que reportan los artículos? Diezmilésimas de Hartree están muy bien dentro de la precisión química (1 kcal/mol) así que no hay de que preocuparse sin embargo es una buena observación.
Sobre el otro comentario que dejaste, las referencias más relevantes son:
Chandra and Nguyen, Int. J. Mol. Sci. 2002,3,310-323, Mendez and Gazquez J. Ame. Chem. Soc. 116, 9298 (1994)
Pero hay muchos reviews sobre conceptual DFT.
Saludos!
#gaussianerror
Dear Joaqquin. First of all thanks a lot for your blog. Super helpful. While I know you have already come to that issue earlier, I still encountering the same issue when I am running DFT calc. : Parse_GFCHK Missing or bad data: RBond.
I have tried your suggestions (independant vs independent and match the basis functions) but unfortunately that haven’t solved the issue. Would you have any other leads to pursue?
I am running a fairly big systems (104 atoms) at the wb97xd/63-1g level.
Thanks again for your help,
All the best,
Jean-Hubert
Dear Joaquin,
Please help me with the optimization. I am trying to optimize Gd(NO3)3 using Gaussian and I have used a charge of 0 and multiplicity of 1 in the input. But Gaussian is giving error stating charge 0 and multiplicity 1 is impossible. My input is given below.
%chk=DB.chk
%mem=3350MB
#p B3LYP/genecp opt gfprint SCF(XQC)
optimization
0 1
Gd -3.05143 2.39037 -0.05126
O -1.21743 3.15416 0.68973
O -1.33542 1.61338 -1.02503
N -0.46965 2.38945 -0.22802
O 0.28070 1.52730 0.49556
O -3.31602 0.61450 1.07296
O -4.58611 1.12975 -0.78640
N -4.37656 0.19206 0.24494
O -3.98571 -0.96127 -0.34338
O -3.42613 4.16897 -1.13673
O -4.45612 3.67766 0.87107
N -4.34974 4.61960 -0.17187
O -3.83643 5.74785 0.36845
O N 0
6-31G(d,p)
****
Gd 0
MWB28
****
Gd 0
MWB28
Thank you.
Gadolinium is a tricky element. It may have a pair number of electrons but in the Gd3+ state (I imagine this nitrate you have here is neutral) it has 7 valence electrons. Try changing the multiplicity up to 8 instead of 1 and it should work.
I hope this helps but please let me know if it did indeed.
Dear Joaquin,
I have tried multiplicity from 2 to 8. For multiplicity 3, 5 and 7 I got the error ” charge 0 and multiplicity #” not possible. For other values I got normal termination. Below I have given the list of energies and corresponding to the multiplicity
E=-1606.737 for Multiplicity 2
E=-1606.726 for Multiplicity 4
E=-1606.835 for Multiplicity 6
E=-1606.942 for Multiplicity 8
I am just confused.Which structure I have take as minimum energy structure ? The structure with the lower energy?
Thanks you.
Of course. Your ground state is most likely an octuplet. Quite supported in the literature of lanthanides’ chemistry
#gaussianerror
Dear Joaqquin. First of all thanks a lot for your blog. Super helpful. While I know you have already come to that issue earlier, I still encountering the same issue when I am running DFT calc. : Parse_GFCHK Missing or bad data: RBond.
I have tried your suggestions (independant vs independent and match the basis functions) but unfortunately that haven’t solved the issue. Would you have any other leads to pursue?
I am running a fairly big systems (104 atoms) at the wb97xd/63-1g level.
Thanks again for your help,
All the best,
Jean-Hubert
Thank you for your kind words about this little blog of mine.
When the Rbond flag shows up it means there is a problem with the number appearing in the Rbond section of the fchk file. Please share more details about this calculation (composition and basis set) as well as a transcript of the Rbond section of the fchk file in this same thread.
Have a nice day
Dear Joaquin,
Thanks much for your answer and sorry it took me so long to get back to you.
So, I was running a Perylene Diimide Dimer (non-covalent). As long as I stick to B3LYP-631G it runs smoothly, the calculation finished and I can open the chk file. Now, if I am using B3LYP-631G on neutral structure (charge 0 multiplicity 1) and increase the optimization to B3LYP-631+G the calculation completes but I can not open the chk and the fchk file (Rbond error message).
What is really weird is that I can open the fchk file with Avogadro but the output structure has been modified with respect to the input structure. For, example new bonds has been created and sp2 O has become sp3 O. This is probably why GV can not open the chk file…just a hypothesis.
The information you will find below are from a Perylene diimide dimer (non-covalent) but with a negative charge. I got the same RBond error message but the calculation did finish successfully as per the log file.
Calculation : # opt wb97xd/6-31g geom=connectivity
RBond R N= 416
1.50000000E+00 1.50000000E+00 1.00000000E+00 0.00000000E+00 1.50000000E+00
1.50000000E+00 1.00000000E+00 0.00000000E+00 1.50000000E+00 1.50000000E+00
1.50000000E+00 0.00000000E+00 1.50000000E+00 1.50000000E+00 1.50000000E+00
0.00000000E+00 1.50000000E+00 1.50000000E+00 1.00000000E+00 0.00000000E+00
1.50000000E+00 1.50000000E+00 1.00000000E+00 0.00000000E+00 1.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 1.50000000E+00 1.50000000E+00
1.00000000E+00 0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 1.50000000E+00 1.50000000E+00 1.00000000E+00 0.00000000E+00
1.50000000E+00 1.00000000E+00 1.50000000E+00 0.00000000E+00 1.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 1.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 1.50000000E+00 1.50000000E+00 1.00000000E+00
0.00000000E+00 1.50000000E+00 1.50000000E+00 1.50000000E+00 0.00000000E+00
1.50000000E+00 1.50000000E+00 1.00000000E+00 0.00000000E+00 1.00000000E+00
1.50000000E+00 1.50000000E+00 0.00000000E+00 1.50000000E+00 1.50000000E+00
1.50000000E+00 0.00000000E+00 1.50000000E+00 1.50000000E+00 1.00000000E+00
0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
1.50000000E+00 1.50000000E+00 1.00000000E+00 0.00000000E+00 1.50000000E+00
1.50000000E+00 1.00000000E+00 0.00000000E+00 1.50000000E+00 1.50000000E+00
1.00000000E+00 0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 1.50000000E+00 1.50000000E+00 1.00000000E+00 0.00000000E+00
1.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 1.00000000E+00
1.00000000E+00 2.00000000E+00 0.00000000E+00 1.00000000E+00 1.00000000E+00
2.00000000E+00 0.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
1.50000000E+00 1.50000000E+00 1.00000000E+00 0.00000000E+00 2.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 2.00000000E+00 1.00000000E-01
0.00000000E+00 0.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
1.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
1.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 1.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 1.00000000E+00 1.00000000E+00
1.00000000E+00 1.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
1.00000000E+00 1.00000000E+00 2.00000000E+00 0.00000000E+00 1.00000000E+00
1.00000000E+00 2.00000000E+00 0.00000000E+00 1.00000000E+00 1.00000000E+00
1.00000000E+00 0.00000000E+00 2.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 2.00000000E+00 1.00000000E-01 0.00000000E+00 0.00000000E+00
1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 1.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
1.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
1.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 1.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 1.50000000E+00 1.50000000E+00
1.00000000E+00 0.00000000E+00 1.50000000E+00 1.50000000E+00 1.00000000E+00
0.00000000E+00 1.50000000E+00 1.50000000E+00 1.50000000E+00 0.00000000E+00
1.50000000E+00 1.50000000E+00 1.50000000E+00 0.00000000E+00 1.50000000E+00
1.50000000E+00 1.00000000E+00 0.00000000E+00 1.50000000E+00 1.50000000E+00
1.00000000E+00 0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 1.50000000E+00 1.50000000E+00 1.00000000E+00 0.00000000E+00
1.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 1.50000000E+00
1.50000000E+00 1.00000000E+00 0.00000000E+00 1.50000000E+00 1.00000000E+00
1.50000000E+00 0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
1.50000000E+00 1.50000000E+00 1.00000000E+00 0.00000000E+00 1.50000000E+00
1.50000000E+00 1.50000000E+00 0.00000000E+00 1.50000000E+00 1.50000000E+00
1.00000000E+00 0.00000000E+00 1.00000000E+00 1.50000000E+00 1.50000000E+00
0.00000000E+00 1.50000000E+00 1.50000000E+00 1.50000000E+00 0.00000000E+00
1.50000000E+00 1.50000000E+00 1.00000000E+00 0.00000000E+00 1.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 1.50000000E+00 1.50000000E+00
1.00000000E+00 0.00000000E+00 1.50000000E+00 1.50000000E+00 1.00000000E+00
0.00000000E+00 1.50000000E+00 1.50000000E+00 1.00000000E+00 0.00000000E+00
1.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 1.50000000E+00
1.50000000E+00 1.00000000E+00 0.00000000E+00 1.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 1.00000000E+00 1.00000000E+00 2.00000000E+00
0.00000000E+00 1.00000000E+00 1.00000000E+00 2.00000000E+00 0.00000000E+00
1.00000000E+00 1.00000000E+00 1.00000000E+00 0.00000000E+00 1.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 1.50000000E+00 1.50000000E+00
1.00000000E+00 0.00000000E+00 2.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 2.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 1.00000000E+00
0.00000000E+00 0.00000000E+00 1.00000000E-01 1.00000000E+00 0.00000000E+00
0.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
1.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 1.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 1.00000000E+00 1.00000000E+00
2.00000000E+00 0.00000000E+00 1.00000000E+00 1.00000000E+00 2.00000000E+00
0.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00 0.00000000E+00
2.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00 1.00000000E+00 1.00000000E+00
1.00000000E+00 1.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00 0.00000000E+00
1.00000000E+00 0.00000000E+00 0.00000000E+00 1.00000000E-01 0.00000000E+00
1.00000000E+00 0.00000000E+00 1.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00
Virial Ratio R 2.005296494750132E+00
SCF Energy R -2.974777824613164E+03
Total Energy R -2.974777824613164E+03
S**2 R 7.897949295905562E-01
S**2 after annihilation R 7.514558611273549E-01
RMS Force R 4.801965430017657E-06
RMS Density R 5.526225375796586E-09
Job Status I 1
Nuclear derivative order I 1
Thanks again for your help and for helping the community.
With very best regards,
Jean-Hubert
Dear Jean-Hubert,
This is one of those weird errors! The R-bond feature ‘draws’ the bonds between atoms in gaussview, so it makes sense that Avogadro is able to open it.
What if you open the log instead? if you need to do some post-processing then you can always load the fchk file upon the log file and get the electronic information from it (it might work!).
I hope this helps
Dear Joaquin,
I know it has been a while but I wanted to share my findings with you and the blog. As you said the Rbond error was one of this weird one. Even with the calculation successfully finishing, I had the bond issue. What I found is that even if GV can not open it the fchk file can be open with Avogadro. The solution I found was to extract the XYZ coordinates from Avogadro and restarting a single point energy calculation in G09. After checking up that this SP calculation runs smoothly I ran opt. This strategy seems to have solved my issue. It looks like in non-covalently bond system, Rbond issues are recurrent.
In any case thanks a lot for your help and for your blogs.
All the best,
JHO
Dear Jean-Hubert,
Thanks a lot for your feedback, do you mind if I use it for a future post? All credit would be paid of course and a link to your site or profile (or any other site you want) would be placed.
The Rbond error must be associated with the changes from the input to the standard orientations during optimizations. Maybe. I guess if we contact the Gaussian people they’d say this is a feature and not a bug.
Best regards
Respected SIr,
I am trying to find first hyperpolarisability using gaussain09 .I want to know if i can use TD-DFT level of theory to compute hyperpolarisability in gaussain09.I tried evalutating but it only evaluated polarisability . I used Polar CPHF=RdFreq , I gave frequency in hartrees as additional inputs but it didnt compute hyperpolariability .I used
6-311G(d) / CAM-b3lyp. Let me know if it is possible ?
Regards
Sarath
At least in principle it is possible. Are you getting any kind of error or just a value of zero?
Have a nice day
Dear Dr Barroso, I´ll try to get the optimisation of big molecule with 220 atoms using differents bases, however whatever base that I used the job end with following error:
Range of M.O.s used for correlation: 1 699
NBasis= 699 NAE= 426 NBE= 426 NFC= 0 NFV= 0
NROrb= 699 NOA= 426 NOB= 426 NVA= 273 NVB= 273
Differentiating once with respect to electric field.
with respect to dipole field.
Electric field/nuclear overlap derivatives assumed to be zero.
There are 3 degrees of freedom in the 1st order CPHF. IDoFFX=0.
3 vectors produced by pass 0 Test12= 3.88D-12 3.33D-08 XBig12= 2.71D+02 5.95D+00.
AX will form 3 AO Fock derivatives at one time.
Could you help me to resolve this problem? Thanks in advance.
Wilson.
Hello Wilson,
I don’t see any problem or error. If these are the last few lines of your output then probably your calculation is being stopped by the system for reasons other to the calculation. Perhaps you are reaching the limit of memory in your computer. If these are not the last lines of the log file then send me more information and maybe I can help you a bit better.
Have a nice day
Gaussian log file is not printing anything as calculations are running in the backgroung
Dears
I am doing QM/MM calculations and trying to optimize a Gaussian input file of about 35000 atoms. But output.log is not printing anything except coordinates even Gaussian calculations are running. Can anyone help me out?
Format of input file;
%chk=/home/SKD/work/gaussian/calculations/g17.chk
%mem=32GB
%nproc=16
#n oniom(hf/sto-3g) opt scf=xqc
Gaussian log file is not printing anything as calculations are running in the backgroung.. Available from: https://www.researchgate.net/post/Gaussian_log_file_is_not_printing_anything_as_calculations_are_running_in_the_backgroung [accessed May 3, 2017].
Hai Sir!!
I was trying to do a tran-cis isomerization scan with Gaussian 09 using CAM-B3LYP and cc-pvDZ. I have given the step size as 10 for 18 steps. In the 13th step, my job got ended and showed an error as follows
New curvilinear step failed, DQL= 6.16D+00 SP=-7.03D-03
Old curvilinear step not converged, using linear step
Error imposing constraints
The command line for dihedral was – D 5 10 29 31 S 18 10.00
Also, I wanted a N-H bond in my system to be frozen. So i gave the command – “B 13 21 F”
I have opened the log file and one of the hydrogens connected to the ethylene double bond is found to be broken and the structure is somewhat distorted (13th step).
So for rectification of the problem, adding the wild card as you explained in the blog is enough ??
ie for my case, adding the * 10 29 * wild card before the dihedral command line. Does this will do ???
Hope I explained my question properly…Waiting for you answer sir.
Thank You!!
Hola estoy ahora leyendo un poco sobre el tema de la fotosintesis y su relación con la cuántica, v una charla tuya en youtube, pero no se ve muy bien hay forma de acceder al ppt que usaste en la charla, te agradezco mucho desde ya saludos
Link youtube: https://www.youtube.com/watch?v=E_-6bhmySiI
Gracias por tu interés en nuestro trabajo, Margarita! Acabo de subir la presentación a Slideshare aunque tal vez se pierde un poco por las animaciones, sin embargo se pueden seguir ambas simultáneamente supongo.
Saludos y espero que te sirva el link abajo!
How can one calculate the electron affinity of a species from a HF calculation?
That is a nice question for it deals with some fundamentals that are often neglected.
Say this species has Ne electrons. In order to get the electron affinity with HF (and only with HF this is valid) you need to calculate the wavefunction for the Ne+1 system; according to Koopman’s theorem then the ionization potential of this Ne+1 species is equal to the energy of the HOMO, and it will be equivalent to minus the electron affinity of the Ne species.
I hope this helps
Hi Dr.
I want to ask something. Can we calculate charge transfer integral directly from Gaussian?
Thank you in advance for your kind help.
i want to know
how to calculate excited states using gaussian 03/ GW09
Hello Dr.
I am just learning gaussian . I tried doing rigid scan of ozone molecule varying both bond length from 1.0 to 1.4 and bong angle from 55.0 to 125.0 degree. I got single one energy in output file. I am unable to understand the output file. Am i doing right or not? hHre is my input and output file. Please suggest me some ideas . I want to plot PES of ozone
%nprocshared=5
%mem=6GB
%chk=0zone.chk
#p scan mp2/6-311+g(2d,p) nosymm geom=connectivity
Title Card Required
0 1
O
O 1 R1
O 2 R2 1 A1
R1 1.0
R2 1.0
A1 55.0
1 2 1.0 3 1.0
2
3
R1 1 2 1.0 S 5 0.1
R2 2 3 1.0 S 5 0.1
A1 1 2 3 55.0 S 5 15.0
output file==::
(Enter /opt/g16/l108.exe)
Scan completed.
Summary of the potential surface scan:
N SCF MP2
—- ———– ———–
1 -223.45064 -224.00773
—- ———– ———–
waiting for your response
Hello!
I think the problem is the numbers after the variables. Instead of writing R1 1 2 1.0 S 5 0.1 you should write only R1 1.0 S 5 0.1
Try it and let me know if it worked.
Hi, Thanks for the platform offered.
I want to know hot to find the range (cut off radius) of Gaussian basis function, say 6-31G(d,p)?
Thanks,
Sunil
*How to find the range (cut off radius) of Gaussian basis function, say 6-31G(d,p)?
Hello. Im glad to know this blog is helpful to you.
I’m not sure I understand your question. A basis function has an asymptotic behavior therefore it doesn’t require a cutoff radius. If you let me know more about what is it that you want to accomplish then I can offer you a better answer.
Have a nice day!
Thank you for the reply. I thought there must be finite range of the basis function beyond which it is zero. I want to find out at what distance, the overlap between two atoms will be zero.
Thank you again.
Sunil
Gaussian 03/ 09 excited states, cubegen, fixed geometry
i want to know how to calculate
excited states and their energies
2 calculate coordinates at fixed geometry. this geometry may not be the equlibrium one
3 calculate radial charge density and static molecular potential
primarily i want to know what should i write in route path etc
i am new to gaussian and hence not so familiar
thank u
hello sir,
i tried that one but it didnot affect any result. the output is as such.
Dear colleagues,
In step 7 of the optimization of a QM/MM ONIOM calculation 2 of the molecules of the high layer have come too close and the calculation has crashed. I obtain this message:
Small interatomic distances encountered:
2 1 0.00D+00
Atoms too close.
And when you see the molecules in Gaussview you can see that from step 6 to step 7 one molecule approaches another one too much.
What can I do?
I am using Gaussian09 with the high layer being a tetramer of my molecule calculated with DFT (wb97xd functional and 6-31G++(d,p) basis set) and the Low layer being a shell of the same molecules calculated with Molecular Mechanics (Dreiding)
You can use the geometry from step 6 and start the optimization from that point. That sometimes helps.
Have a nice day!
how to optimise geometry of a molecule at other than than its natural symmetry.
i want to know what should i write in route etc path
Hey Dr. Joaquin,
I’m studying silicium nanowires and I’m using abinit to optimize the geometry. I would like to know if you have worked with this program. If the answer is yes, do you know how to choose the number of processor that i can use?
Respected Dr. Joaquin.
hope you are doing good.
kindly guide me,How can I convert Debye-ang (polarizability), Debye-ang**2 (first hyperpolarizability) and Debye-Ang**3 (second hyperpolarizability) intto atomic unit?
Respected Sir ,
Can help me on tell me what i need to to calculate silicon nanowire band structure using abinit software..i have confuse ….which tutorial can help me? and what is the znucl number for silicon nanowire or is it same like the bulk silicon?
Hi everyone,
recently I stumbled upon problem: visualizing high level MOs from G09 ONIOM calculation. I’m PhD student working on huge complex combining ONIOM and PCM, with goal to calculate excited states. My job ended succesfully, I managed to extract linear spectra, but have troubles in creating .cube files for visualization of molecular orbitals. Cubegen is not working for any of my ONIOM calculations, and there appears error like this:
Could not find Alpha MO coefficients on formatted checkpoint file.
Error termination via Lnk1….
Segmentation fault
I have tried loading *log and *fchk file in jmol, gaussview, molden and avogadro. Only jmol managed to show me some orbitals, but they were all on LOW level, and my goal is to see orbitals from HIGH level, since QM part of the molecule is the most important for my analysis. So my question is: Did anybody managed to visualize orbitals from high level of their ONIOM/PCM calculation, and how? I hope somebody has time to send me any clue. Thank You in advance.
Kind regards,
Marty
Hi Marty,
I know it is very old question, but I am facing the same issue and unfortuantely I could not find any solution at moment, did you manage to visualize the orbitals in the end ?
Thanks,
Carmine
i want to run Co2 molecule in D2H point group instead of D infinity H using Gaussian 03. how to do that ?
Hi every one
I am facing one problem related to my DFT calculation. When i upload my input file having set to gaussian then it gives an error : Problem with the distance matrix. Error termination via Lnk1e in C:\G03W\l202. so, how i can remove it ??? I am working with Ruthenium dye.
#Optimized structure of Ionic liquid using Gaussian09#
Dear Sir,
I intend to simulate a protein of interest in the ionic liquid,1-Butyl-3- methylimidazolium chloride (BmimCl) in GROMACS. In order to generate the topology and coordinate files of the IL, I tried optimizing the structure through Gaussian09. Kindly clarify my doubts regarding the same.
1. Should the cation and anion structures be generated separately in vacuum? or should it be generated by using water as solvent?
2. If it is to be generated in vacuum, I guess Gaussian needs solvent descriptors (eps, epsinf and hydrogen bond acidity etc to be specified when using SCF=SMD and Solvent= Generic). In that case, how do I give these solvent descriptors separately for anion and cation?
I am a novice in Simulation and so, my questions may sound naive. It is your blog I turn to when I am completely perplexed and your comments really helped me understand the whole Molecular Dynamics world better.
Any information could really help. Thanks in advance for your time.
Regards,
Vidya
Dear Sir,
Can you please share the link for Gaussian 5 free download software.
Can it be download to windows?
I initially download the free software but its giving ” file location error”.
Many thanks,
Best Regards,
FYS
I think you mean GaussView 5, and unfortunately it is not free. I’m sorry I cannot help you this time.
I am doing PBC calculation using Gaussian 09. In the optimization calculation the following error is coming-
‘ Possible problem detected with PBC diagonalization:
FLenRc= 6.34D+00 SDif= 3.02D+01 STest= 1.92D+02 ThrSDi= 1.00D+01.
Alpha NIter= 39 Fermi level: -185.587155436
= 237.999999904307 NE= 238.000000000000 Err=-9.57D-08 Lim= 2.38D-08
Possibly not enough cells included in PBC.
Numerical problems in PBC.
Error termination via Lnk1e in /home/arindam/Gaussian/Gaussian/g09/l502.exe’
What does it mean and how to resolve it? Thank you.
Hi Arindam,
I am also facing same problem. Did you find any solution for that?
Dear Sir,
Could you please guide me when and where for we do “toprot calculations” and some points/ procedure to follow for these calculations.
Thanks.
Sir,
I just need to know how to generate a .wfn file from an optimised structure using gaussian 09
This may be helpful…
https://www.researchgate.net/post/How_to_generate_wfn_or_wfx_file_from_gaussian
Monu Joy
Use geom=check guess=(read,only) output=wfn in the route section. Do not forget to type the charge and multiplicity as well as a name for the requested wfn file.
Have a nice day
Hi
How can I calculate rotational component of velocity from MD simulation? I am using Lammps software, from where I can get x,y and z components. Thank you.
Hi Dr.
I want to know whether we can calculate charge transfer integral (t) directly from Gaussian output?
Thank you in advance for your kind help.
I want to calculate two photon absorption cross section of simple imidazo[1,2-a]pyridine. How we can calculate with gaussian 09 software?
As per the paper:
Chemical Physics Letters 374 (2003) 446–452
Calculations of two-photon absorption cross sections by means of density-functional theory
I’m not sure how to do it with Gaussian, do you have QChem available?
Hi, I want to know the Input keyword to ignore the convergence in single point energy calculations in GAUSSIAN for specific number of scf cycles.
Hello Dr. Joaquin barroso
I have a question on use mixture of solvents in Gaussian, Is possible to optimize a molecule in a mixed solvent (Acetonitrile-Water in rate of 3:1) using Gaussian 09W?
Can you please suggest me an input file of this issue?
Your pleased reply can help me significantly.
Thank you very much
Farshad shiri
farshadshiri@outlook.com
please reply me by email
Hello Farshad,
I’m afraid it is not possible to do so with Gaussian, and even when you can define your own solvent parametrizing it is quite challenging and would be a research paper on its own. I suggest you either run your calculations in acetonitrile (since it is the major component) or find out what the polarity of the mixture is and then select a solvent defined in G09w whose polarity resembles that of the mixture.
Have a nice day
Hi,
Correct me if I wrong. I guess there is a way by which this can be done but I am not sure of the accuracy and reliability of the results.
For implicit solvation in Gaussian, we need to define the dielectric constant and refractive index of the resultant binary solvent system. For ACN-H2O system, you can refer to these papers to get these values for the ration you have mentioned. 1) Org. Biomol. Chem., 2003,1, 575-580, 2) J. Chem. Eng. Data, 2007, 52 (3), pp 1103–1107 and 3) https://link.springer.com/chapter/10.1007/978-3-540-75291-2_359.
Hope this helps.
Regards
Elvis M.
In fact you are right, but the problem is that defining all those data, as you said, will not give you a reliable result. They should be benchmarked somehow.
Thanks for the references!
Dear Dr. Barroso,
first of all thank you very much for this blog! It is very appreciated.
Is there any way of running the new composite scheme PBE-2hc in Gaussian? I successfully run it in ORCA, but unfortunately for now I can run only G09 (rev E) in cluster…
Thank you!
Thanks a lot for your kind words.
For what I know (and by that I mean I know very little) it is not available in G09 and neither it is in G16. I guess you could define it yourself and plug it in if you have the source code. What are you trying to achieve with G09 now that you have it working in ORCA?
Have a nice day
I am doing something exceptionally simple in Gaussian 09 as an exercise for physics grad students trying to learn about molecules (which can scare them). Basically, I want to use the PES scan capability for simple diatomic molecules to look at 1D potentials and shifts from neutral to anionic to cationic states. I am using a z-matrix formalation for the diatomic and listing my diatomic bond length as a variable with the required “s” scan parameters (at least as I understand the gaussian manual).
h2 calculations for phys7810
0 1
h1
h2 1 rhh
rhh .7 s 50 0.05
The output reads the variable in as a scan variable, but exits promptly (see below)
—————————-
h2 calculations for phys7810
—————————-
Symbolic Z-matrix:
Charge = 0 Multiplicity = 1
h1
h2 1 rhh
Variables:
rhh 0.7 Scan 50 0.05
NAtoms= 2 NQM= 2 NQMF= 0 NMic= 0 NMicF= 0 NTot= 2.
Isotopes and Nuclear Properties:
(Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM)
in nuclear magnetons)
Atom 1 2
IAtWgt= 1 1
AtmWgt= 1.0078250 1.0078250
NucSpn= 1 1
AtZEff= 0.0000000 0.0000000
NQMom= 0.0000000 0.0000000
NMagM= 2.7928460 2.7928460
Leave Link 101 at Sat Oct 14 16:39:13 2017, MaxMem= 26214400 cpu: 0.0
(Enter /usr/local/gaussian/g09/l114.exe)
NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-
NUMERICAL EIGENVECTOR FOLLOWING MINIMUM SEARCH
INITIALIZATION PASS
CALL FROM INITNF: BAD IC ENTRY FOR VARIABLE 1
Error termination via Lnk1e in /usr/local/gaussian/g09/l114.exe at Sat Oct 14 16:39:13 2017.
Job cpu time: 0 days 0 hours 0 minutes 0.1 seconds.
File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1
What am I doing wrong? There couldn’t be a simpler application in Gaussian 09 than calculating a PES for H2!!!
I’ve noticed that the scan facility in Gaussian has undergone a lot of syntax changes in different versions. Is my syntax just wrong?
Thanks!
David
Dear David, Sorry for such a late response. Have you solved this issue yet? If anything I would object the variable rhh .7 as it should read rhh 0.7. Also, why labeling h1 and h2? there is no need for that and you could only leave the atomic symbols.
I hope this helps.
Dear Dr. Barroso, I would like your opinion. I’m simulating NO3- and ClO3- as oxidizing agents in aqueous medium, to start I did opt-freq in gas phase, and then in water (using opt-freq with SCRF=PCM) when I check results I can note a large difference between SCF energy and enthalpies/free energy in gas phase, then when I check the solvatation energy the difference is appreciable . E.g.: for ClO3-: ΔE=-28 / ΔH=-176 / ΔG=-177 (kcal/mol) and for NO3-: ΔE=-63 / ΔH=-126 / ΔG=-126 (kcal/mol).
In my opinion, the charge is stabilized in the aqueous medium and by the dipole interactions that are formed around the molecule, but when I check Mulliken charges there is no appreciable difference between the phases. My question is, have you seen a difference like that before between E and H or G? Do you think there is an error in my calculates?
Cheers!
Camila
Hello everyone,
I am trying to calculate frequency for large molecule (212 atoms) after that I made optimization of the structure, of course, using DFT. I know with this kind of big molecules, It´s better to use partial hessian vibrational analysis, and I have been using the following procedure after the matriz of the molecule:
$molecule
Matriz
$end
$rem
MEM_TOtal 5000
BASIS 6-31G*
JOB_TYPE freq
METHOD b3lyp
PHESS TRUE
N_SOL 9
$end
$alist
1
2
3
4
5
6
22
23
24
$end
But when I further try to run frequency calculation using the optimized geometry , I get this as follows and stop the calculation:
Calculating MO derivatives via CPSCF
CPSCF will be done in 4 segments to save memory.
Partial Hessian Calculation
Hessian Limited to Following Atoms
I At.No. X Y Z
1 6 -3.26177 -10.02592 -0.45296
2 6 -3.28487 -8.66717 -0.77821
3 6 -2.68582 -7.74134 0.08067
4 6 -2.06855 -8.15281 1.26980
5 6 -2.65385 -10.45247 0.74180
6 6 -2.04677 -9.51280 1.59493
7 6 -4.55831 -10.66426 -2.36468
8 6 -1.59645 -12.57124 0.72946
9 6 -0.93904 -9.15208 3.69200
Cold you help me to understand What´s the problem with this job? Thanks, in advance.
Wilson.
1) Is the bonding description of a molecular system obtained via NBO method always reliable?
2) Is it necessary to have special care when analyzing NBO results?
1) most of the times. There is a line saying which percentage of the electrons are described by a Lewis structure. If that percentage is above 99 then you’re good to go.
2) Yes. always.
Hello Sir,
I am doing a optimization of a Perovskite Structure using Gaussian.
After running for 5 hrs I get an error ” NB too large for integers in this machine ”
%mem =150 MW
Please let me know how to resolve this error.
Dear Dr. Barroso,
I would like to know how to prepare an input file using M06-L correlation functional and two different basis sets (6-311 and 3-21) for a system of about 120 atoms in G09,
I would be so grateful if you could provide me a sample input file,
Thank you in advance for your reply,
Safa.
Estimated Dr. Barroso,
I have a problem optimizing a ts of water as a leaving group in an oxonium to form a carbocation. I optimized the ts first with am1, and then HF/6-31g* and both worked out great, but when I try to optimize it with b3lyp/6-31g* the structure keeps converging to the one related to the water rotating.
What do you suggest?
Thanks for your time
Hello Marie,
I would suggest using a different functional such as PBE or related just to check if the level of theory is working adequately, which most would argue is hardly ever the case with B3LYP. Are you trying to use QSTn or just a regular scan? Try using QST3 and use the previously optimized geometries of all three steps (you can even get them by optimizing those that you already optimized at lower levels of theory).
I hope this helps.
Hello,
Can anyone tell me how to plot electron difference contour maps using multiwfn in red and blue colour? Basically in two colours which represents the areas of increase and decrease in electron density.
#beginner #materialsstudio
Can you please guide me on how to draw a 16-carbon fatty acid in materials studio and test its behaviour in a 111 plane of a simple cubic crystal system? Thank you!
I’m using Gaussian 09. I want to calculate proton affinity, gas phase basicity of aromatic compounds like hydroquinone (C6H6O2).
I’m also interested in calculation entropy ∆S of a system like reaction between hydroquinone and methanol to produce protonated hydroquinone. Please help me in details, because I’m very new in theoretical chemistry field.
You should run a thermochemistry calculation with the keyword FREQ in your input.
I hope this helps.
#Gaussian error #ADMP-MD Simulation
Hi Sir
I have been studying DFT and quintessentially involved in hydrogen storage. I am testing ADMP-MD simulation for C,B,Al (up to 20 atoms) with 10 hydrogen molecule.I have a cluster of 4 Nodes (64 processor). But i am unable to run ADMP even for 100 fs as the job get terminated running for some time(20 cycle) giving a error message “GEWDen is stupid about Cholesky+NBsUse<NBasis., failed to open excel file" .Is there any way or efficient keywords to run ADMP for the described molecule for at least 1000 fs in my cluster.
I have used the keywords
B3LYP/6-311++G(d,p) ADMP=(MaxPoints=300,FullSCF) Geom=Crowd Integral=Ultrafine Iop(1/82=300)
The job get terminated after 20 cycle.Is there any efficient keywords for this.
Plz give me a solution
Thnk u
#Gaussian #NBO_Analysis
Please find my doubt here
https://docs.google.com/document/d/1eP-Nm-lMmAk_TTnt0m6LfUbvnfWgbsr3twiEtdvIHng/edit?usp=sharing
You have two lone pairs on each oxygen atom. Namely, for the first compound, NBOs 67 and 68. They are labeled as
67. LP ( 1) O 7
and
68. LP ( 2) O 7
The number in parenthesis is a label for each of the lone pairs; so one of them has a stronger delocalization energy to the 605 BD* orbital than the other.
I hope this helps
Joaquin
I found your comments on generating Gaussian basis sets for pesky atoms like Iodine very helpful. It makes me suspect you would understand the answers to some long standing questions that have been in my mind.
Q1) I am interested in how charges move around in CH2I as a function of the vibrational excitation of the symmetric and asymmetric CH stretches. I run the calculation in C2v symmetry to find the equilibrium (planar) geometry and the vibrational normal modes (which I do in high precision with the keyword hpmodes). This generates x,y,z displacements of each atom to 5 sig figs, which I can then easily use to find the geometry of a vibrationally excited radical with say Q = 0.1. Why shouldn’t the sum of mass weighted displacements of the atoms for any vibrational mode add up to zero? (I am using the masses stated in the program, good to 8 digits)
Q2) If my reference geometry is such that the z axis is along the CI bond and the xz plane contains the HCH atoms, why is it that my normal mode displacements are sometimes not exactly symmetric (to 5 digits at least)?
Thanks!
David
Dear David,
Thanks for your kind comments and once again please forgive the lateness of my other response.
About Q1, I think you should use reduced masses instead; I’m sure there is a reason for that hidden in classical mechanics.
Q2 is trickier. They should be entirely symmetric, are you constraining the symmetry with symm=tight or symm=follow? that might constrain the C2v symmetry of your molecule. Please let me know if you find a solution to this issue.
Joaquin-
Thanks for taking the time to respond. The Gaussian manual is not so transparent at times. At times I’m convinced it is not even bug-free code (horrors!) and that it takes people raising these issues to improve the software.
Regarding Q1, I don’t think reduced masses are the answer. Any true normal mode should not move the center of mass at all, otherwise it would transform, at least in part, as a translation rather than a vibration. Indeed, when they transform out the 6 low frequency modes (corresponding to translation and rotation), that is presumably exactly what they are doing. So why would they leave a small (but not < 10^-5 small) piece of translational motion in with the vibrations, if the calculations are good to 5 digits?
When I sum the mass weighted displacements (using the exact isotopic masses that Gaussian is using), I get a vector with components very close to zero, but not exactly (perhaps 10^-3 or 10^-4 amu Angstroms or less). So I know I am close to having the correct result – but I am confused as to why a normal mode analysis that gives 5 sig figs accuracy wouldn't yield a zero mass weighted displacement vector to at least that many sig figs. I'd be happy enough if the terms were .00001 or ,00002 amu Angstroms, but typical numbers with .00xx (x not equal 0) amu Angstroms seem unreasonable.
Regarding Q2, I am running the calculation in NoSymm to maintain the exact same reference geometry (so I can rather accurately subtract the equilibrium and vibrationally shifted wavefunction densities). But I do request very tight optimization
#p b3lyp/gen gfinput IOP(6/7=3) FormCheck Opt(z-matrix,verytight,maxcycles = 200) pop = nbo freq=(readiso,hpmodes,anharmonic) NoSymm
Does this jiggle loose some other thoughts?
Thanks again
David
Hello Sir.
#CompChem.
How will confirm (Excited State Intra-molecular Proton Transfer) ESIPT process with the help of DFT?
Hello,
Can you let me know resources/tutorials on how to setup a 2D PBC calculation in Gaussian? I’m interested particularly in studying adsorption of organic molecules on silver and other metal/semi-metal surfaces.
Thanks!
dear
From simulation data, I have a system of K+(NH3)2(H20)4 with unsymmetrical octahedron shape. Two of NH3 are adjacent. I used NBO to investigate the ion-ligand interaction type. The orientation of O and N of ligands are directly faced to K ion. I found that the Wiberg bond index indicating for a non covalent interaction. But, I also found that the highest stabilization energy of donor acceptor come from CR of ligand (O and N) to LP* of K ion. In my opinion, the highest stabilization energy should come from LP of ligand (O and N) to LP* of K ion. I have no idea how to explain this situation. Do you have any suggestion regarding to the system?
Thanks
Dear Joaquin,
I am trying to calculate absorption spectrum of an excited state.
Is there a method to calculate the absorbing wavelength of a molecule on an excited state?
In other words, I want to know absorption spectrum of molecule on S1 or T1, not S0 (ground state).
Which keyword or method can be applied ?
Thanks.
Dear Joaquin, I am having difficulty in calculating energy barrier of racemization. How you please suggest me how to calculate it? I am using gaussian 16. And i also have another question. I want to use Avogadro instead of Gaussian view. will there be any difference?
Hi Joaquin,
I am trying to calculate the excited state potential energy surface. My input file contains the root section as follows.
==================
%mem=4GB
%chk=pxfcntd22.chk
#p CAM-b3lyp/6-31g(d) opt=modredundant td=(nstates=30, singlets) nosymm
pxfcntd22
–
–
–
–
–
D 4 5 32 31 F
D 4 5 32 31 S 6 10.0
===================
But the job is terminating within few hours.
It shows the error messages
“Excited state symmetry could not be determined.”
and
“Segmentation fault (core dumped)” at the end.
Can you please suggest what could be the problem and how can i solve it.
Eagerly waiting for your reply.
Thank You.
Regards,
Tessy
Hello Tessy
Please copy and paste the full lower section of your output, specially the lines after “Excited state symmetry…”; that line is not a problem, it merely states there is no symmetry to be found (probably), although it is weird since you asked for nosymm. Send me more details.
Hello Sir, I am doing polarization calculation . I am using the key word polar=gamma in gaussian 16, in that we need to give at what frequencies we need to find frequency dependent polarizabilities. I have doubt in giving that frequency. Should we find the absorption frequency of that molecule using TD DFT and give that one sir? Also I want to understand how can we use it to find non linear effects. If possible can you please give some notes on them?
Take a look at:
Have a nice day
Dear Sir, Im Habeeba,Research Scholar. In my research lab gaussian 03 and 09 softwares are available.Is it possible to optimize CZTS molecules using Gaussian 09 software?.Because CZTS contains large number of molecules. Or which type of gaussian version is very easy to run these molecules Please clarify me sir, Thank you.
It all depends on the level of theory you want to use. Please make a better description of your intentions so I can give you a better answer.
Dear prof. Joaquin, I had been working with Q_CHEM in order to calculate Frequencies of a molecule using:
$rem
BASIS = 6-31G**
GUI = 2
JOB_TYPE = Frequency
METHOD = B3LYP
SCF_CONVERGENCE = 8
MEM_TOTAL = 12000
MEM_STATIC = 2000
$end
However, this work ending with the following text:
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 22395 RUNNING AT n003
= EXIT CODE: 9
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
remove work dirs /scratch/qchem22382.0 — /scratch/qchem22382.0
rm -rf /scratch/qchem22382.0
rm -rf /scratch/qchem22382
And I don’t know what part of the job is getting problem. Could you help with that? Thanks in advance.
Wilson.
Hi Wilson,
I’m still not too familiar with QChem, unfortunately, but it would seem that you need to take a look at the scratch directory despite the message of doing otherwise. I’m sorry I cannot give you a better answer.
have a nice day
Dear prof. Joaquin! If a species has one calculated frequency very close to 0 cm 1 what does that tell you about the (calculated) potential energy surface in that region? in my case I have optimized my transition state and I made an IRC, then I reached the minimum and optimized the same but in the case of the reactants I obtained a low negative frequency. If possible can you please give some notes on them?
Thank You.
Regards,
Mario
You want your negative frequencies to be large enough as to not being considered noise, so if your negative frequency (for validating the finding of a TS) is -5cm⁻¹ then it is probably just noise. My rule of thumb is having them lower than -50 but some people go as low as -100 cm⁻¹.
I hope this helps!
Dear Friends,
I will be really thankful if you could find a solution to my problem with Gaussian calculation of transition TS using QST2 method each time I get error message saying ‘Old curvilinear step not converged, using linear step’ that causes the program to stop.
Thanks
You probably need to re-define your input geometry or your TS guess.
Dear professor Joaquin,
I have known your blog and become a follower for 6 months, I find it is really helpful for me, especially in TS optimization. Thank you so much for your work. I am trying to find TS state for a reaction, after going through some steps I have a geometry with several imaginary frequencies, in which I noticed two highest values, the first one is -110 (cm-1) but it is not the mode I am concerned, the second is -73 (cm-1) that is my interest. If possible could you give me some suggestions if I want to follow the second mode? I also tried to use QST2 and QST3, but they do not work in my case.
Thank you.
Dear Dr. Joaquin,
I am trying to find a transtion state for the reaction between aminoguanidine and a acetylenedicarboxylate derivative. After several trials, I found a TS with an imaginary frequency (-704.15) using QST2. My supervisor thinks that it is not the TS we search for. Now I am confused and I am not sure whether it is satisfactory. Is it possible to send you the log file? I will be very happy if you make any suggestion about it?
Thank you in advance.
Dear Sir,
I am trying to learn the potential energy surface (PES) scan of the small donor molecule/PCBM complex. So, I was making an attempt to reproduce the result of Figure S1 1(a) of the Y. Cui et al. paper (d.o.i – 10.1021/acs.jpcc.6b09927). I have introduced two dummy atoms, one is on the center of the C-C bond of the DPP ring and another on the center of the hexagonal ring of PCBM. Next, I have constructed input with keyword
#p opt=modredundant M062X/6-31G(d,p) scf=maxcycle=3000
after inserting the cartesian coordinates of SM/ Molecule, I have fixed the distance between the two said dummy (atom no -172 and 173 respectively) atoms by using keyword-
B 172 173 S 10 -0.100000
But, I have failed to reproduce the result of the said paper. I have performed relaxed PES scan. will I have to perform rigid PES scan using Z-matrix? As the SM/PCBM complex structure is very big, so how to perform the scan for this type of donor-Acceptor complex?
Thanking you,
Labanya
Hi There,
Thank you SO MUCH! I was actually holding my breath as I followed these directions. It worked beautifully!
I am having a collection with 7 Columns and around 1000 rows. In that 1000 rows, some rows are duplicate.
How can I delete those duplicate rows from collection?
Anyways great write up, your efforts are much appreciated.
Thank you,
Shasha
Dear Sir, i am trying to find intermolecular hydrogen bond interactions in dimer structure of an organic compound for example in methanol dimers. what do i need to do for computing
or optimizing these structures, and how i can do it?
i will be really happy if you can inform me for this subject.
Thanks you very much in advance
Dear Professor, explain to me how to get the Fukui functions from the Gaussian output. Thank you very much.
Please check this tutorial in this same blog. You cannot get the numbers from the Gaussian output but you can use those output files to calculate them yourself very easily with MS Excel
Click on the following link
Is there a way to set frequency range when calculating a VCD/IR spectra? I am interested in 1100 to 1600 cm-1 range? Thanks
Dear professor Joaquin,
I am studying in the first year for PhD study at Charles University in Prague, I am using Gaussian 09 for all my calculations. I have problem when calculating NBO presented as follow:
United Atom Topological Model (UA0 parameters set).
UA0: Hydrogen 24 has 2 bonds. Keep it explicit at all point on the
UA0: potential energy surface to get meaningful results.
Error termination via Lnk1e in /opt/QChem/g09/l301.exe at Thu Jun 7 13:27:02 2018.
I tried to use the keyword SPHEREOnH=24, unfortunately, it does not work.
I hope you could give me some suggestion to solve this problem. Thank you very much
Hello Nguyen,
This problem is not related to NBO but to the use of SCRF. I imagine you are using SCRF=Read to include that sphereonh keyword. Make all atoms explicit with SCRF=Read and then in the reading list at the bottom of the file include radii=bondi or radii=pauling. Take a look at https://joaquinbarroso.com/2009/09/07/pcmg03/
Dear Dr. Joaquin,
I am doing some broken symmetry calculations using Gaussian 09. For that when I am trying to guess fragments so that I am getting following error “Bad data into FinFrg” although my input files are correct in my knowledge. Please help me to solve this. I will be grateful to you. Waiting for your kind response.
Hi, could you please provide more details on your calculations as well as a larger section of the ending of your log file? Thanks
I’m getting the exact same error with my fragment guess calculations. Any advice?
I found the solution and posted it here: https://www.researchgate.net/post/Why_does_a_gaussian_error_Bad_data_into_FinFrg_in_DFT_optimization_for_radical_system_appear
input section
%mem=32GB
%nproc=14
%chk=job-3-mult-10-N-at-C60-trimer
#P UB3LYP/6-311G* EmpiricalDispersion=GD2 guess=(fragment=4,only)
fragment guess of opt of N-at-C60-trimer AFC with dispersion
0,4 0,-4 0,4 0,4 0,1
N(Fragment=1) 0.,0.,0.
N(Fragment=2) 0.,0.,-8.8162680081
N(Fragment=3) 0.,0.,8.8162680081
C(Fragment=4) -3.4926757003,-0.6952391166,0.
C(Fragment=4) -3.0405756329,-1.4224818711,-1.1692102362
C(Fragment=4) -2.3138483855,-2.5833561795,-0.7236974256
C(Fragment=4) -2.3138483855,-2.5833561795,0.7236974256
;
;
;
;
;
;
;
;
;;
;
End section of *.log file
Total kinetic energy from orbitals= 6.885288062630D+03
Leave Link 601 at Thu Jun 14 15:48:00 2018, MaxMem= 536870912 cpu: 230.4
(Enter /home/RAMACHANDRAN/g09/l122.exe)
CPIOFr: IOpCl= 1 IRwI=-1 IRwCP= 731 ICalc= 4 LCPTot= 16455249 Len1MO= 32580071 IndFrg= 179355604
CPIOFr: IOpCl= 1 IRwI= 2 IRwCP= 731 ICalc= 0 LCPTot= 16455249 Len1MO= 32580071 IndFrg= 49035320
CPIOFr: IOpCl= 1 IRwI= 1 IRwCP= 731 ICalc= 0 LCPTot= 16455249 Len1MO= 32580071 IndFrg= 49035320
CPIOFr: IOpCl= 1 IRwI= 2 IRwCP= 731 ICalc= -1 LCPTot= 16455249 Len1MO= 32580071 IndFrg= 16455249
CPIOFr: IOpCl= 1 IRwI= 2 IRwCP= 731 ICalc= 0 LCPTot= 16455249 Len1MO= 32580071 IndFrg= 49035320
FinFrg: NACore= 183 NAVal2= 363 NAVal1= 3 NBCore= 183 NBVal2= 363 NBVal1= 6
NA= 549 NB= 552 NAE= 552 NBE= 549
Bad data into FinFrg.
Error termination via Lnk1e in /home/RAMACHANDRAN/g09/l122.exe at Thu Jun 14 15:48:02 2018.
How to calculate Frank Condon integral using Gaussian for anions/ cations say LiH+/ LiH- ? a step by step explanation would be aappreciated
# How to calculate Frank Condon integral using Gaussian for anions/ cations say LiH+/ LiH- ? a step by step explanation would be aappreciated
I optimized the geometry of a ligand using Gaussview 5, DFT. the final file was a log. file format. I saved the log file. Now I want to see the intermediate geometrics of the ligand, as well. What should I do?
You should open the log file with GaussView and tick the box “load intermediate geometries” in the open dialog window.
Hi, I am working TDDFT with various XC functionals with varying Hartree-Fock exchange (exact exchange). Can someone please tell me if there is any
functional with HFX between 20 and 40 and 60 and 100. For. e.g. M062X has 54 % of HFX, I want a functional to work with, which has HFX between 54 and 100.
Hi, there is an M06 version called M06HF or M06-HF which includes 100% of HFX. I’m not aware of another with such a high percentage of HFX.
I hope this helps
Hi
I was doing a calculation for organometallic complex but it terminated suddenly showing the comment that
NSgBfM= 533 533 538 539 539 MxSgAt= 67 MxSgA2= 67.
Leave Link 302 at Thu Jun 21 21:02:59 2018, MaxMem= 1073741824 cpu: 18.0
Returned from execl, istat=-1, errno=5!
Returned from execl!
could you please tell me how I can sort out this problem
Hi, this is just the outing message from Gaussian, it doesn’t say what the error is. Please copy a few more lines before these so I can give you an answer.
Hola, buenas tardes.
Estoy deseando hacer cálculos de Fe con los electrones distribuidos de diferentes formas en los orbitales. Por ejemplo la configuración de Fe es Fe:3d64s2, quisiera obtener la energía de Fe:3d8. Según entiendo su puede hacer con Permute o Alter del keyword Guess.
Espero me pueda ayudar.
Hola Juan Luis,
No estoy seguro que ninguna de las dos opciones pueda lograr lo que quieres, en cualquier caso, la opción guess controla la función de onda de prueba, es decir, la función de onda inicial de donde partirá el SCF con lo que buscará la configuración de mínima energía. Tal vez con QChem se pueda hacer algo así.
Saludos
Hi,
I am using ONIOM the tackle something big but it still takes ages (months…) I have the feeling that the high-level shell does not need as many iterations as the low-level. The coordinates of the high-level structure barely change from step to step while the low-level structure undergoes obvious changes. Is there a way to tell Gaussian to calculate the high-level only every Xth time? And what would be a reasonable value for X to start with?
Thank you for your help!
Regards,
Simon
Hi,
Unfortunately that is not possible with any version of Gaussian, but maybe you can perform two different optimizations using the Opt=ReadOpt keyword (search for partial optimizations within this blog) and thus launch a first partial optimization of the HL structure (freezing the rest) and then optimize de LL structure with the HL section frozen.
I’ve never tried this before but it might do the trick. Whatever the outcome, please let me know.
I hope it helps!
Thank you for your answer. I will give it a go.
Hello Dr. joaquin barroso
I am doing open shell calculation for metal system using Gaussian 09 software.
I could see in the output, it has the MOs like this: Alpha occ. Eigenvalues and
Beta occ. eigenvalues. For this case, which value I have to take for HOMO, LOMO
and how to define the HOMO-LUMO gap of this system?
Looking forward to hearing from you.
Hi, I’m actually writing a post on this issue. HOMO-LUMO gap is kind of meaningless in an open shell calculation. Depending on what you want to learn, you can take the gap between the closest occupied-empty orbitals of the same spin symmetry (i.e. no alpha-beta but rather the alpha-alpha or beta-beta whichever is smaller). However, if you are into calculating transition then you need to go into TDDFT or at least some ZINDO depending the size of your molecule. I hope this helps
Dear Dr. Joaquin barroso
I am optimising Fe3O4 small cluster using Gaussian09. Can you please tell me what change and multiplicity I should consider get the correct base state ?
Thanks
Sada
CConnectionGFCHK::ReadFile()
Cannot find file
This is the error message while opening the .chk files. This started to happen just recently and the same method used to work previously. Any solution?
Thanks
Dear Dr. Joaquin barroso
I often use opt ub3lyp / 6-31g (d) to calculate the triplet energy of a molecule. I have calculated and derived several times.
However, when I did this calculation and read the chk file into gaussview, I got the message “CConnectionGFCHK :: ReadFile () Can not file file”.
There was no difference from previous calculations. Can not be converted to fchk file. How should I solve it?
Thanks
Seokhoon
#PES USING gAUSSIAN
Sir
I am using Gaussian to plot PES for ground and excited states of diatomic molecule CO carbon monoxide. i observed a very peculiar situation and unable to understand
1
i run USING THE 2 COMMANDs
# opt td(states=6) b3lyp/6-311G* and # opt=(modredundant) td(states=6) b3lyp/6-311G* test
job 1 results in optimised output of 1st excited state geometry, energy
when i run
opt=(modredundant) td(states=6) b3lyp/6-311G* test scanning over large points now my minimum energy corresponds to a different geometry (other than obtained from above)
my two commands are doing geometry optimisation. hence i feel both approaches should give the same value of minimum energy at same distance as i am using same coordinates in both. which is not the case.
summarising
(A) # opt=modredundant td=(nstates=6, root=1) b3lyp/6-311G* (B) # opt td=(nstates=6) b3lyp/6-311G*
Energy SCF -113.322616303 -113.273146359
1st excited state energy (optimised) -113.04978 -113.049957180
geometry 1.24288 angs 1.35695223
excitation energy 7.42 ev 6.0733 eV
how can we explain this variation
2 how can i perform the correct scan so that i get minimum energy at 1.356 angs
note the optimised GS is at 1.1269 angs
pl help
regards
Hai,
How to generate the excited state potential energy surface diagram? I’m using gaussian (g09) for calculating ground and excited state potential energy surface diagrams. I have generated the ground state potential energy surface diagram using this root line and the input is here,
#p b3lyp/6-31g(d) opt=modredundant scrf=(pcm,solvent=acetonitrile) freq=noraman”
0 1
6 -0.975197597 0.704827932 -1.821832072
6 -1.817017083 0.016206245 -0.944190618
6 -1.292695393 -0.680207007 0.163655172
D 4 5 32 31 F
D 4 5 32 31 S 12 10.0
But whenever doing the excited state calculation, with the root line,
#p opt=modredundant td=(nstates=3, root=1) b3lyp/6-31g(d) scrf=(pcm,solvent=acetonitrile) nosymm “, i’m not getting the complete scan graph. The abstract of the job is as follows,
SCF Done: E(RB3LYP) = -1263.74976846 A.U. after 9 cycles
Total Energy, E(TD-HF/TD-KS) = -1263.66641948 .
what could be the reason for this incomplete scanning?..initially my jobs were getting terminated with an error message like segmentation fault, core dumped. But now i’m not facing that issues. Jobs are running but it is incomplete. Can you please suggest me a solution?
Hello Dr. Barroso,
I am currently trying to complete NBO calculations on Gaussian 16, however all my calculations end without normal termination and without any error.
The last line in the log file always contains “Symmetry”
I tried increasing the memory allocation, reducing the basis set size, even testing smaller molecules.
A clipped sample of my input file:
%mem=48000MB
%nproc=32
# rhf/3-21g POP=NBO
test
0 1
C -1.5461810 1.0001760 0.9999880
“etc”
$nbo bndidx $end
Thank you very much!
Try changing NBO for NBORead. Don’t forget to leave a blank line at the end of the input file. I hope this helps but if it doesn’t let me know
Unfortunately the calculation still halts at “Symmetry”
Please post the last 30 or 40 lines of your output so I can understand better what is going on.
The calculation ends after ~2-3 minutes
Hello, Dr Barroso, I was wondering how to make an input file that contains both Gen keyword and multi step jobs. I was calculating emission spectra the way provided in http://gaussian.com/scrf/.
Please help me.
uploading the input.
%nprocshared=8
%mem=24GB
%oldchk=step-2.chk
%chk=step-3.chk
# m062x/Gen scrf=(iefpcm,solvent=acetonitrile,read) Geom=check Guess=read Pseudo=Read
Step 3.1- State specfic non-eq solvation by saving the solvent reaction field from the ground state in M06-2x
0 1
C H O Cl 0
6-31+G(d)
****
I 0
Lanl2dz
****
I 0
Lanl2dz
Noneq=write
–link1–
%chk=step-3.chk
%nprocshared=8
%mem=24GB
# m062x/Gen td(Nstates=15,root=1) scrf=(iefpcm,solvent=acetonitrile,ExternalIteration,Read) Geom=check Guess=read Pseudo=Read
Step 3.2- read non-eq solvation from ground state and compute energy of the first excited state with state-specific method
0 1
C H O Cl 0
6-31+G(d)
****
I 0
Lanl2dz
****
I 0
Lanl2dz
Noneq=read
What could be modified?
It looks fine to me, so having a copy of your error message would help me to know what is going on. Perhaps you should remove the guess=read and pseudo=read keywords from your second calculatoin if you are leaving the gen keyword anyway.
I hope this helps-
what the solution for this question when in thermal equilibrium at t=300k the ratio of the level population N2/N1 for some particular pair of levels by 1/e . calculate the frequency for this transtion . in what region of e.m spectrum does thus frequency fall
Dear Joaquin, I am trying to find BDE values and for that I have to complete the enthalpy formula Total Enthalpy= E0 + ZPE+ DHtrans + DHrot + DHvib + RT
Based on research I have a basic idea about how can I obtain these values. But I still have doubts regarding the output informations given by GAMESS.
First of all I used the keyword RUNTYP=HESSIAN and have obtained the output bellow. Can you help me to find the appropriate values in the output? I do not know which unit to use either.
Thank you very much.
—————–
ENERGY COMPONENTS
—————–
WAVEFUNCTION NORMALIZATION = 1.0000000000
ONE ELECTRON ENERGY = -3112.3562800292
TWO ELECTRON ENERGY = 1302.8610096182
NUCLEAR REPULSION ENERGY = 1043.5884666515
——————
TOTAL ENERGY = -765.9068037595
ELECTRON-ELECTRON POTENTIAL ENERGY = 1302.8610096182
NUCLEUS-ELECTRON POTENTIAL ENERGY = -3872.3550425693
NUCLEUS-NUCLEUS POTENTIAL ENERGY = 1043.5884666515
——————
TOTAL POTENTIAL ENERGY = -1525.9055662995
TOTAL KINETIC ENERGY = 759.9987625400
VIRIAL RATIO (V/T) = 2.0077737511
——————————-
THERMOCHEMISTRY AT T= 298.15 K
——————————-
USING IDEAL GAS, RIGID ROTOR, HARMONIC NORMAL MODE APPROXIMATIONS.
P= 1.01325E+05 PASCAL.
ALL FREQUENCIES ARE SCALED BY 1.00000
THE MOMENTS OF INERTIA ARE (IN AMU*BOHR**2)
1320.99780 11616.11222 12363.77065
THE ROTATIONAL SYMMETRY NUMBER IS 1.0
THE ROTATIONAL CONSTANTS ARE (IN GHZ)
1.36494 0.15522 0.14584
7 IMAGINARY FREQUENCY VIBRATION(S) IS(ARE) EXCLUDED
FROM THE FOLLOWING THERMOCHEMICAL ANALYSIS.
14 – 87 VIBRATIONAL MODES ARE USED IN THERMOCHEMISTRY.
THE HARMONIC ZERO POINT ENERGY IS (SCALED BY 1.000)
0.227292 HARTREE/MOLECULE 49884.884527 CM**-1/MOLECULE
142.628185 KCAL/MOL 596.756327 KJ/MOL
Q LN Q
ELEC. 1.00000E+00 0.000000
TRANS. 1.35388E+08 18.723656
ROT. 4.93058E+06 15.410968
VIB. 2.10041E+02 5.347301
TOT. 1.40211E+17 39.481925
E H G CV CP S
KJ/MOL KJ/MOL KJ/MOL J/MOL-K J/MOL-K J/MOL-K
ELEC. 0.000 0.000 -0.000 0.000 0.000 0.000
TRANS. 3.718 6.197 -46.415 12.472 20.786 176.462
ROT. 3.718 3.718 -38.203 12.472 12.472 140.605
VIB. 618.409 618.409 583.501 173.279 173.279 117.085
TOTAL 625.846 628.325 498.883 198.222 206.536 434.151
VIB. THERMAL CORRECTION E(T)-E(0) = H(T)-H(0) = 21653.109 J/MOL
E H G CV CP S
KCAL/MOL KCAL/MOL KCAL/MOL CAL/MOL-K CAL/MOL-K CAL/MOL-K
ELEC. 0.000 0.000 -0.000 0.000 0.000 0.000
TRANS. 0.889 1.481 -11.093 2.981 4.968 42.175
ROT. 0.889 0.889 -9.131 2.981 2.981 33.605
VIB. 147.803 147.803 139.460 41.415 41.415 27.984
TOTAL 149.581 150.173 119.236 47.376 49.363 103.765
VIB. THERMAL CORRECTION E(T)-E(0) = H(T)-H(0) = 5175.217 CAL/MOL
Dear Anne,
That right there is one of the reasons why I don’t quite like to work with Gamess, their output isn’t as straightforward to me as that of other programs.
Anyway, most of what you need to look for you can find it at the section below the THERMOCHEMISTRY flag.
The terms of your equation can be found as follows:
E0 is the TOTAL ENERGY (in your case -765.90 au)
THE HARMONIC ZERO POINT ENERGY is your ZPE (0.227 Ha; 142.63 kcal/mol or 596.75 kJ/mol)
Then look to the section below E H G CV CP S (There are two of these sections one in KJ and the second in Kcal, select the one consistent to your unit needs).
Take the second value on the line for TRANS, ROT, and VIB (the second is the H, third is G, fourth is CV and so on). Finally RT is just your ideal gas constant and the Temperature of interest.
Espero que isso ajude (I gather from your last name you are a Portuguese speaker, sorry if it’s not the case)
Hello,
Thank u for reading. I have a preblem when doing a rigid scan with G09.
After adding keyword “scan” and “R bondlength steps stepsize” after molecule deffination, only the atom itself moves. But how can i make the wholle molecular groups move along the way the the atom moves?
Use the following keywords. Say you want to scan the bond 1 – 2 but you want all atoms attached to 1 and 2 to move together with the bond:
* 2
1 *
1 2 s 1.0 5 0.1
This should help (in this example the initial R12 is 1.0 Angstroms and will increase it five times by 0.1 Angstroms until it reaches 1.5 A)
Hello
Could you please help with the following error in Gaussian
Error: User-specified g09 input file, SG_4_Lan.com, does not exist
Thanks
#bondbreaking #carboxyl #deprotonated
Hello, I’m trying to do an optimization on a big molecule (+/- 100/120 atoms) with a deprotonated carboxyl function covalently attached. However the optimizations always reach a point where the carboxyl group detaches itself from the big molecule and obtains a CO2 geometry. I’ve tried optimizing with a small basis set (3-21g) and it ends up ok, but when I add a larger basis set (6-31+g(d)) this bond breaking error always happens. Curiously this only happens in the gas phase, when I applied the SMD solvent model I could optimize with the larger basis set without any problem. I’m using the input like this now:
# opt=(calcfc,GEDIIS,verytight) rm062x/gen geom=connectivity scf=yqc int=ultrafine
Can you help me?
p.s. I’m using the 6-31+g(d) basis on the carboxyl and 3-21g on the rest of the structure through the gen keyword
Is there any reason why you need this optimization in the gas phase? If you can stick to the solvated models that would be better in the overall sense. The cavity imposed by the SCRF hinders the CO2 from escaping your molecule.
If you must study the gas phase state then try the wB97XD functional and see if you can keep the CO2- attached.
I hope this helps
Hello Doctor,
Are there any post-bac. positions available in your group for the 2019-2020 academic year?
Always! The problem is we have no funding available at this point. Will post it when there is any
good evening I do not know how to make fukui clues in our molecule by the molecular orbital HUMO and LUMO, thanks
how to know from the energies of toluene and benzene that toluene is obtained from benzene?
Dear Sir,
Can you please tell me why i am not getting the calculated IR frequencies after optimizing the geometry of a molecule with B3LYP using def2-TZVP basis sets. I used M3 and M4 grid and could optimize the geometry. But the IR frequencies are not produced with the same set up.
Add the keyword freq to your route section
Dear sir,
I am trying to optimize positively charged metal-complex with the counteranion, in the presence of solvent. The problem that I am facing is during the optimization the counter-anion is distorting the metal-complex and leading to different geometry (I am keeping the counteranion as far as possible). By different geometry, I mean that changing metal oxidation state by forming a bond between two negative ligands i.e. hydride.
Can you suggest me a better approach to deal with such system??
Loose the counteranion and work only with the positive complex.
I have to correlate the data with the experiment. So, there is a need of doing it with counteranion.
It is quite a effective point! Really wanna express gratitude for that information you have divided. Just keep on creating this form of content. I most certainly will be your faithful subscriber. Thanks again.
Sir ,how to optimise the transtion state of “ch3cloh using gusian view ?i optimise in 3 to4 different way but all the optimisation wouldn’t completed ,the link died abnormaly ,so plz tell me the proper method to optimise the above molecule
Hi Dr. Barroso,
I am doing studies on a Uranium complex bound to a carbon nitrogen based ligand and I have a couple questions on what approach i should take. I am interesting in what is the best way to calculate the electrostatic potential, especially with regards about calculating the esp while using a ecp basis set for the U atom. I have read elsewhere that esp calculations dont work well when using ecp’s, do you have any experience in this?
Thank you for your response,
D
Check out the Basis Set Exchange website and try using a medium core ECP, that is one that only substitutes half the number of electrons in the core instead of all 86 of them; this will take longer to calculate but will increase the accuracy of your predictions.
I hope this helps
Dear Sir,
I am getting following error in my gaussian 09 calculations.
” Failed to find a lower point in StbLin”
Please let me know, how one can solve this. I will be grateful to you.
Dear Dr. Barroso,
I am a beginner in Comp Chem.
How do you locate a minima or maxima on a PES? What does the negative sign on a computed frquency mean? May you kindly please explain it with an example if possible.
Regards,
Bryan
Minima are found trhough optimization of the geometry (opt option in gaussian). A maxima corresponds to a Transition State (look for ‘the art of finding transition states’ in this blog). After the optimization you perform a frequency analysis, if they are all positive then you have a minimum, if you have only one negative then you have a Transition State (TS), if you get more than one then you have something meaningless.
Sometimes you get a negative frequency when you want a minimum, animate that frequency and it will tell you what the molecule wants to do, i.e. how does it want to move to ‘be more comfortable’.
I hope this helps
Thank very much Sir, highly appreciated!
Dear Dr. Barroso,
I try to calculate molecular complex Freq and NMR with Gaussian. Geometry optimization for neutral species using these commands:
#P B3LYP cc-pVTZ Opt(GDIIS, Z-matrix) NMR Freq SCFCYC=250 NoSymm
Error: symmetry not used in fofcou
Can you suggest me a solution to deal this problem??
Regards
Try deleting the NoSymm keyword and look for the NMR post we wrote last year in this post.
Dear Dr. Barroso,
I have the following Cartesian coordinates of a Gold complex and have been struggling to get the corresponding charge and multiplicity. I would like to run a calculation for Opt and Freq. May you kindly please help.
Au 1.360814 1.469089 4.400746
C 5.307642 1.389607 6.843985
H 5.507275 1.229404 5.910229
H 4.870358 2.257890 6.915128
C 6.510720 1.389607 7.612332
H 7.089684 2.096802 7.304637
H 6.959811 0.547877 7.509174
H 6.306354 1.532993 8.538974
C 1.456104 -1.956071 7.162351
H 0.690196 -1.468381 7.503839
H 1.363535 -2.024224 6.198359
C 1.488953 -3.274870 7.738612
H 0.666753 -3.731582 7.532296
H 1.584937 -3.205832 8.690153
H 2.226021 -3.766101 7.374002
I 1.201101 1.134698 1.820913
I -0.420347 3.370638 4.490387
O 4.402687 0.338108 7.352659
O 2.673550 -1.232944 7.482496
P 3.034067 0.042485 6.682134
Se 3.109165 -0.249598 4.533606
Se 1.591287 1.649826 6.831890
That is hard to say, you should know what the oxidation state of Au is in this complex, because charge and multiplicity will change whether this is Au(0), (1) or (3). Also there are some weird signs that I’m guessing were oxygen atoms almost at the bottom of your list. Sorry I cannot be of any help.
Dear Dr. Barroso,
I ran a Gold complex in Gaussian09 with the following exact Route Section “PBE0/LANL2DZ Opt Freq NoSymm” and
it gave me this error message ” QPErr — A syntax error was detected in the input line.
#T PBE0/LANL2DZ Opt Freq NoSymm” .
May you kindly please assist me.
This was the input file:
#T PBE0/LANL2DZ Opt Freq NoSymm
au1i2se2pc4h10o2
0 1
Au 1.360814 1.469089 4.400746
C 5.307642 1.389607 6.843985
H 5.507275 1.229404 5.910229
H 4.870358 2.257890 6.915128
C 6.510720 1.389607 7.612332
H 7.089684 2.096802 7.304637
H 6.959811 0.547877 7.509174
H 6.306354 1.532993 8.538974
C 1.456104 -1.956071 7.162351
H 0.690196 -1.468381 7.503839
H 1.363535 -2.024224 6.198359
C 1.488953 -3.274870 7.738612
H 0.666753 -3.731582 7.532296
H 1.584937 -3.205832 8.690153
H 2.226021 -3.766101 7.374002
I 1.201101 1.134698 1.820913
I -0.420347 3.370638 4.490387
O 4.402687 0.338108 7.352659
O 2.673550 -1.232944 7.482496
P 3.034067 0.042485 6.682134
Se 3.109165 -0.249598 4.533606
Se 1.591287 1.649826 6.831890
I think the NoSymm keyword is now deprecated. Try eliminating it and run it again. Also, There is something weird with the fifth and fourth to last atomic symbols, maybe is the pasting into the browser but I guess they were supposed to be oxygen atoms, right?
Dear Doc.,
I ran the calculation without the “NoSymm” keyword and it still gives me an error message. Here is the error text:
#T PBE0/LANL2DZ Opt Freq
————————
QPErr — A syntax error was detected in the input line.
#T PBE0/LANL2DZ Opt Freq
‘
Last state= “GCL”
TCursr= 3523 LCursr= 3
Error termination via Lnk1e in /apps/Gaussian/09D/g09/l1.exe at Fri Mar 22 11:18:13 2019.
Job cpu time: 0 days 0 hours 0 minutes 0.0 seconds.
File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1
Thank you.
Hello,
I am studying mercury halides formation in the atmosphere and apply TST to find favorable pathways. I would be grateful if you could explain to me or give the link to where to find the information on how to find kinetic data for the studied reaction by transition state theory?
Is it, in general, possible to evaluate somehow rate coefficients from studying a single act of reactions with TST? how to deal with temperature in this case?
Thank you so much for this blog. It helps a lot
Hi,
QPErr — A syntax error was detected in the input line.
# opt=restart (calcfc,ts) ub3lyp/6-311+g
‘
Last state= “GCL”
TCursr= 3523 LCursr= 14
Error termination via Lnk1e in /share/apps/packages/gaussian//g09/l1.exe at Tue Apr 9 13:00:28 2019.
Job cpu time: 0 days 0 hours 0 minutes 1.8 seconds.
I got the following error while restarting the file on Gaussian, I am optimizing a complex,
Have i out the key-words correctly?
%mem=25MW
%nprocshared=16
%chk=G-1.chk
# opt=restart (calcfc,ts) ub3lyp/6-311+g(d,p) scf=qc geom=check guess=read
Optimization
0 2
N -0.19242149 0.86832452 0.07298009
C 1.09154582 0.71229219 0.09495347
N 1.98075778 1.87453271 -0.04432711
H 2.55966058 1.75653545 -0.85114071
Hello Everyone,
I put my question short.
How the partial atomic charge (Mulliken/NPA/MK/CHELPG) of D-H…A atoms (D=Donor, H=Hydrogen, A=Acceptor of Hydrogen bond) change before and after hydrogen bond formation?
hi,
for open shell species how to calculate occupancy from nbo?
Dear Sir,
I’m trying to run a dft calculation with the following job input but it fails to converge:
%chk=bp34.chk
%nprocs=4
%mem=8GB
# PBEPBE/Gen Pseudo=Read Opt Freq NoSymm
auc16ph18se2i2
0 1
Au 7.5267262431 7.6191903263 4.1403668471
C 3.0251959453 6.663147335 2.9316546043
H 2.4056329416 5.9002146547 3.441036955
H 2.3563481736 7.4559452209 2.5457710752
C 3.8498035423 6.0284096611 1.7852080233
H 4.472383945 6.8105159402 1.3121784704
H 4.5404749658 5.2757091494 2.208521869
C 2.9228860363 5.3873274802 0.7596436096
C 2.54262546114.0261073256 0.8790990623
H 2.9539479169 3.4199154099 1.6963068714
C 2.3994027341 6.1490122442 -0.3163926769
H 2.6996171971 7.1983616682 -0.4319793416
C 1.6581997794 3.4391351814 -0.0535928233
H 1.3810491755 2.3837002062 0.0461688392
C 1.5148147751 5.5656221846 -1.2508361469
H 1.1259131021 6.1640623499 -2.0822930671
C 1.1396434719 4.2084452237 -1.1205973691
H 0.4579619665 3.7531268036 -1.8474933272
C 2.9366391898 8.1810947401 5.5779935622
H 2.0828423212 8.5963350937 5.0070274721
H 2.5778600451 7.3195499329 6.1712300968
C 3.5603826205 9.2655210667 6.4933756602
H 4.014233169 10.0558406131 5.8677431585
H 2.7139868227 9.734394453 7.0340992975
C 4.5816114676 8.7293079769 7.4898557914
C 5.9579403965 9.0383352875 7.35819318
H 6.2934831192 9.6852198593 6.5389152017
C 4.1671199239 7.9005558858 8.5642616756
H 3.1011075349 7.6689023648 8.6947989936
C 6.9042547886 8.5132104367 8.2668148969
H 7.9668158083 8.7452730095 8.1367309486
C 5.1094215689 7.3774272739 9.4761393053
H 4.7754708606 6.7394769364 10.3023489684
C 6.4833917764 7.6785559271 9.3257478417
H 7.2174595256 7.2664759135 10.0268065518
I 9.254580283 9.4805923376 3.156219778
I 9.475412192 5.9619604308 5.0661659648
P 4.1144238313 7.4658885075 4.2629612356
Se 5.5578351692 9.0913548355 3.3158178093
Se 5.763808213 5.9555767526 5.0499301353
@/home/bpmoloto/test/basissets/def2-TZVP_H.gbs
****
@/home/bpmoloto/test/basissets/def2-TZVP_C.gbs
****
@/home/bpmoloto/test/basissets/def2-TZVP_P.gbs
****
@/home/bpmoloto/test/basissets/def2-TZVP_Se.gbs
****
@/home/bpmoloto/test/basissets/def2-TZVP_I.gbs
****
@/home/bpmoloto/test/basissets/def2-TZVP_Au.gbs
****
@/home/bpmoloto/test/basissets/def2-TZVP_Au_ECP.gbs
@/home/bpmoloto/test/basissets/def2-TZVP_I_ECP.gbs
It gives me this error text:
SCF Done: E(RPBE-PBE) = -6494.02226510 A.U. after 129 cycles
NFock=128 Conv=0.18D-02 -V/T= 2.0787
Convergence failure — run terminated.
Error termination via Lnk1e in /apps/Gaussian/09D/g09/l502.exe at Thu Apr 18 00:54:52 2019.
Job cpu time: 1 days 7 hours 19 minutes 33.5 seconds.
File lengths (MBytes): RWF= 398 Int= 0 D2E= 0 Chk= 13 Scr= 1
Dear Joaquin
First of all, thank you for having this section, and for your time. Here it is my question
How can I get the Vda (strenght of donor-acceptor coupling) using Gaussian?
I have a limited knowledge in computational chemistry and Gaussian (using GaussView as graphical interface), but it is a very interesting topic and useful for the molecular rotor we are studying. I managed to produce the HOMO, LUMO frontier orbitals using DFT (6-31G+) calculations plus the GS, ES geometries. But I want to go further and compare the Vda with other published rotors. If anybody could help me describing step by step what should I do (formula, etc…), I’d be happy to read it. thanks
Answer
Hello Dr. Joaquin Barroso-Flores,
I would be grateful if you could explain to me that how can I prepare the Gaussian input file for multilayer QM/MM ONIOM calculation from the CIF file. Also, I request you to please advise me how can I calculated the investigate the absorption and emission features of organic molecules (in QM/MM ONIOM).
I find out the similar work in the following articles (DOI: 10.1021/acs.jpcc.7b00488 (J. Phys. Chem. C 2017, 121, 5747−5752); https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.24282 ) but I am not able to prepare the input file. Hence, I write this request to you.
Thank you very much in advance,
Venkatesan
Hello Joaquin
I am using Gaussian’s ONIOM software for my QM/MM calculation. And receive the following error message :
Missing atomic parameters for atom 234 IAtTyp= 0
Missing atomic parameters.
I have tried to use the parmlookup function in addition to trying multiple keyword combinations but I cannot seem to get past this error. Atom 234 in this case is a carbonyl carbon that links the QM region to the MM region of my calculation
My job input is as follows:
#p oniom(B3LYP/6-311G(d,p):amber=hardfirst) nosymm scrf=(smd,solvent=water,oniompcm=x) geom=connectivity iop(2/15=3) test opt=quadmac
I’ve also tried the following keywords are replacements:
amber=softfirst
opt=quadmarco
This error occurs after 12 PCMM matrix inversion algorithm cycles and the MM parameters for the model system are supposedly made.
Do you have any ideas on how to resolve this issue?
Thank you in advance,
Eric Hantz
Dear Dr. Barroso,
I have been trying to run the attached job (See the input file ) and receiving an error text in its log file:
General basis read from cards: (5D, 7F)
QPErr — A syntax error was detected in the input line.
‘
Last state= “Top”
TCursr= 2832 LCursr= 0
Error reading general basis specification.
Error termination via Lnk1e in /apps/Gaussian/09D/g09/l301.exe at Mon May 13 15:27:11 2019.
Job cpu time: 0 days 0 hours 0 minutes 21.7 seconds.
File lengths (MBytes): RWF= 23 Int= 0 D2E= 0 Chk= 1 Scr= 1
******************
Input File
%chk=bp43.chk
%nprocs=16
%mem=12GB
# PBEPBE/Gen Pseudo=Read Opt Freq NoSymm
au4c64p4h72s8e
0 1
Au 5.906433 2.552097 6.337790
C 6.627190 1.995485 10.019892
H 5.748924 2.109682 9.624882
H 6.526666 1.431745 10.802957
C 7.141892 3.343298 10.456628
H 7.166402 3.926877 9.681908
H 8.054218 3.235439 10.768185
C 6.337256 4.033504 11.552641
C 6.390804 5.414753 11.644439
H 6.873152 5.897994 11.012980
C 5.739525 6.080018 12.654217
H 5.790836 7.006652 12.702897
C 5.022505 5.397664 13.581933
H 4.589332 5.853050 14.267636
C 4.942138 4.039168 13.501262
H 4.438932 3.568378 14.125767
C 5.606222 3.357306 12.495656
H 5.555911 2.428981 12.459494
C 9.340625 0.981007 9.577592
H 9.922216 0.530628 8.946133
H 9.703494 1.869225 9.725026
C 9.382138 0.222583 10.891973
H 8.813097 0.674748 11.534559
H 9.023887 -0.667773 10.754276
C 10.780847 0.106797 11.469188
C 11.056058 0.598212 12.725151
H 10.381794 1.007768 13.217523
C 12.322681 0.489073 13.259249
H 12.494709 0.823026 14.110467
C 13.318255 -0.099724 12.556855
H 14.169748 -0.175220 12.924047
C 13.063377 -0.586312 11.292546
H 13.745955 -0.980058 10.798784
C 11.787444 -0.489506 10.758449
H 11.613928 -0.832656 9.911403
P 7.701907 1.152183 8.825266
S 8.022163 2.277827 7.174710
S 6.999013 -0.729641 8.538467
Au 4.955785 -0.319694 7.570999
C 4.235029 0.236919 3.888898
H 5.113294 0.122721 4.283907
H 4.335552 0.800658 3.105833
C 3.720327 -1.110895 3.452162
H 3.695817 -1.694473 4.226881
H 2.808001 -1.003036 3.140605
C 4.524963 -1.801101 2.356149
C 4.471414 -3.182349 2.264351
H 3.989066 -3.665590 2.895810
C 5.122693 -3.847615 1.254573
H 5.071382 -4.774249 1.205892
C 5.839713 -3.165261 0.326857
H 6.272887 -3.620647 -0.358847
C 5.920081 -1.806765 0.407528
H 6.423287 -1.335974 -0.216977
C 5.255997 -1.124903 1.413133
H 5.306308 -0.196578 1.449296
C 1.521594 1.251396 4.331197
H 0.940003 1.701776 4.962656
H 1.158725 0.363178 4.183764
C 1.480080 2.009821 3.016816
H 2.049121 1.557655 2.374230
H 1.838332 2.900176 3.154513
C 0.081371 2.125606 2.439602
C -0.193839 1.634191 1.183638
H 0.480425 1.224635 0.691267
C -1.460462 1.743331 0.649540
H -1.632490 1.409377 -0.201677
C -2.456036 2.332127 1.351934
H -3.307529 2.407623 0.984742
C -2.201158 2.818715 2.616243
H -2.883737 3.212461 3.110005
C -0.925225 2.721909 3.150341
H -0.751709 3.065059 3.997386
P 3.160312 1.080221 5.083523
S 2.840056 -0.045424 6.734080
S 3.863206 2.962044 5.370323
Au 6.608455 5.934382 6.238982
C 3.910488 8.673639 7.252043
H 3.061059 8.275453 7.007248
H 3.707269 9.509168 7.701297
C 4.608366 9.020326 5.984952
H 4.872645 8.198246 5.542653
H 5.418175 9.510245 6.201929
C 3.802441 9.833539 5.034982
C 3.925703 9.605706 3.638539
H 4.530696 8.979976 3.313074
C 3.122118 10.338476 2.763676
H 3.187745 10.197527 1.847087
C 2.248899 11.250003 3.240748
H 1.713843 11.723238 2.646843
C 2.141092 11.483069 4.531484
H 1.543159 12.126418 4.836086
C 2.893940 10.793455 5.421646
H 2.792762 10.973540 6.328499
C 3.407124 7.364521 9.761188
H 2.631470 6.951093 9.352270
H 3.749265 6.746040 10.426029
C 2.948683 8.635777 10.481664
H 3.691028 9.010683 10.980989
H 2.663304 9.292820 9.826560
C 1.805514 8.334507 11.424680
C 0.497656 8.653943 11.101996
H 0.321465 9.111512 10.310586
C -0.541981 8.306565 11.926787
H -1.412891 8.531534 11.691728
C -0.308378 7.629978 13.097907
H -1.014908 7.396369 13.655650
C 0.972666 7.302684 13.433109
H 1.138782 6.837270 14.221737
C 2.025514 7.658356 12.613881
H 2.894693 7.442009 12.864239
P 4.674175 7.581840 8.484918
S 4.943684 5.708328 7.786558
S 6.232574 8.523958 9.360059
Au 7.773941 8.631185 7.669807
C 10.471907 5.891929 6.656747
H 11.321337 6.290114 6.901541
H 10.675127 5.056399 6.207493
C 9.774029 5.545242 7.923837
H 9.509751 6.367322 8.366137
H 8.964220 5.055322 7.706860
C 10.579955 4.732028 8.873808
C 10.456693 4.959861 10.270250
H 9.851699 5.585592 10.595716
C 11.260278 4.227091 11.145113
H 11.194650 4.368040 12.061702
C 12.133496 3.315565 10.668042
H 12.668553 2.842329 11.261947
C 12.241303 3.082498 9.377306
H 12.839236 2.439150 9.072703
C 11.488455 3.772113 8.487143
H 11.589633 3.592027 7.580290
C 10.975272 7.201046 4.147601
H 11.750925 7.614474 4.556519
H 10.633131 7.819527 3.482761
C 11.433712 5.929790 3.427126
H 10.691368 5.554884 2.927800
H 11.719091 5.272747 4.082230
C 12.576882 6.231061 2.484110
C 13.884740 5.911624 2.806794
H 14.060930 5.454056 3.598204
C 14.924376 6.259003 1.982003
H 15.795286 6.034034 2.217061
C 14.690774 6.935589 0.810882
H 15.397304 7.169199 0.253140
C 13.409729 7.262883 0.475681
H 13.243614 7.728297 -0.312948
C 12.356882 6.907211 1.294908
H 11.487702 7.123558 1.044550
P 9.708221 6.983727 5.423872
S 9.438712 8.857239 6.122232
S 8.149821 6.041609 4.548731
@/home/bpmoloto/test/def2-tzvp/def2-TZVP_H.gbs
****
@/home/bpmoloto/test/def2-tzvp/def2-TZVP_C.gbs
****
@/home/bpmoloto/test/def2-tzvp/def2-TZVP_P.gbs
****
@/home/bpmoloto/test/def2-tzvp/def2-TZVP_S.gbs
****
@/home/bpmoloto/test/def2-tzvp/def2-TZVP_Au.gbs
****
@/home/bpmoloto/test/def2-tzvp/def2-TZVP_Au_ECP.gbs
Kindly please help.
Regards,
Bryan
Dear Dr. Barroso,
attached is the initial portion of a UNOCAS calculation I am doing at a certain point. I have obtained UNO orbitals with UHF. then I prepared this input file with CHEMCRAFT using .fchk file from UHF UNO orbital calculations. but the problem is my energy eigenvalues with CAS is higher than that in UHF. Can you please help me with the input? where am i making mistake?
%chk=MeCbl270cas.chk
#p CASSCF(2,2)/gen/tzvpfit guess=cards iop(5/7=-1)
CoC23N6H28
1 1
6 -0.066673049 -0.948366409 3.922516939
6 0.046388549 -1.281783356 2.593903936
7 -0.083240451 -0.143750672 1.819162244
6 -0.270366419 0.867562308 2.660752517
7 -0.266594405 0.417237087 3.944263912
27 -0.014896819 0.018147798 -0.315524651
6 -0.050588156 0.253390234 -3.005020561
7 -1.256378027 -1.459149473 -0.473400487
6 -0.900680538 -2.796874384 -0.511499188
6 -2.133539605 -3.676629253 -0.534645386
6 -3.296465513 -2.672629069 -0.588803375
6 -2.604714218 -1.331167262 -0.503119228
6 0.386433381 -3.281635902 -0.522412225
6 1.535029834 -2.445614654 -0.561214809
7 1.450183972 -1.138039649 -0.526547810
6 2.772541586 -0.508491033 -0.755821060
6 3.766717616 -1.612921312 -0.367808789
6 2.974777647 -2.902470757 -0.692932043
6 2.724023404 0.809909812 0.007359510
7 1.343128964 1.312365467 -0.194829592
6 1.311199224 2.620597923 -0.268911939
6 2.702942580 3.215772073 -0.190470247
6 3.609993259 1.986477824 -0.434994406
6 -3.292864959 -0.120151664 -0.475835865
6 -2.716486518 1.145550473 -0.430649251
7 -1.384142085 1.390065976 -0.355729544
6 -1.144107311 2.751504737 -0.426852888
6 -2.442623395 3.515046838 -0.588823066
6 -3.520583990 2.425601335 -0.469399997
6 0.095361418 3.346965744 -0.387498859
1 2.851133107 -0.275291949 -1.835788596
1 2.854991730 0.594750576 1.085687789
1 -4.381633411 -0.168485329 -0.522157739
1 0.147137640 4.432963943 -0.466558391
1 0.529149889 -4.362081175 -0.546609750
1 0.398195711 1.239226345 -3.119619202
1 0.547856566 -0.605545824 -3.305542760
1 -1.125997892 0.178950786 -3.160350927
1 0.209871416 -2.256693772 2.147464476
1 -0.408291683 1.907908454 2.384800869
1 -0.392841805 0.987813615 4.774905100
1 -0.024203240 -1.542683684 4.828079730
1 3.840533931 1.896470717 -1.507971043
1 4.559399470 2.036764310 0.112538074
1 -4.014801768 -2.796686505 0.235079442
1 2.849998837 4.022964100 -0.921765595
1 -2.464871568 4.009059930 -1.572428875
1 2.866484714 3.656639937 0.808247465
1 -4.232452233 2.424261553 -1.307014623
1 3.981550757 -1.562130842 0.711311374
1 4.718275186 -1.544302183 -0.909666507
1 3.163378715 -3.251108524 -1.723225880
1 3.207164794 -3.743851946 -0.024933137
1 -2.538806318 4.309284658 0.164765355
1 -2.112255514 -4.355300133 -1.399218202
1 -4.118143756 2.524683620 0.450993246
1 -2.169167358 -4.311037679 0.363868059
1 -3.874436540 -2.745500179 -1.523073561
1
S 6 1.0
13575.349700000000 0.000606455036
2035.233370000000 0.004697908889
463.225624000000 0.024332477595
131.200196000000 0.097399968280
42.853015900000 0.301955842939
15.584185800000 0.662336090867
S 2 1.0
6.206713850000 0.655953085205
2.576489650000 0.375856333118
S 1 1.0
0.576963394000 1.000000000000
S 1 1.0
0.229728314000 1.000000000000
S 1 1.0
0.095164440000 1.000000000000
P 4 1.0
34.697232200000 0.011327220006
7.958262280000 0.076169659240
2.378082690000 0.301922522160
0.814332082000 0.727850273385
……………………
……………………
it is a very long input file.
I am waiting for your reply. Thank you!
-Saurav
Dear Dr. Barroso,
I am getting the following warning
” Warning X atom .. may be hypervalent but has no d function”
while running an optimization job in gaussian 09.
“X” may be atoms like P, S, Br etc
As per some suggestion (available on internet) by other group I have added an additional keyword “extrabasis” and some additional lines at the end of the file. For instance in case of Phosphorous (P)
P 0
D 1 1.0
0.55 0.100D+01
****
Can you please describe what does the values in line2 and line3 represent and what should be their values for sulphur (S) and bromine (Br)?
Thanks
Shyam
I think you can find answer at EMSL site
https://bse.pnl.gov/bse/portal
retrieve basis set data as the gaussian format
Dear Dr. Barroso,
Hi I have an ‘Out of memory’ error while I am running “room temp.” vibronic spectra simulation with Gaussian 16, Revision A.03, version in Ubuntu 64bit.
However, without keyword [Temperature=value=298.15] calculation runs well.
Does current version do not support temperature effects on vibronic spectra?
Because In the Gaussian 16, Revision B.01, (window10 64bit) It runs well and it’s same computer. (I run gaussian with ubuntu app in windows store)
How can I consider temperature effects in linux version. Please I need your opinion.
I also share my step by step vibronic calculation input files
Step 1.
===========Ground states============
%mem=27GB
%nprocshared=10
%chk=bandshape_1_GS.chk
#p opt freq=savenormalmodes b3lyp/6-31g(d) geom=connectivity
bandshape_1_GS
0 1
structure
==================================
Step 2.
===========Excited states============
%mem=27GB
%nprocshared=10
%chk=bandshape_1_ES.chk
#p opt freq=savenormalmodes td=(nstates=10,root=1) b3lyp/6-31g(d)
geom=connectivity
bandshape 1 ES
0 1
structure
==================================
Step 3.
===========Vibronic calculation========
%oldchk=bandshape_1_GS.chk
%mem=27GB
%nprocshared=10
%chk=bandshape_1_Abs.chk
#p freq=(savenormalmodes,fcht,readfcht,readfc) b3lyp/6-31g(d)
guess=read geom=allcheck
Spectroscopy=OnePhotonAbsorption
Temperature=value=298.15 <————————–this keyword makes an out of memory error
Advanced=(forceFCCalc)
SPECHWHM=200.0 MAXBANDS=5 MAXINT=1200 PRTINT=0.0001 ALLSPECTRA
bandshape_1_ES(2).chk
==================================
Hi Dr Barroso,
Last time I asked a question here it was very helpful so here I go again.
I am studying a Metal-Ligand complex and want to look at the nature of their bonding. I am interested in determining the metal contribution (f-orbital) to this bonding and how it changes when changing the M. I have relaxed these structures and performed nbo analysis. I am somewhat confused as to where to proceed from here. Any suggestions? This might be somewhat unclear, but any further information I would be happy to provide.
D
Buenas Joaquín.
Hace poco comencé a trabajar con el programa AIMAll (QTAIM). Al realizar el cálculo de propiedades integradas en el sistema que estudio, me encontré de que, a pesar de que el programa termina el calculo de manera correcta, los valores de “carga” y los demás de algunos átomos solicitados no fueron resueltos. Despues de varios intentos (creyendo de que se trataba de algun problema de compatibilidad entre las versiones, ya que realizo el cálculo en uno y la visualización en otro ordenador) revisando el archivo de texto de éstos atomos en cuestión me encontré con lo siguiente:
“Failed to connect BCP 2 to RCP4. Aborting because cannot triangulate surface”
Sería de gran ayuda si me dijeras de que se trata, y alguna sugerencia para corregirlo.
Gracias.
Hi Sir,
I am a researcher working on the structure property relationship of organic crystals through quantum chemical computations.
While doing the NBO analysis I came across an enormously high E2 value between n1(N1) and σ (O2-O3) of Nitro group attached to pyridine ring in my organic molecule. Can you please help me out in finding the reason for it. My level of theory is # B3LYP/6-31G(d) POP=NBO
Hello Dr. Barrosso, I have been doing a frequency calculation on amylopectin for three weeks now with the DFT (B3LYP) method associated with the 631 ++ G base (d, p) but the computation does not converge. I need your help to get around this problem. I enclose the last sentences of the output file:
dumping/ fiocom/, unit =3 NFiles= 1 SizExt =524288 WInBlk=512
defal= T Lstwrd =67072 FT ype=2 FMxFil=10000
Number 0
Base 20480
End 67072
End1 67072
Wr Pntr 20480
Rd Pntr 20480
Length 46592
Error termination in NtrErr:
NtrErr called from FIOCnC.
Thank you so much!!!!
Dear Dr. Barrosso,
I am trying to use cubegen to generate an electrostatic potential cube for some simple anionic molecules that I optimized in #gaussian. My command, which successfully generates the cube is this:
cubegen 12 potential dianion.fchk dianionpotential.cube 80
The problem is that the resulting cube file only contains positive values. The (negative) charges are clearly correct in the input files. I’m not sure what I’m generating, but it is not an electrostatic potential map!
Hi William,
You are generating a potential energy surface, not a potential energy mapped surface. If this is what you want to display then you should check the option ‘display both values’. However, my guess is you wanna use density=scf instead of potential and then generate a mapped surface on that one with the charges from your output. Here is a fair video on how to do that:
Dear Dr. Barroso
I was looking for a demonstration of why the Coupled Cluster theory in quantum chemistry is size consistent, i.e. E(A+B)=E(A)+E(B).
I haven’t found anything interesting in the literature, do you have any hint on that?
Best regards
Demetrio
That is an excellent question. The origin of the size consistency in CC stems from the definition of the exponential operator, i.e., Psi = e ^T (psi-HF), where T is the cluster operator. You should check “Reviews in Computational Chemistry” and look for the review by Henry F. Schaefer III on coupled cluster, maybe even in Szabo and Ostlund you could find a nice explanation but I don’t have it near me right now.
Have a nice day
I am trying to calculate NICS (0 and 1) values for heterocyclic compounds using Gaussain 09. I am placing the ghost atom (Bq or 0) at the center of the ring. I am using the method/basis set (B3LP/deft2tzvp) as reported in the paper JPC A, 2017, 121, 7282.
But when I run the job I am getting the following error.
‘Standard basis: def2TZVP (5D, 7F). Atomic number out of range in Df2TZV. Error termination via Lnk1e in C:\G09W\l301.exe at Thu Jul 11 11:44:14 2019.’
This is occurring because of the ghost atom (Bq or 0) present at the center of the heterocyclic ring.
I am not sure why this is happening.
Kindly help me to overcome this error.
This is just a guess but since the def2 family of basis sets is associated with a pseudopotential and the ghost atoms have no core electrons to be removed then that is probably why your calculation is crashing. Try using a different basis set for the ghost atom as large as you want but an all-electron one.
I hope this helps
Dear Dr. Barroso:
I´m running (using Gaussian) a “# opt freq b3lyp/6-311+g(d,p) pop=full geom=connectivity” calculation and sudenly this calculation is cutoff on a 2070 error.
I guess the problem here is referred in this sentence in the output file: “Integral buffers will be 131072 words long.
Raffenetti 2 integral format.
Two-electron integral symmetry is turned on.
g_write”
I´m using 150MW.
I´m not able to overcome this problem.
Can you helpme to end this calculation?, any sugestion will be welcome.
Thank you.
Hi, I guess you’re requesting too little memory. Try requesting more depending on the computer you’re using and the number of shared memory processors in use. I for instance, use nprocshared=16 mem=32GB (2GB per proc) for demanding calculations in a sort of a brute force way in a big cluster.
I hope this helps, have a nice day
Just out of curiosity, I have submitted an opt+freq calculation with Huckel as keyword. Optimization doesn’t lead to any other point and taken initial geometry as minima. Frequency calculation has all the frequency with zero value and showing the vibrations. How we can explain that zero magnitude frequency with vibration?? Any comment on optimization…
Did you by any chance use guess=(huckel,only)? that way it would end right after creating and printing the initial guess wavefunction. There was also an IOP option to exit the program after generating the guess but I can’t remember what was it.
Can you please share your input file at least the route section so I can get a better understanding of your issue?
Have a nice day
Hi,
I am trying to figure out how to interpret an ECP basis set file. For example, the LANL2DZ file for Zn is provided below. The first section is clearly the description for the double-zeta valence. The second section is clearly the ECP, but I am not sure what the various terms are describing. I assume that the “ZN-ECP 3 18” line is describing that three core shells are present, and that the Ar core is being used (i.e., a large-core ECP). The remaining sections appear to be describing gaussian primitives being used to make contracted gaussian functions, but I am unclear as to what exactly they are modelling. My guess is interactions between the core and valence, but don’t really know for sure. Any help with this would be appreciated.
!———————————————————————-
! Basis set: LANL2DZ
! Description: LANL2DZ
! Role: orbital
! Version: 0 (Data from the Original Basis Set Exchange)
!———————————————————————-
Zn 0
S 2 1.00
0.7997000 -0.6486112
0.1752000 1.3138291
S 1 1.00
0.0556000 1.0000000
P 1 1.00
0.1202000 1.0000000
P 1 1.00
0.0351000 1.0000000
D 4 1.00
68.8500000 0.0258532
18.3200000 0.1651195
5.9220000 0.4468212
1.9270000 0.5831080
D 1 1.00
0.5528000 1.0000000
****
ZN 0
ZN-ECP 3 18
f potential
5
1 386.7379660 -18.0000000
2 72.8587359 -124.3527403
2 15.9066170 -30.6601822
2 4.3502340 -10.6358989
2 1.2842199 -0.7683623
s-f potential
5
0 19.0867858 3.0000000
1 5.0231080 22.5234225
2 1.2701744 48.4465942
2 1.0671287 -44.5560119
2 0.9264190 12.9983958
p-f potential
5
0 43.4927750 5.0000000
1 20.8692669 20.7435589
2 21.7118378 90.3027158
2 6.3616915 74.6610316
2 1.2291195 9.8894424
d-f potential
3
2 13.5851800 -4.8490359
2 9.8373050 3.6913379
2 0.8373113 -0.5037319
Hello Kai
The LANL2DZ is a quasirelativistic effective core potential which replaces the core electrons and simulates their presence along with some of the relativistic effects affecting them. For a more detailed explanation you may wanna check the original Hay and Wadt papers:
Hay PJ, Wadt WR. J. Chem. Phys. 1985;82:299.
Roy LE, Hay PJ, Martin RL. J. Chem. Theory Comput. 2008;4:1029.
Hay PJ, Wadt WR. J. Chem. Phys. 1985;82:270.
Wadt WR, Hay PJ. J. Chem. Phys. 1985;82:284.
Hi,
I m trying to calculate the freq+opt of the transition states using G09.but the computer stays working 17 days, can u tell me please how to reduce the time for calculation in gaussian
Thank you so much in advance.
filoroi
Hi, i would like to study the chemical reaction between two organic molecule in presence of HCL. I have tried to find the tutorial but have not got any. I am using mopac and while creating the data file. i am confused how to make two molecule to run and how much time i have to run. Please help me if you have any suggestion or if you have any tutorial for chemical reaction study for example A+B in-presence of Hcl -> new molecule
Thankx
Raj
I’m sorry but I’m not familiar with MOPAC. I hope you find the help you need.
Have a nice day
Thank you for the reply. please kindly suggest other tool, if you have i can use. I want to see how two organic molecule interact in presence of HCL. The reaction may form bonds between them. Please kindly advise me the steps.
Regards,
Raj
Hi, I am trying to perform EOM-CCSD calculations for my molecule, due to its computational cost we generally take active window and perform EOM-CCSD calculations only with those orbitals (keyword for this is: Window Keyword and Frozen Core Options).My desired orbitals are not near HOMO and LUMO, so i want to get them into the active space by reordering the orbitals near HOMO and LUMO with them. I want to know how to reorder the molecular orbitals into this active space.
Your help is highly helpful and genuinely appreciated,
Many thanks in advance,
Bharath
Sir, greetings. How do I calculate MO contribution while calculating UV spectrum in Gaussian. I am getting Homo to Lumo with oscillator strength. But not getting MO in %.,like H to L (70%),. My question is how can I get this % value.
Hi
Is it possible to run dft calculations of Ti2O3 in Gaussian? If yes what keywords should I use? I am currently using 6-31G* basis set but not sure about it.
Thanks
Hi! I was wondering what the difference is between using a custom basis set option in Gaussian v.s. using the gen keyword.
Thank you so much!
Karl
Hello Karl,
If one wants to use a basis set that is not defined within gaussian, the GEN or GENECP keywords must be used. Also, these keywords may be used to make use of different basis sets for different atoms, these sets can be the ones defined within gaussian.
I hope this helps
Dear Dr. Barroso,
could you explain how to calculate Raman optical activity (ROA) spectrum with Gaussian. Geometry optimization for neutral species using these commands:
#P B3LYP cc-pVTZ Opt=CalcAll Freq SCFCYC=250
Regards
Good day,
I want to ask how can I calculate vibrational circular dichroism (VCD) spectrum with Gaussian? Could you tell the keywords? I can’ t found it
hi, Dr. Joaquinbarroso.
I am trying to optimize and find the global minimum for my molecule, I used #opt freq aimed to see the value of imaginary frequency to confirm the global minimum structure. My process goes through optimize that molecule with low computational model B3lyp/3-21G then come to high computation model M06/6-31+G*. Of course this process in gas phase and there is no problem with them when optimization finish (mean that imaginary frequency = 0). Then I need to optimize that molecule in solvent DCM, but after several trials the optimization still gave back to me the value of imaginary frequency is 1. So, do you have any suggestions for me in this case. Thank you so much and Best regards.
Good evening,
I am trying to calculate excited states using single-excitation CI. I use this command:
#P B3LYP STO-3G Opt=CalcAll Freq CIS(D) integral=NoXCTest SCFCYC=250 NoSymm or without NoSymm, but it is written ,, symmetry not used in fofcou” and ,,Tx NOT orthogonal to T”
Many thanks in advance,
Urte
Dear Urte,
This error means the excited state you’re trying to obtain is not a stable one at least not from the ground state geometry input at the level of theory selected. Maybe changing from a minimal basis set could help but it usually doesn’t.
On a separate note, there is no need to specify a freq job if you’re using opt=calcall since the latter will launch a freq job at the end, if anything you could use freq=noraman to decrease the computing time. Also, I can tell you’re using an old version of gaussian because the scfcyc keyword is no longer admitted 🙂 now SCF(MaxCyc=N) is the way to control the number of cycles for the SCF calculation.
I hope this helps
Good day!
I would like to freeze all atoms only at z axes during the optimization. Have you ever tried to do that in Gaussian?
Thanks
Hi Gottlib,
No, I’ve never tried that but it does sound interesting. If I understand correctly, you want to perform a sort of 2D optimization, right? If that is the case you can try to use the symmetry of the layer you want to optimize to your advantage by constraining the point group with PG=pointgroup (say d6h for a suitable graphene sheet) but you’d need to reorient the molecule on the xy plane first.
I hope this helps
Dear Joaquin Barosso! I appeal to you as an expert in working with the GaussView 5.0 and Gaussian 09W programs. I very need your help. Could you tell me how to build anion and cation radical derivates for the molecule 2,3-dihydro-3,5-dihydroxy-6-methyl-4H-pyran-4-one. Tell me, please, about generation anion and cation derivates different molecule. Among them phenolic antioxidants. I will be very grateful to you.Sincerely, Irina Skorohod! Zabolotny Institute of microbiology and virology, NAS of Ukraine.
Dear Prof. Barroso,
I have pop=readradii and opt=modredundatn in a route section. Coordination is cartesian.
When I want to run a job I got an error message :
“Found a floating point number as input.
46 97 2.76 S 10 -0.2
?”
My important part of the input file is:
#p opt=(Modredundant) UB3LYP/6-31G NOSYM Geom=connectivity Pop=ReadRadii
-2 4
C 54.71600000 54.32900000 51.37900000
.
.
blank line
46 97 2.76 S 10 -0.2
blank line
Fe 1.32
I tried many configurations for that but I still got the error.
Any helps would be appreciated.
Dear Farzad,
I’m not sure what is it you’re trying to achieve here. First of all, the ReadRadii option is used when you want to get fitted charges for instance to input them in a molecular dynamics simulation (this is what the antechamber program does), this is called Restrained Electrostatic Potential (RESP). So in your input you’re missing the kind of charges to be calculated: could be pop=(MK,ReadRadii) or pop=(CHelp,ReadRadii) etc.
Since this is a population analysis related calculation, maybe you can try to perform it as a single point and not along a relaxed scan, unless you need to find the fitted charges at every point of the scan for any reason.
If you’re only trying to get a scan while defining a different vdW radius for any given atom(s) I’m afraid that is not going to work because (ab initio or DFT) optimizations do not rely on such parameters.
I hope this helps
Dear Prof. Barroso,
I want to do the geometry optimization of a molecule with a negative charge from the sulfonate ion, which is bonded to the aromatic ring, and a radical cation from the aromatic ring. How should I assign the charge and the spin multiplicity to create the input file?
Do you have some suggestion? Any help would be very appreciated.
Dear Jie Xu
You should always work with the total charge of a molecule, therefore if you’re studying a zwitterion, your total charge is zero. If additionally you have one unpaired electron then your multiplicity is a doublet. So, in short you should go for 0 2 in your charge multiplicity section.
Dear Prof. Barroso,
I very much appreciate your kind reply. I’m a beginner of Gaussian. Your blog is very much helpful for beginner, like me. Thanks.
Dear Joaquin Barosso
I am a first-year PhD student, and even if I am synthetic chemist, I am intrigued by quantum chemistry. In my spare time, I have tried to calculate the activation energy for the protonation of two amines. In particular, I have two amines that are very similar, but one of two is totally inert. I have optimized both structures and calculate the NBO, Molecular electrostatic potential, Fuki function, the charges etc. they showed slight differences, but I was wondering if there is a way to calculate the activation energy for a protonation and (maybe) showing that there is a very high activation energy for one of the amine. I have recently read one of your paper: “Aromatization of pyridinylidenes into pyridines is inhibited by exocyclic delocalisation. A theoretical mechanistic assessment “(https://doi.org/10.1016/j.tet.2016.05.058), and I would like to replicate one of your experiment (imagine S6 in supplementary data: relative energy kcal/mol vs reaction coordinate).
How I can run an experiment like this? in my case it would be X+ H+-> XH+
If I understood well, I have to prepare the reagents and product structures and calculate opt+fre QST2, and then “check” the optimizations steps
That is my input file:
%mem=8GB
%chk=Amine_protonated_qst2.chk
# opt=(calcfc,qst2 ) cam-b3lyp/6-31g(d) nosymm
geom=connectivity gfinput pop=full
Amine and proton
Cartesian Coordinates
Protonated amine
Cartesian Coordinates for products
But, unfortunately, it gave an error. Hence, here the questions: Do you think that is the right approach? And if so what is the error in my input file? I hope that is clear. Thank you so much for your help
Dear Joaquin Barosso,
it is me again, with another dumb question :D, I’ve found the following error regarding the opening of .fchk files in GaussView 6.
“Missing or bad data: Atom (or atom modified) types line number 4789
here the line:
#100C_3 #100C_3 #100C_3 #100N_R #100C_3
#100C_R #100O_R #100C_3 #100C_3 #100C_R
#100O_R #100N_R #100N_R #100C_3 #100C_R
#100O_R #100C_3 #100N_R #100C_3 #100C_R
#100O_R #100N_R #100C_3 #100C_R #100O_R
#100C_3 #100C_3 #100C_R #100O_R #100N_R
#100N_R #100C_3 #100C_R #100O_R #100C_3
#101S_3+4 #100N_R #100C_3 #100C_R #100O_R
and here the related input file:
%nprocshared=6
%mem=30GB
%chk=OCH3_cut.chk
# opt oniom(b3lyp/6-31+g(d,p):pm6:uff) scf=(qc,noincfock) geom=connectivity
STRUCTURAL PROTEIN
The job terminated without any problem. What is wrong with that lines? Thank you for your help.
Kind regards,
Carmine
#transition states #inputcoordinates
I am trying to find the barrier energy for the isomerization of maleic acid to fumaric acid. I am using Gaussian 16 and Gaussview for the first time this semester. Previously, I had only used WebMO but only for one semester. I am still a novice Gaussian user..
My professor has suggested replacing the double bond with a single bond + the needed H atoms, manually varying the dihedral angle for one side of the reactant molecule in a B3LYP/6-311G opt+freq run, then looking for an imaginary frequency.
I am hoping for something more efficient than this tedious trial and error approach. After reading your blog posts “On the ‘art’ of Finding Transition States”, I want to try using the opt=qst2 keyword suggested in Method 1. When I create the reactant and product coordinate input files, do I need to do anything special to deal with the double bond in each molecule, or do I just use the coordinate map from an optimization of each molecule with the double bond intact?
Thank you for your assistance
David Toelkes
sir,
i want to know how to prepare Gaussian input file for a binary solvent
Sir, while optimizing cluster structure I am getting Error Termination via Lnk1e in /home/g16/l101.exe . with message that RWCPar cannot convert versions. what does it mean?
Dear POONAM BHADORIA,
I am facing same error. can you suggest solution of this error?
I am using gaussian 09 d for optimisation of sulphur containing compound. I have used b3lyp as functional and def2svp for all atoms with scf=QC. Eventhough, first scf cycle is not converging and showing zigzag pattern. Could you please help me asap?
Take on of the structures in the zigzag and use it as a first step for a new optimization.
Hello
I am going to optimize partially ionic organic molecule, so I don’t know where to put the counter ion(chloride ion) in gaussview. whether I put it close to the positively charged atom in organic molecule or performing a 2-D scan.
Could you please let me know what can I do for this situation?
Hi! I have a problem with my molecule in Gaussian. I want to launch a calculation but appears this error:
Severe Error Message # 2070. The processing of the last link ended abnormally. All processing has been aborted.
Run Progress: Link died!
The following are the outfile.
Entering Link 1 = c:\program files\G09W\l1.exe PID= 4848.
Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009, Gaussian, Inc.
All Rights Reserved.
This is part of the Gaussian(R) 09 program. It is based on
the Gaussian(R) 03 system (copyright 2003, Gaussian, Inc.),
the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.),
the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.),
the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.),
the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.),
the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.),
the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon
University), and the Gaussian 82(TM) system (copyright 1983,
Carnegie Mellon University). Gaussian is a federally registered
trademark of Gaussian, Inc.
This software contains proprietary and confidential information,
including trade secrets, belonging to Gaussian, Inc.
This software is provided under written license and may be
used, copied, transmitted, or stored only in accord with that
written license.
The following legend is applicable only to US Government
contracts under FAR:
RESTRICTED RIGHTS LEGEND
Use, reproduction and disclosure by the US Government is
subject to restrictions as set forth in subparagraphs (a)
and (c) of the Commercial Computer Software – Restricted
Rights clause in FAR 52.227-19.
Gaussian, Inc.
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—————————————————————
Warning — This program may not be used in any manner that
competes with the business of Gaussian, Inc. or will provide
assistance to any competitor of Gaussian, Inc. The licensee
of this program is prohibited from giving any competitor of
Gaussian, Inc. access to this program. By using this program,
the user acknowledges that Gaussian, Inc. is engaged in the
business of creating and licensing software in the field of
computational chemistry and represents and warrants to the
licensee that it is not a competitor of Gaussian, Inc. and that
it will not use this program in any manner prohibited above.
My molecule is a pentasaccharide and I used DFT, 6-311G+(d,p), with CPCM as solvation method. What is wrong?
Thank you for your assistance
Myriam
Dear Dr. Borroso,
I have been trying to perform AIM analysis using the AIM2000 package. The molecular system is a tetramer form, with nearly 170 atoms. The wavefunction file (.wfn) are around 20MB size. However, when I trying to open the .wfn file using AIM2000 package, it shows ‘illegal primitive centre’.
Kindly help me out in comprehending and troubleshooting the issue. Is it sue to the large molecular system, which is resulting in heavy size .wfn file and thus AIM2000 cannot open it up??
Looking forward to your response
Thanks and regards
Pankaj
Happy New Year, dr. Barroso! I want to ask about radical calulation with gaussian. If I have neutral radical (charge=0), the multiplicity should be ,,2″? If charge -1 or +1 , multiplicity is also should be 2? Or I should use additional command like URHF?
My calculation:
#P B3LYP 6-31+G Opt Freq NoSymm SCRF=(Solvent=Water,Read)
Do you have some suggestion?
#gaussianerror
Dear Dr. Borroso,
I am trying to monitor the binding energies of metal ions (+2 and +3) with crown ethers and other macrocycles. I would like to monitor these in both gas and solution phases and potentially use B3LYP/6-311G++(d,p) and LANL2DZ basis sets. However, my ions do not want to be anywhere near the inner diameter of my cavitand despite everything that I have read. I have experimental data and I would like to visualize/ calculate the structures.
Can you help?
I can email my input files.
# B3LYP/genECP opt freq
# scf=(tight,maxcycle=5000) 5D
****
2 1
Pb -1.55760 1.08190 0.00000
O 11.19850 7.38130 -4.70100
C 12.44490 7.24020 -5.38520
H 12.67870 8.07390 -5.82420
H 12.37540 6.54810 -6.06060
C 13.49530 6.87640 -4.38610
H 13.27960 6.02700 -3.97010
H 14.35690 6.79390 -4.82390
O 13.53980 7.90830 -3.40270
C 14.44990 7.61320 -2.35100
H 15.35750 7.59740 -2.69230
H 14.24980 6.74280 -1.97330
C 14.31390 8.67110 -1.30280
H 15.03300 8.59210 -0.65650
H 14.36330 9.55010 -1.70960
O 13.05380 8.50520 -0.65330
C 12.73000 9.60280 0.18480
H 12.68290 10.41680 -0.34000
H 13.41660 9.71610 0.85970
C 11.40940 9.34270 0.83990
H 11.45780 8.53530 1.37550
H 11.17770 10.08260 1.42240
O 10.42110 9.19470 -0.17540
C 9.11180 9.09880 0.38220
H 8.79970 9.97910 0.64470
H 9.13030 8.53460 1.17030
C 8.18670 8.51660 -0.63710
H 8.47250 7.61820 -0.86550
H 7.28870 8.46560 -0.27350
O 8.18970 9.33540 -1.80570
C 7.17360 8.96210 -2.73470
H 7.20070 9.58100 -3.48160
H 6.31110 9.06780 -2.30160
C 7.26260 7.54480 -3.28430
H 7.08190 6.92610 -2.55950
H 6.56110 7.42990 -3.94470
O 8.50690 7.18060 -3.88410
C 8.92500 8.08910 -4.89680
H 9.15010 8.94350 -4.49570
H 8.20130 8.23200 -5.52530
C 10.11800 7.54340 -5.61890
H 9.89660 6.68820 -6.01960
H 10.37830 8.15150 -6.32830
C O H 2
6-311G(d,p)
****
Pb 2
LANL2DZ
****
Pb 2
LANL2DZ
I fully believe that you should update this site ASAP
Hi everyone,
I’m looking for a transition state of a nitrogen nucleophilic attack to a protonated formaldehyde. I perfomed a relaxed scan varying the N-C distante from 1.5 to 3.0 A but there is no a maximum in the energy surface.
Have you already had a similar problem?
There might not be a transition state in this case. Please try the QST2 or the TS options before going to the scan.
I hope this helps
Hi Joaquin,
I have a question regarding the “DoVacuum” tag in Gaussian 09.
My understanding is that when using this tag, G09 will compute the free energy of solvation by performing optimisation in the gas and solvent phases.
I’m curious about the procedure used by G09 and I imagine it must be one the following but I’m unsure as to which it is:
1. Solute structure optimised in solvent with frequency calculation in solvent + gaseous structure optimised in vacuum with frequency calculation in vacuum,
2. Solute structure optimised in solvent with frequency calculation in solvent + gaseous structure used from solvent output but placed in vacuum with frequency calculation in vacuum,
or
3. Solute structure optimised in solvent with frequency calculation in vacuum+ gaseous structure used from solvent output but placed in vacuum with frequency calculation in vacuum.
I imagine G09 must used ideal gas statistical mechanics equations to compute the free energy change. I’m not sure how physically sounds it is to use procedures 1 and 2 in this case which leads me to believe 3 is most likely. Though I wonder if you can offer any insight.
Thanks.
Best wishes,
Matt
P.S. your blog has proven to be very useful!
Nb -0.48 & C – 0.026 . Nb ration shell not exceed 16:1 . what is the answer
Hello, if I want to calculate the electron-phonon factor of my system in Gaussian 16, what should I set in input files?
Thank you very much!
Hello,
How do I set-up a calculation in gaussian to calculate the electronic strucutre of a periodic system? For example, if I want to calculate the electronic structure of PZT using DFT keyword LSDA, how do I set-up a calculation to generate the electronic structure of the periodic system?
Thank you so much!
Michael
Hi
I’m tried to study the excited state for BODIPY organic solar cell that have 564 electrons using the following input file on orca program.
“!RIJCOSX RI-B2PLYP def2-TZVP def2/j def2-TZVP/c Grid5 finalgrid6 gridx6 TightSCF CPCM(Chloroform) pal4
%maxcore 4000
%tddft
nroots 20
tda false
end
* xyzfile 0 1 5_geoopt_chcl3.xyz”
But the calculation end by “orca finished by error termination in MP2” and it end before doing MP2 iteration!
So how I can solve this proplem?
Hi,
I am trying to do B2PLYP calculation using aug-pc2+2d basis set developed by JL Martin for HClO4 and Cl2O7 molecules. My calculation stops after doing 1st SCF calculation without giving any error messages. Can you please help me with this.
Thanks,
Tanusree
Hi,
I am trying to optimize two noncovalently interacting molecules with desired orientation. For free optimization the orientation changes, so I have tried with freezing few atoms. Can please tell me the exact difference between free and freeze optimization? am I going to lose any important chemical quantity for this specific optimization?
Hi,
I am beginner of Gaussian. I have a difficulty in draw the structure. I have the available geometric parameter of structure, but when I use the builder to change the dihedral (x) then I change the the bond lengh. But after that the dihedral(x) will be change,so is there any way to fix it? (I just draw the structure, not yet calculate) I know we can use modredundant to fix the bond lenght, but it use to fix the geometric parameter after finishing calculation, for me, I just want to draw the structure with the geometric parameter that I want and then calculate and see how the parameters change.
Thank you.
Hi everyone,
I am a beginner of Gaussian and have to run an ONIOM calculation on a protein-ligand complex. For the unknown ligand I had to specify the connectivity. I add it below the atomic informations and now I get this error, which markes the first line of this added connectivity:
Error parsing secondary structure:
QPErr — A syntax error was detected in the input line.
5703 5704 3.0 5705 1.5
‘
Last state= “Top”
TCursr= 101 LCursr= 1
Here are the calculation specifications:
%rwf=DYRK.rwf
%nprocshared=16
%mem=10000MB
%chk=DYRK.chk
# opt oniom(b3lyp/3-21g:pm6:amber)=embedcharge
scrf=(solvent=water,oniompcm=x) maxdisk=50000MB
I created the input file with GaussView but had to adjust the hydrogen link atoms and add the connetions of the ligand.
Can someone tell me what I have done wrong? I thougth of the emty line between atom informations and connectivity entries or do the connetivity needs to start with the first atom?
I am clueless, please help.
Dear Sir,
I installed UCA-FUKUI on Win 7 (64X) perfectly but there are some problems , sometime I deal with an error by this content ”Run-time error ’62’: Input past end of file”.
How should I remove this error?
I would be appreciate by your guidance.
Hello,
I am in the beginning of my research and I am facing a certain problem of finding transition state for my reaction. I found in literature the TS but I don’t succeed in finding it with Gaussian.
I am scanning the bond I want to break and take the highest energy point from the scanning profile. For that point I tried to do opt(ts), opt=qst2 and qst3 but none of them gave me the transition state.
The TS is a bi-radical so I did stable=opt to confirm that it is actually an open-shell(unrestricted). From that stable.log file, I did further scanning but it shows no result (there is no option for viewing a scan profile).
Can you explain me why is it like that and what is my mistake?
Thanks in advance
Hi Dr. Barrosso!
I’m struggle to get an optimized structure of triphenyl phosphine sulfide. It seems that Guassian has a hard time in general with tetrahedral phosphorus centers with multiple phenyl groups! Calculations run for days without converging or land on transition states. The jobs take numerous steps of nearly the same energy, which might hint at a flat PES surface?
I’m using Gaussian 16 with a M06-2X/6-311G+(d,p) method with keywords opt freq=noraman scrf=(solvent=acetonitrile). My original geometry came from an xray crystal structure
I’ve tried an initial freq calculation, a freq calculation at every step, changing the max step size from 30 to 10 and confining the geometry to C3v, none of which panned out!
Do you have any advice? I’ve asked just about everyone in the my department (UCSD) and I’m getting a little desparate!
Hi John,
Indeed you may have a hard time getting to a minimum with such a molecule. I would pre-optimized it with Hartree-Fock and then move to a second optimization with DFT. You will end on a minimum which most likely wont be the global minimum. These flat PES surfaces are pesky to get so it depends on what you need to learn from the system, if you need to calculate some electronic properties, maybe you wont see much difference between minima. If you need to learn something from the crystal at the crystallographic structure I would only optimize the H atoms.
You can use the SCF=QC or XQC in either method to help the convergence.
Additionally you may run a single point and a freq calculation, and try distorting the molecule in the direction of the negative frequencies to get the initial structure of your optimization.
I hope this helps.
how do I calculate the vibrational polarizability and hyperpolarizability using gaussian?
Hi Dr. Barrosso!
First of all , thanks for your blog. It is very helpful and I learned a lot.
I am trying to estimate the ionization spectra for simple molecules ( less than 10 atoms )
can you guide me to the steps I should follow. ( I am using Gaussian 16 )
I mange to calculate the ionization energy to the molecules , but my question is how I can estimate the spectrum ?
From where I can get the intensities ?
I used CIS and TDDFT to calculate the excitation states. How I can plot the spectrum.
Dear Abdur,
I’m afraid I don’t know how to do it, but if you find out please share it with the community either here or elsewhere.
Sorry I couldn’t help.
Hi
I’m going to optimize an organometalic anion via gaussian.
I’d like to know if optimization of molecular ion is possible via gaussian in a way that the complex remain in its charged state or not, if yes, then how?
By the way, I’m a geologist and the complex I’m going to optimize is stable at pH=2
its a gold (I) ion bond to to dodecanethiol that with charge=-1
——–
here is my input:
%mem=1GB
%nprocshared=1
%chk=C:\Users\Tick_PC\Desktop\Au-ddt\Au-charged\RSAuSR.chk
# opt b3lyp/6-311+g(d,p) pop=mk extrabasis iop(5/13=1)
Title
-1 1
S -11.15100000 -2.23000000 -0.20000000
C -4.09800000 -0.13400000 -2.82700000
C -3.15100000 1.00200000 -3.22500000
C -5.49200000 0.35500000 -2.41900000
C -1.73600000 0.52200000 -3.56500000
C -6.44700000 -0.78100000 -2.04200000
C -0.80600000 1.64200000 -4.03400000
C -7.84400000 -0.28900000 -1.64600000
C 0.59200000 1.10600000 -4.34800000
C -8.77500000 -1.41800000 -1.18900000
C 1.51300000 2.21600000 -4.85500000
C -10.17000000 -0.93500000 -0.78800000
C 2.89300000 1.68100000 -5.20100000
H -4.19100000 -0.83500000 -3.66600000
H -3.65700000 -0.69500000 -1.99300000
H -3.57100000 1.53000000 -4.08900000
H -3.09200000 1.72900000 -2.40500000
H -5.39800000 1.04300000 -1.56900000
H -5.92700000 0.93000000 -3.24600000
H -1.79800000 -0.24500000 -4.34800000
H -1.30200000 0.03500000 -2.68100000
H -6.01600000 -1.35000000 -1.20900000
H -6.53800000 -1.47500000 -2.88700000
H -1.23000000 2.11800000 -4.92700000
H -0.74000000 2.41400000 -3.25800000
H -8.29800000 0.23300000 -2.49700000
H -7.75100000 0.44500000 -0.83600000
H 1.02300000 0.65100000 -3.44900000
H 0.52000000 0.31700000 -5.10700000
H -8.86200000 -2.15200000 -2.00100000
H -8.31000000 -1.93500000 -0.34000000
H 1.07700000 2.68500000 -5.74600000
H 1.60900000 2.99700000 -4.09200000
H -10.65000000 -0.43300000 -1.63400000
H -10.09500000 -0.20900000 0.02800000
H 3.37100000 1.23200000 -4.32300000
H 3.53600000 2.49100000 -5.55800000
H 2.83400000 0.92200000 -5.98600000
S -14.63000000 -3.09900000 -3.08200000
C -21.91700000 -6.16300000 -2.92200000
C -23.27600000 -6.24000000 -2.22100000
C -20.91800000 -5.24500000 -2.20900000
C -24.29900000 -7.10100000 -2.97000000
C -19.55100000 -5.18500000 -2.89700000
C -25.63400000 -7.24000000 -2.23700000
C -18.55100000 -4.27600000 -2.17400000
C -26.61700000 -8.09900000 -3.03600000
C -17.21100000 -4.14900000 -2.90700000
C -27.93800000 -8.27400000 -2.28900000
C -16.20800000 -3.24000000 -2.19400000
C -28.90500000 -9.15600000 -3.06400000
H -21.49300000 -7.17300000 -2.99600000
H -22.06100000 -5.80500000 -3.95000000
H -23.13400000 -6.64400000 -1.21100000
H -23.68100000 -5.22700000 -2.10400000
H -21.33700000 -4.23300000 -2.15100000
H -20.78500000 -5.59300000 -1.17700000
H -23.87200000 -8.09900000 -3.13400000
H -24.47300000 -6.66500000 -3.96300000
H -19.68400000 -4.82900000 -3.92500000
H -19.13200000 -6.19800000 -2.96300000
H -25.46400000 -7.69200000 -1.25200000
H -26.06600000 -6.24700000 -2.06700000
H -18.37600000 -4.66300000 -1.16200000
H -18.99000000 -3.27700000 -2.06000000
H -26.80300000 -7.63600000 -4.01200000
H -26.17200000 -9.08500000 -3.22700000
H -16.77800000 -5.15100000 -3.02200000
H -17.39800000 -3.76500000 -3.91800000
H -27.75400000 -8.72400000 -1.30500000
H -28.40100000 -7.29600000 -2.11600000
H -16.00100000 -3.62500000 -1.19000000
H -16.62700000 -2.23500000 -2.08200000
H -29.13500000 -8.72000000 -4.04200000
H -29.84400000 -9.26600000 -2.51300000
H -28.48500000 -10.15300000 -3.22300000
Au -12.89100000 -2.66400000 -1.64100000
Au
Def2TZVP
****
Dear Ahmad
As you probably already notice, once you define the charge of your system, that remains the same throughout the course of your calculation, which is normal since the charge results from the difference between the number of electrons and the number of protons and both numbers are fixed.
What you cannot do is fixing where that charge will be located. That will depend on the most stable state obtained by your calculation, which is ultimately what you want to obtain.
I hope this helps.
Sir
I am trying to optimize a rhodium complex having 81 atoms including Rh, N,P, C, H. I am using # opt b3lyp/gen geom=connectivity pseudo=read. Its been a week and the program is still running. Please suggest what to do.
Chhandasi
Dear Chhandasi,
Well, if it is still running let it be. Sometimes these things take a long time particularly if they have too many electrons as seems to be the case with your Rh and I atoms (even if you’re using pseudopotentials).
Hello.
I’m doing CCSD(T) and CCSD calculations on a series of small molecules in Gaussian09. Several calculations terminated without any problems but one CCSD(T) calculation and one utilizing CCSD gave me this error after about 20 minutes.
‘UNABLE TO DETERMINE LAMDA IN FmD114′
Without these remaining calculations, several months’ worth of work is incomplete. I will appreciate any suggestions. I’ve searched a lot of chemistry forums but nobody seems to know the solution.
Here’s my route section for one calculation:
#p opt=(ts,z-matrix,noeigentest) freq=noraman rccsd(t)/genecp nosymm maxdisk=15950MB
and for the second calculation:
#p opt=(z-matrix,noeigentest) freq=noraman rccsd/genecp maxdisk=15950MB
Hi Alex,
Try using freq=(noraman,calcall), it will take longer but may take care of those pesky calculations.
I hope this helps, please let me know.
Thank you. I usually use calcall by default when locating transition states. But it’s for methods that have analytic 2nd derivatives. If this keyword is used in G09, Gaussian produces an error message stating that no 2nd derivatives are available for this method.
Hi Joaquin,
Long time lurker (thanks for all the info so far!), first time poster.
I’m trying to run a TD calculation on a relatively large organic system (197 atoms, already optimised) in g09 (009e01). The size of the system prevents it from completing within the 12h wall time limit of our HPC cluster, even with nstates=2. I can’t figure out how to restart the job using either the chk or rwf files.
Using the following route section:
#P wB97XD/6-31++G** TD(nstates=10, restart) scf=yqc scrf=(pcm, solvent=water) Int(grid=ultrafine) NoSymm Test
I receive the error:
No CIS info on chk file.
Trying to restart via the RWF doesn’t work either.
Is there a way to reliably restart TD-DFT calculations? I’ve tried using DMTCP checkpointing as an alternative but can’t get it to work.
Thanks very much,
Charlie
Hello Charlie,
It seems your computational resources are very limited if you cannot complete the calculation for nstates=2 in 12 hours. My guess is the number of processors you’re using is too low for it to work.
The restart keyword should be working but another way to do it is by calculating just a few states, say nstates=5 and then run a second calculation with (nstates=5,add=5) geom=check guess=read in order to read the first few calculated and then add another set of states.
Another way it could work would be if you performed a CIS calculation first with only singlets but your level of theory and the number of atoms seems too large for such a short computing time available.
I would try to use a more crude approximation by decreasing the number of basis functions, say 6-31G or even 3-21G just to get it started and find the source of the problem. Also I would remove scf=yqc and Int keywords just to let the calculation move forward and then progressively increase the number of keywords just to isolate the error.
I hope this helps
Dr. Barroso – I am using turbomole and it generates .wfn file. Do you have any idea on converting .wfn files to .wfx file?
Thanks
Subrata
Hi,
I just came across your page as I searched an error from my log files of my calculations. I’m a masters student and I am struggling some of my test DFT calculations and getting this error..
%chk=toluene.chk
%mem=400mw
%nproc=4
Will use up to 4 processors via shared memory.
————————–
#N opt freq b31yp/6-31g(d)
————————–
QPErr — A syntax error was detected in the input line.
#N opt freq b31yp/6-31g(d)
I’m new to computational chemistry as project is organic based but due to everything happening I cant go into the lab. Could you please help me?
Also do you have any tips on calculating the transition state
Hello,
The name and syntax of the functional you’re trying to use is B3LYP but you typed B31YP so you need to change that number 1 for the letter L. Gaussian is not case sensitive.
For TS calculations, please search for a series of posts on this blog titled “the art of finding transition states”.
I hope this helps
#guassian #grouptheory #symmetry #Irrep
Dear Joaquin,
I noticed that when I run calculations in Gaussian of molecules with C2 or Cs symmetry, the irreducible representations of the molecular orbitals are not printed in the ‘Molecular Orbital Coefficients’ section of the log file.
The calculations are running with the appropriate point group symmetry, as the ‘Full point group’ line says C2 or Cs.
I use the ‘pop=full’ keyword. In the ‘Population analysis using the SCF Density’ section, in the ‘Orbital symmetries’ section, the irreducible representations of the orbitals in the appropriate point group are listed.
However, in the ‘Molecular Orbital Coefficients’ section, the irrep is not listed next to the occupancy. For example, my calculations with C2v symmetry print ‘(A1)–O’ for an occupied orbital with A1 symmetry, but the Cs and C2 calculations just print ‘O’ without the irrep. This is what happens in my calculations with C1 symmetry, but I do not know why it happens with C2 and Cs point groups too.
I tried the keywords ‘IOp(4/9=100)’ and ‘symmetry=on’ but they did not remedy the problem.
Thanks in advance,
Jack
Dear Jack,
Have you tried re-orienting the molecule? Try making your Cs or C2 axis lie over the z-axis and use the cartesian frame of reference to define your symmetry operations, e.g. place the atoms which are supposed to be on the sigma-v plane on the xz plane and so on.
Gaussian tries to re-orient the molecule to get advantage of the symmetry but it’s better to help it.
I hope this helps!
Hello Professor, I’d like to know what the entropy variation of a system translates into. I would be grateful for your help.
#visualization #psi4
Respected Sir,
I want to know which visualization software you prefer to visualize Psi4 outputs.
Thanks in advance.
Rohan
I don’t use Psi4, sorry. Maybe try Chimera or VMD, those are free. Chemcraft is my favorite but GaussView is just very easy to use and I’m getting lazier by the minute.
I hope this helps
Hello. I am doing a CCSD(T) geometry optimization on a series of molecules. One of the geometry optimizations took about 2 weeks even though an analogous molecule with the same number of basis functions took less then 2 days to converge to a minimum. After 30 iterations, the calculation aborted with the ‘error’ message about exceeding the maximum number of iterations. I checked energies at different geometry optimization steps and noticed that the optimization had taken the molecule further from the minimal energy value so far. Furthermore, the bondlengths are more reasonable for the optimization step corresponding to the minimal energy value so far: the molecule should be symmetric (and it is at the 4th optimization step) but it’s becoming a bit too asymmetric as the optimization progresses. Also, the energy seems to only change by a miniscule amount in the last iterations. I used the optimized geometry obtained from a CCSD calculation as the initial guess, so my initial guess should be fine.
My route section:
#p opt=z-matrix freq=noraman rccsd(t)/genecp maxdisk=15950MB
A mixed aug-cc-pVTZ-PP/aug-cc-pVTZ basis set was used in both CCSD and CCSD(T) calculatons.
Now, I’m not sure that simply increasing the number of iterations will help… Any advice would be greatly appreciated!
Dear Dr Joaquin Barroso
I am trying to calculate the Spin Orbit Coupling (SOC) of some molecules.
I calculated the absorption and emission wavelength in singlet state
Could you help me, how to calculate SOC from S1 (or S2… ) to T1 (or T2…) transition states.
Please tell me the method and process.
Thank you very much
Dear Dr. Joaquin Barroso,
I want to do BSSE correction of H3O+(H2O)4 system, So for this, I am giving keyword conterpoise=5, But getting error.
Can you please tell me what keyword I should use or how to do BSSE calculation of H3O+(H2O)4 system.
Thank you
hello professor,I am trying to create a wfn file for guanidinium and water interaction.to optimize the structure ,I am getting following error,
Add virtual bond connecting atoms H12 and H9 Dist= 3.27D+00.
Error parsing secondary structure:
QPErr — A syntax error was detected in the input line.
gua_inta.wfn
‘
Last state= “Top”
TCursr= 104 LCursr= 0
Error termination via Lnk1e in C:\G09W\l101.exe at Sat Jul 04 10:50:05 2020.
Job cpu time: 0 days 0 hours 0 minutes 0.0 seconds.
File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 1 Scr= 1
I have used the input below,
%chk=C:\Users\Soumyadeep Saha\Documents\gua_inta.chk
# opt freq b3lyp/6-31g density=current geom=connectivity counterpoise=2 out=wfn
gua_inta
0 1 0 1 0 1 0 1 0 1
C(PDBName=C,ResName=UNL,ResNum=1,Fragment=1) 0 -5.75200000 2.63500000 -0.45700000 H
N(PDBName=N,ResName=UNL,ResNum=1,Fragment=1) 0 -5.05200000 3.80600000 -0.09700000 H
N(PDBName=N,ResName=UNL,ResNum=1,Fragment=1) 0 -5.03300000 1.52100000 0.01000000 H
H(PDBName=H,ResName=UNL,ResNum=1,Fragment=1) 0 -4.00500000 1.53100000 0.03200000 H
H(PDBName=H,ResName=UNL,ResNum=1,Fragment=1) 0 -5.46900000 0.68300000 0.37400000 H
N(PDBName=N,ResName=UNL,ResNum=1,Fragment=1) 0 -7.01900000 2.64200000 0.16600000 H
H(PDBName=H,ResName=UNL,ResNum=1,Fragment=1) 0 -7.86300000 2.41400000 -0.35000000 H
H(PDBName=H,ResName=UNL,ResNum=1,Fragment=1) 0 -7.15900000 2.98700000 1.10900000 H
H(PDBName=H,ResName=UNL,ResNum=1,Fragment=1) 0 -4.14500000 3.96400000 -0.44500000 H
O(PDBName=O,ResName=HOH,ResNum=2,Fragment=2) 0 -2.36200000 2.74400000 0.03800000 L
H(PDBName=H,ResName=HOH,ResNum=0,Fragment=2) 0 -1.39200000 2.74400000 0.03800000 L
H(PDBName=H,ResName=HOH,ResNum=0,Fragment=2) 0 -2.68600000 3.10200000 -0.80400000 L
1 2 1.0 3 1.0 6 1.0
2 9 1.0
3 4 1.0 5 1.0
4
5
6 7 1.0 8 1.0
7
8
9
10 11 1.0 12 1.0
11
12
gua_inta.wfn
Dear Dr. Barroso
I am doing a optimization of a organic polymer.
After running for 5 hrs I get an error ” NB too large for integers in this machine ”
Thank you
Dear Carlos,
It seems you need a bigger computer :-S
Try performing a partial optimization
Or try optimizing a shorter section. Or try going to a lower level of theory; I ignore which one you’re trying but go to a semi-empirical method or even to Molecular Mechanics methods.
I hope this helps
Hi Dr. Barroso,
I have a couple questions regarding TD-DFT calculations. I am looking for change in dipole moment between ground and excited states on a relatively simple organic compound. I am curious as when to use the keyword ‘density’ in my calculations. The use of density gives me back very different results for the dipole moment.
I appreciate all the help,
thank you
DM
Hi Daniel,
Very cool question, it might even get a post on its own but for the time being here’s a quick answer.
If you do TDDFT and don’t use the DENSITY keyword, you’re implying the use of DENSITY=CURRENT which applies to the lowest excited state of the number of states you’re requesting in the route section, say TD(NSTATES=5), you’re getting the density of the first excited state which may or may not be the state of interest.
I would run three calculations: 1) DFT for the ground state. 2) TDDFT, request as many states as you need/want, analyze the previous calculation and select which is the transition you’re most interested in, and 3) request the density of the Nth state of interest to be recovered from the checkpoint file with the following route section:
# TD(Read,Root=N) LOT Density=Current
Guess=Read Geom=AllCheck
replace N for the Nth state which caught your eye in 2) and LOT for the Level of Theory you’ve been using. That should give you the dipole moment for the Nth excited state and you can compare it with the one in the ground state calculated in 1).
Let me know if it worked for you.
Have a nice day!
This worked great! I was able to determine a large increase in dipole in the excited state in comparison to the ground state. Thank you very much!
I’m glad I could help 🙂
Dear Joaquin
I want to do Hirshfeld surface analysis with MultiWFN, but I get this error:
Couldn’t find Gaussian path defined in “gaupath” variable in settings.ini
Input the path of Gaussian executable file, e.g. “d:\study\g03w\g03.exe”
Unfortunately I don’t know how I must do.
Please help me.
Thank you in advance
Dear Dr. Joaquin Barroso,
I have a trivial test.gjf file that runs to completion in the following x86_64 processor type and gaussian version combinations:
AMD EPYC + g09
Intel + g09
Intel + g16
This combination however ends with a very short test.log and no “Normal termination …” at the end.
AMD EPYC + g16
This is using the recompiled bsd binary distribution from the Gaussian installation CD.
Are you familiar with a reason this might happen?
Thank you in advance –
JW
Dear Virginia,
I’m afraid I’m not. Can you run other test calculations in the AMD EPYC g16 combo? I would request the assistance of Gaussian directly for matters regarding installation; their software is expensive enough so as not to take advantage of their excellent online service.
Have a nice day!
Dear Joaquin,
I did run a series of DFT calculations with both Gaussian09 and Gaussian16. Quite a lot of my structures have a small negative frequency in the G09 calculations while G16 calculations on the exact same geometry show no negative frequencies. The motion of the vibrations are all the same, it is only that the assigned frequencies differ.
I tried to find out how the two version treat the vibrations differently but couldn’t find a lot information. Do you by any chance know what is happening here?
Thanks in advance and for keeping this webpage alive!
JB
Dear Julian,
The official website specifies some changes between versions in the speed with which they’re calculated, some differences are to be expected, I suppose.
https://gaussian.com/gdiffs/
Now, when you say small negative frequency, I assume you mean in value and not intensity. A rule of thumb is to consider a negative vibration between -100 and 0 cm^-1 (some may cut it at -50 cm^-1) as noise. Therefore, if your neg freq is -10cm^-1 is hard to know if it is -10 or +10 (due to the accuracy with which they’re calculated). I wouldn’t worry too much if that’s the case but you could try to stick to a version, and modify the structures according to the neg frequency (should there be one) and reoptimize them in order to get rid of those pesky negative values.
I hope this helps.
Thank you for reading, that is what truly keeps this webpage alive.
Cool initials, BTW 😉
Dear Joaquín,
First of all thank you very much for running the blog – it has helped me a lot with my comp chem education (still a total beginner by the way)!
Just a small question here: let’s say that I have the optimised structure of the ozone (O3) molecule in hand, and now would like to obtain the optimised structure of the first excited state of O3 (guess we can call it ‘O3*’ for the sake of this argument) by promoting one electron from the non-bonding MO to the pi* MO. In particular, I’m interested in the energy levels of FMOs of O3*. Thus, I was wondering if Gaussian could be used for this purpose, and how should I approach this type of calculation (I’ll admit this part might be time-consuming for you!)? I had a look into SAC-CI and CASSCF, but the lack of quantum chem background doesn’t help me much!
Really appreciate your time reading this comment, and I hope to hear back from you!
Best Regards,
HD
Dear Huan Do
I’m glad to know you’ve found the blog useful.
If I understand your question correctly, you could benefit from a couple of posts in here about Natural Transition Orbitals.
https://joaquinbarroso.com/?s=natural+transition+orbitals
Let me know if this helps.
Dear Joaquín,
Thank you very much for your reply – NTOs are certainly very helpful with the nature of my study, however they’re just a tad short in terms of information about the energies of the frontier orbitals of the excited state (1st E.S. for simplicity).
To clarify further, let’s take your student Gus’ latest post about NTOs (https://joaquinbarroso.com/2020/08/27/orbital-contributions-to-excited-states/) on the 27th of Aug as an example: The MOs #35 and #36 (HOMO and LUMO respectively) with the occupation number of 0.88135 are no doubt the FMOs of interest. Is there any way we can extract their respective energy (in hartrees) from NTO method?
Once again thank you very much for your time reading through the comments, and I hope to be able to hear back from you!
Best Regards (and stay safe!),
Huan
Hello Sir
Help in fixing this error
Subroutine NAOANL could not find a f-type valence orbital on atom La
Seems like you’re using a very small basis set. Try increasing it but without further information it is very hard trying to provide a solution.
Have a nice day
Hello Sir
Is it possible to calculate excited state using CASPT2 in Gaussian 16 program package? If you possible CASPT2 calculation, would you please help me by giving an input/output file.
Thanks in advance.
Hi,
I am new to computational chemistry and my project now involves the use DFT calculations to find my best sensizer to use in DSSC I am trying to find the best compound.and i want group or team research to work with and have thier advices Do you have a suggestions of that
and first i want to interpret NBO terms such as BD CR RAY.. etc and how to interpret them as pi and sigma and pi* and sigma*. Any advice would be much appreciated!
thankyou alot
Hello Joaquin. First of all thanks for the blog, it is extremely useful. I am new to computational chemistry and theoretical calculations and use of gaussian. I can scan molecules but I don’t know how to do a double scan, that is, modify two dihedral angles simultaneously. When I try to do it in the same way that I modify a single angle, with modreduntat, the system crashes and I get these errors: Old curvilinear step not converged, using linear step
Error imposing constraints
Error termination via Lnk1e in
What could I do?
Thank you very much!
Hello Agustín,
Welcome to CompChem! You can indeed perform a double scan with Gaussian. Say you want to rotate two bonds, then you’re scanning two dihedrals, your modredundant section would look like this:
* 2 3 *
1 2 3 4 S 4 90.0
* 6 7 *
5 6 7 8 S 4 90.0
This would fully rotate bonds between atoms 2-3 and 6-7. You would then get ALL the combinations of those two scans. This is important because sometimes people want to get the two rotations simultaneously, i.e. both bonds rotating synchronically but this is not possible, instead you have to extract the diagonal elements of the scan (that is 0,0; 90,90; 180,180; 360,360 for the case above).
Now the only problem is that if your molecule is too large, or too bulky, or the two scanned bonds are too close, atoms will clash or collide into each other causing the error you’re describing. I’m guessing that is. In that case you conclude they cannot rotate simultaneously.
I hope this helps, have a nice day
UPDATE. As I finished writing the previous reply I realize that I’m no longer sure you can do it with modredundant but even if you can’t, the SCAN option I’m sure it can.
Let me know how it went.
Muchísimas gracias Joaquin!! Pude hacer el scan de dosn angulos diedros con modredundant usando HF y DFT pero con la STO-3g como base, con el resto no deja seguir el cálculo cuando llega a una determinada estructura, seguramente como decís vos los átomos se acercan demasiado. Con “scan” debería armar la Matriz Z no? Nuevamente muchas gracias!
Hola Agustín
Que bueno que te sirvió. Para usar el scan efectivamente requieres la matriz-z pero la puedes generar automáticamente con algún visualizador como GaussView
Hi,
I would like to calculate the properties of the MOF structures or any similar periodic morphology using G09. Is that possible? Any help would be appreciated.
Thank you so much in advance.
nasim
Hello Nasim,
It is in principle possible to calculate periodic structure properties with Gaussian by using PBC (Periodic Boundary Conditions) but depending on what you’re trying to achieve, Gaussian won’t give you a good description; you can’t even get band structure out of it. The best idea would be to move towards VASP or some other code which handles periodic solids and density of states.
I hope this helps
Dear Prof.,
I am doing some TD calculation to find the UV-vis specra using gaussian.
My question is that the curve produced by gaussian is oscillator strength vs the wavelength.
However I need to find the spectrum of the absorbance vs wavelength.
So how to find the absorbance vs wavelength spectrum?
Is there any equation I can apply of software that uses the gaussian output?
I really appreciate your help.
regards
Hassan
Hello Hassan,
Are you using GaussView for visualizing it? If you have the latest version (6.0) allows you to exchange from oscillator strength to wavelength in the setting of the spectrum window.
I hope this helps. Have a nice day
Dear Prof.,
I was trying to obtain NBO plot files of a dimer for visualization of oribtals in multiwavefunction. I used the keywords pop=nboread and $NBO plot file=name $END. I got the results for two systems. But for a third dimer system calculation abruptly stops at the following point in the log file:-
‘NATURAL LOCALIZED MOLECULAR ORBITAL (NLMO) ANALYSIS:
NLMO: NTime= 10000 OffTop= 3.45D-04 Done= 1.00D-06’ without showing any error. 0.38 and 0.39 files come up empty. What could be the issue? This particular system is large with 40 atoms in one molecule, contains 4 Bromine,2 N and 4 oxygen (I have used a dimer) atoms. This is Gaussian 16 and NBO version 3.1. Is there any keyword that can force the job to be completed?
Thank you very much for any help and consideration that you may give to this matter!
Regards,
Remya
Hi Remya,
There has to be something wrong with your input so this isn’t about forcing it. Please copy your full input file here (you may skip the coordinates and connectivity matrix should there be one).
Instead, tryi sending those NLMOs to the checkpoint file with pop=(NBO,SaveNLMOS) in the route section. then you can use your chk and fchk files to visualize them.
I hope this helps. Have a nice day
How to sloppy freeze a dihedral angle within a range in gaussian 09/16 optimization?
I have a very big molecule and I want to optimize the molecule with two dihedral angles being optimized within a certain range. I am using opt=modredundant method in Gaussian 16, Revision B.01.
After some search, I have used the input command as follows:
# opt=modredundant cam-b3lyp/genecp scrf=(iefpcm,solvent=dichloromethane) geom=connectivity scf=(xqc,maxcycle=1200)
.
.
.
.
392 393 1.0 394 1.0
393
394
* 103 220 *
91 103 220 208 F -0.5 -2.0
* 23 300 *
11 23 300 288 F -0.5 -2.0
C H N O 0
6-31G(d)
****
Zn 0
LANL2DZ
****
Zn 0
LANL2DZ
But this method did not work out. It shows the error mentioned below:
The following ModRedundant input section has been read:
D * 103 220 * B
Wanted an end-of-line for input.
Found a floating point number as input.
91 103 220 208 F -0.5 -2.0
?
Error termination via Lnk1e in /opt/Gaussian/g16_expt/g16/l101.exe
Please suggest me how to optimize my molecule by restraining the desired dihedral angles to be optimized within the mentioned range.
Hello Bapan
Sloppy freeze optimizations in Gaussian are a pain in the neck. These calculations are usually cumbersome and not necessarily informative but can be useful sometimes, yet for some reason Gaussian has made some changes around the syntax without much clarification. So, from what I understand there are several things to try, here are some ideas:
Use opt=(modredundant,z-matrix); the syntax requires min max values in that order and since -0.5 > -2.0 that could be causing a confusion but I doubt that’s it; Define your z-matrix in such a way that max and min dihedral angle values are positive quantities instead of -0.5 and -2.0 degrees, you may also achieve this effect by selecting atoms other to 208 and 288 around the bond you’re trying to sloppy freeze. You may also just freeze it in the middle, say -1.2°, since your range is quite tight anyway.
Now, in G16 there is an option called Generalized Internal Coordinates (GIC) with many options to achieve the sloppy freeze, you can exclude values, restrain an upper bound, a lower bound or both (the range you’re trying to get). I’m not familiar with it so I wouldn’t know the exact syntax but if I get some time I’ll play around with it and report it.
I hope this helps
Hello,
I am new to computational chemistry aspects. I have been started using gaussian one year ago. I am using iop(3/124=30) command in g09 revision C01 to include dispersion correction. Is it fine to do so?
There is another issue. I am getting a positive solvent correction value in pcm model. Is it an artifact? Should I take it as zero and move forward with the sole gas phase energy or there is some other path. Please, suggest how to handle such issues.
Dear Abishek,
You will soon realize that most decisions in computational chemistry depend on what you’re trying to achieve. I don’t know what is it you’re trying to do here but if you’re using DFT you could just use empirical dispersion models, say, B3LYP-D3, this will add a dispersion correction to your calculation. You can also use Stefan Grimme’s website and add it after your calculation is done. Search for Grimme’s dispersion in this very same blog. Here: https://joaquinbarroso.com/2017/03/08/grimmes-dispersion-dft-d3-in-gaussian-compchem/
Now for the second part, a positive solvation energy means your molecule is “not soluble” in that solvent, strictly speaking that the solvation is endergonic and therefore not spontaneous.
I hope this helps. Have a nice day
Hi Dr. Barroso
I have a question regarding TD-DFT and orbital visualization. I have optimized the excited state for a compound and I would like to visualize the orbitals. I am having a bit of trouble understanding what orbitals I should be looking at. After excited state optimization (opt td=root1), should I be looking at the homo or the lumo of the resulting optimized S1 structure. I assume I should be looking at the LUMO (major contributor to my excited state) of the excited state structure as the excited electron still have not relaxed down to a ground state. Is it possible that I look at the NTO of the optimized excited state structure?
Hi again!
I’m using a Z-matrix to fix the dihedral angle during optimization of a large molecule (Erbium bis-phthalocyanine). The calculations run fine for a while, but after a seemingly arbitrary number of successful optimisation steps, the calculation fails with the error:
Bond length on Z-matrix line number [x] is not positive. (repeated for several values of x)
Problem with the z-matrix.
Error termination via Lnk1e (etc etc)
Is there a way to prevent Gaussian moving to negative bond lengths? The most recent geometry in chemcraft looks fine, so it seems like a problem with the next step.
Route section:
#P B3LYP/Gen pseudo=read scf=xqc EmpiricalDispersion=GD3BJ Opt=(Z-matrix, maxcycle=3000) Test NoSymm
I’m using the Stuttgart large-core ECP for Er (4f electrons not explicitly treated) and 6-31G* for the rest (tried using Def2SVP but optimisation kept getting stuck in a loop)
Thanks,
Charlie
Hello Charlie
I don’t think I’ve ever found such a thing but you could either use Generalized Internal Coordinates (GIC) if you’re using Gaussian 16 or just define your z-matrix in a different way. Check your final structure and let me know what does having a negative length means, are the attached groups to the bonded atoms interpenetrating each other or what? My guess is this has to do with the way the Z-matrix is defined at the following step of the gradient.
One thing I’d do is take an intermediate geometry (it could be also the one that you call the most recent geometry), one that is going in the right direction, and take it as a starting point for a new optimization, probably re-arranging the atom list to prevent a wrong definition of the problematic bond length.
I hope this helps
Hi Dr. Barroso,
i am studying semi-conducting polymers’ design. In energy calculation of some tetramers, pentamers and hexamers at 6-31G+(d) and 6-31+(d,p) levels i got an error mesage like below:
LinEq1: Iter=993 NonCon= 1 RMS=2.65D-10 Max=4.41D-09
LinEq1: Iter=994 NonCon= 1 RMS=2.75D-10 Max=5.78D-09
LinEq1: Iter=995 NonCon= 1 RMS=2.58D-10 Max=4.89D-09
LinEq1: Iter=996 NonCon= 1 RMS=2.57D-10 Max=4.68D-09
LinEq1: Iter=997 NonCon= 1 RMS=2.68D-10 Max=5.48D-09
LinEq1: Iter=998 NonCon= 1 RMS=2.66D-10 Max=5.00D-09
LinEq1: Iter=999 NonCon= 1 RMS=2.74D-10 Max=5.64D-09
LinEq1: Iter=*** NonCon= 1 RMS=2.78D-10 Max=5.27D-09
CPHF failed to converge in LinEq1.
Error termination via Lnk1e .
Please, help me to handle with this problem.
Pınar
Hi Pinar,
It seems to be a problem with the convergence, start by trying a new initial geometry or a different convergence scheme
I hope it helps.
Hello Sir
Is it possible for a molecule to absorb and emit at the same wavelength? What is the reason behind it?
I’m working on charged Tin porphyrins and got the excitation and emission (fluorescence) wavelength around 400nm.
Hello Joaquin,
I am trying to calculate relativistic effects on Gaussian using DKH2 command. I need to optimize my file and I use the following keywords
#p opt=readfc guess= core M11/gen int=DKH2 scf=(tight,maxcycles=200) .
I am only using a Rh and a 3 main group elements. The basis set is ANO-RCC.
I continuously get this error no matter what I have tried:
Warning: this job cannot use analytic gradients
and so will do many energy evaluations.
If you have the time, could you explain what this means? I hope I am asking the right question.
Thank you,
Pirouz
Hi Pirouz
It means the readfc option is not available. Try deleting it and also maybe the guess keyword.
I hope this helps
Hi Joaquin! You answered my question I feel really dumb but I believe I have found the solution to my problem.
I was using int=DKH2 on my optimization calc. I am guessing these two being mixed together on gaussian give an error. Would you have a more detailed explanation as to why? Basis set ANO-RCC and XC M11.
Thanks!
#EnsurenumberofTS#
Respected Joaquinbarroso,
How can we know that how many transition states will be there in a reaction? I have found one transition state of my reaction but not sure whether this is the only TS?
Hello Sir
Sorry for the repetitive comment Sir.
Is it possible for a molecule to absorb and emit at the same wavelength? What is the reason behind it?
I’m working on charged Tin porphyrins and got the excitation and emission (fluorescence) wavelength around 400nm.
Could you please help me sort out this Sir?
Thank you
H,0,-6.51894045,0.30679045,-0.62172274
H,0,-5.92981156,0.43976535,1.05586158
H,0,-5.45709918,-2.67522149,-1.07145284
H,0,-5.19573423,-1.35237519,-2.23400053
H,0,-3.80329644,-2.22243148,-1.55255149
N,0,3.84990732,-0.54243216,3.01202041
N,0,4.8694467,-0.3879246,3.62996877
N,0,2.86399209,-0.69198799,2.4146221
Na,0,6.63118935,-0.10719016,4.6815026
Recover connectivity data from disk.
Sir getting this towards the end of a g09 calculation, the calculation in neither completing nor terminating.
Pls help!!
Hello mister,
I am trying to compute harmonic frequencies (as part of my PhD program) for malononitrile molecule (C3H2N2) with Molpro Version 2015.1. Level of theory and basis sets are CCSD(T)-F12/cc-pvTZ-F12, even dough optimization converged properly, frequencies with new optimized geometry stops at HESSIAN and never terminated. I tried insistently with different optimized geometries without success. What can we do here? Many thanks, Juan
Some info at the end of the out.file:
PROGRAM * HESSIAN
*** Long output written to logfile /ddn/home3/r2653/Malono/C3H2N2_CCSDT_freq.log ***
Computing numerical hessian using default procedure for command CCSD(T)-F12
Using no symmetry in wavefunction calculations
Running default procedure: HF-SCF000 CCSD(T)-F12
Numerically approximating hessian using central energy differences
Task list generated. Total number of displacements: 462
46 tasks completed, CPU=2d 13h 43m 36s Elapsed=15h 54m 18s
92 tasks completed, CPU=5d 3h 38m 1s Elapsed=1d 7h 50m 38s
138 tasks completed, CPU=7d 15h 30m 50s Elapsed=1d 23h 15m 22s
————————————
and at the end of the log file is wrtitten…
DF-MP2-F12 energy corrections:
==============================
Approx. Singlet Triplet Total
DF-MP2-F12/3*C(DX,FIX) -0.060356509570 -0.006234683467 -0.066591193038
DF-MP2-F12/3*C(FIX) -0.058539670475 -0.006054805992 -0.064594476467
DF-MP2-F12/3C(FIX) -0.058541338948 -0.006200441261 -0.064741780209
DF-MP2-F12 correlation energies:
================================
Approx. Singlet Triplet Ecorr Total Energy
DF-MP2 -0.544152316887 -0.326308804801 -0.870461121687 -224.601165285113
DF-MP2-F12/3*C(DX,FIX) -0.604508826457 -0.332543488268 -0.937052314725 -224.667756478150
DF-MP2-F12/3*C(FIX) -0.602691987362 -0.332363610792 -0.935055598154 -224.665759761579
DF-MP2-F12/3C(FIX) -0.602693655834 -0.332509246062 -0.935202901897 -224.665907065322
SCS-DF-MP2 energies (F_SING= 1.20000 F_TRIP= 0.62222 F_PARALLEL= 0.33333):
============================================================================
SCS-DF-MP2 -0.856019369918 -224.586723533343
SCS-DF-MP2-F12/3*C(DX,FIX) -0.932326540004 -224.663030703429
SCS-DF-MP2-F12/3*C(FIX) -0.930034409327 -224.660738572753
SCS-DF-MP2-F12/3C(FIX) -0.930127028996 -224.660831192421
Symmetry transformation completed.
Number of N-1 electron functions: 12
Number of N-2 electron functions: 78
Number of singly external CSFs: 3408
Number of doubly external CSFs: 5808936
Total number of CSFs: 5812345
Length of J-op integral file: 755.87 MB
Length of K-op integral file: 942.34 MB
Length of 3-ext integral record: 0.00 MB
Memory could be reduced to 347.56 Mwords without degradation in triples
I solved the issue changing the symmetry from off to 0. Thanks and cheers!
after the optimization, it was found that some bonds are missing from the molecule in the optimized structure. i use the basis set LANL2DZ bonds between the cobalt atoms and the oxygen atoms are destroyed (octhedral CoO6)
how i can solve this problem
#fluorescence emission band shape
Hello Sir,
I am interested in simulating fluorescence spectra, I have followed the steps given Guassian SCRF page. I got the emission energy, from that emission wavelength. But I need to calculate the band shape of emission spectra with percentage transition probabilities i,e., LUMO-HOMO (%).
Thanks in advance
#NQR (nuclear quadrupole resonance)analysis
Hi,
can you give me idea about NQR analysis ( how to perform it on gaussian 16 and how to evaluate its .log file)?
Hi Joaquin!
I am doing some calculation with the presence of background charges in Gaussian16. I was wondering if there is any way to visualize the background charges? That way I could be sure that I put them in the right coordinates.
Nishat
Hi,
I used the following input: #p opt=calcfc freq um06l/gen guess=read scf=xqc for finding the optimized structure from the already optimized wavefunction of the stability calculation at the same multiplicity. While I got the following termination: Symmetry not used in FoFCou.
Anyone can help me with this calculation? All the previous discussions about this error were a little far from my input method.
Regards
Karam
Hi Joaquin ,
I want to know how to setup a calculation in Gaussian 09 for a Lithiated quinone. What I want to achieve here is to show that Li-ion has an affinity for the carbonyl moiety. I want to use this calculation to support my mechanism for the Li-ion binding sites. Looking foward to your suggestions. Also, any pointers to a tutorial article that can help me will be amazing.
Thanks a lot!
Ram.
Related question: How to understand QTAIM properties at BCP?
Good day Dr. Barroso,
The concepts that I would like to understand better are (and what I understand about them):
*****K, Schrödinger kinetic energy density: Kinetic energy density tells whether a bond is stabilizing or not. In addition, it indicates how much electron density accumulates at the BCP as the respective electron clouds of the involved atoms approach.
*****L = K – G, Lagrangian density = (-1/4) DelSqRho: I do not understand this property.
*****DelSqVrep = Laplacian of the repulsive contribution to virial field V: I don’t quite get it. What I understand, it would be how shared the electrons are at the BCP.
The question is: how those properties can be understood properly?
Thank you so much in advance,
Andrew
Dear Sir
I am trying to find vibrational frequencies modes for Aminoimidazole carbonitrile. I have optimized the structure using DFT B3LYP functional and started with STO-3G basis to 6-311g(d,p) basis and calculated frequencies. I have encountered one negative frequency. From literature, this is the stable tetramer of HCN. I would like to know if negative frequency always implies a transition state or there can be some reason for this negative frequency.
Thank you,
Chinmai Sai
Dear Dr. Barroso,
Thank You for the great post on the topic and especially for the algorithm block scheme in “The “art” of finding Transition States Part 2 https://joaquinbarroso.com/2016/05/31/the-art-of-finding-transition-states-part-2/“. I wanted to mention, though, that the quick templates for the jobs in these two posts do not include any title section, apparently because it is counted into the molecule specification. As I have never done QST before, I did not expect the title section belonging to the molecule specification, I assumed it is a characteristic of the job. Maybe You should add a footnote in the posts? It took me one additional Gaussian failure and manual read to correct for this <:-)
In deep respect,
Igors Mihailovs
Dear Professor J. Barroso,
Presently I am working on a phosphazene based system. I need to calculate the Electrostatic Activation of the system. I am using a neutral molecule, a distance anionic substituent, and a cationic substituent for interaction with a cyclic aromatic ring for an addition reaction respectively. I am using Gaussian-16W and M06-2X/6-31+G(d,p) level of theory. I also need to work in the gas and SMD solvent model. I need to know what kind of keywords should I use for the job? I designed, 1. optimizing the structures with the above level of theory, then need to check may be stabilization and lastly need to calculate for electrostatic effect or activation from remote charge functional group and external electric field. Could you please suggest to me that the plan is ok and what kind of keywords should I use? I also need to consider the NBO analysis, free energy barrier, and thermocyclic parameters.
Keshab K. Adhikary
Ghent UniversityGlobal Campus,
Incheon, Korea
Dear Sir,
I am using Gaussian 09 software to calculate Excited-state properties. I am using the TD-DFT method to find the excited states, I had given inputs for no of states and also the root of interest. But I am unable to see the excited state energy of that particular state in the output file. Do I need to add any function in the input file for it to show the Energy Value of that state?
Dear Mahesh
The output of a TD-DFT calculation is quite straightforward. I here copy an example taken from the Gaussian website:
Excited State 1: Singlet-A2 4.0147 eV 308.83 nm f=0.0000
=0.0008 -> 9 0.70701
The excitation energy for this particular excitation is 4.0147 eV however, it shows an oscillator strength value of f=0.000 therefore it will not take place.
The output will list in this same format all the requested excitations therefore you can read which of them are the likeliest to take place and with what energy.
I hope this helps
PS I forgot to mention that the excitation energy is expressed in that list in two units: as wavelength in nm (more of a spectroscopists unit) and the equivalent amount in eV (more of a physicists unit).
Have a nice day
Dear Dr. Barroso,
I’m running a vibrational frequency calculation for a molecule using g16. While the calculation seems to finish (Normal termination of Gaussian 16), the results can’t be viewed by GaussView5. I checked the .out file, and there’s the error “Unable to Open any file for archive entry.”
Would you have some guidance where the problem is from?
Thank you,
Arlene
From the .out file:
“Leave Link 607 at Wed Jan 13 18:33:11 2021, MaxMem= 2147483648 cpu: 47.3 elap: 2.0
(Enter /opt/gaussian/16.C.01/g16/l9999.exe)
Unable to Open any file for archive entry.
……
…….
The archive entry for this job was punched.”
Dear Arlene,
Have you solved this problem. I’m encountering the same error in my Gaussian NMR calculation and wondered if you could help if you’ve found the solution.
Thank you,
Ling
Found the answer. It isn’t an error after all. The calculation ran successfully. Thanks
Dear Dr. Barosso,
I am getting a problem regarding NBO calculations.The job ends once the NLMO calculation starts. There is no error termination in the output file, still in error file it s showing segmentation violation. Please help me.
Thank you.
Suvam
Dear Suvam,
I am not sure if my answer will solve your issue, but let’s hope it does.
When running a calculation with Gaussian on a server, that needs NBO/NPA etc calculation, the requested memory for your job should be greater than that you allow to Gaussian.
For instance, when I perform NBO calculations on a server:
– when requesting the same memory (for instance 4G, 8G, 16G, 32G) for BOTH the job and Gaussian, the calculation stops at some point and the error message is left in the output file ‘oom kill’ (oom = out of memmory)
– when requesting twice the memory for the job than Gaussian is allowed to (for instance 8G allowed for Gaussian and 16G requested for the job), I don’t have any problem.
I hope it helps,
Best regards.
Dear Sir,
I have optimized a metal complex through DFT Gaussian software, before optimization the geometry of the complex ( Cu(II) Complex) was square pyramidal but after optimization, we don’t get the same geometry. Kindly comment upon this. Is this optimized structure is accurate?
Dear Joaquin,
Thank you for the great blog and all the excelent tutorials.
I have been trying to get the excited state geometries for a given molecule, using gaussian. After getting the vertical excitations and inspecting the transitions I have been optimizing geometries of S1 and S2 with the following input, from the chk or the vertical excitations:
#CAM-B3LYP/6-311G** TD=(read,NStates=6,Root=N)
#test Geom=Check Guess=Read OPT=(ReadFC)
When changing N=1 to N=2, while the starting geometry is different, the optimized one is the same (same geometry, same energy and same frequencies from a posterior job).
Can this be because both ES geometries are converging to the same minimum in the PES of the ground state? Since I would like to understand what is beyond a large Stokes shift, it would be important to know the geometries for each of these ES. Is it possible to get the geometries of the ES before relaxation to the GS?
Thank you in advance
Best regards
Nuno
#basisset #diffusefunction #hydride
Dear Dr. Barroso,
I have a question concerning the good choice of diffuse functions for hydrogen atoms. I am currently studying a reaction involving a hydride transfer.
Browsing various basis sets on BasisSetExchange, I looked into the basis functions and coefficients for hydrogen atoms and noticed this:
– the difference between 6-311+G** and 6-311++G** is an added ‘s’ function
– the difference between def2-TZVP and def2-TZVPD is an added ‘p’ function
What is the reason for the differences in Pople vs. Karlsruhe basis sets?
Why is the diffuse function an s orbital in one case, and a p orbital in the other ?
How important is that difference and what impact can it have on the accuracy of the calculation?
Thanks in advance!
Hi,
I trying to do BSSE calculation at CCSD(t)/aug-cc-pVTZ level of theory. But it is not going beyond this following massage. I don’t konw why is it not going after 16 iteration Nr.
Can you please help me in this?
Integral buffers will be 131072 words long.
Raffenetti 1 integral format.
Two-electron integral symmetry is turned on.
One-electron integrals computed using PRISM.
NBasis= 614 RedAO= T EigKep= 4.50D-05 NBF= 614
NBsUse= 614 1.00D-06 EigRej= -1.00D+00 NBFU= 614
ExpMin= 2.53D-02 ExpMax= 4.56D+05 ExpMxC= 1.44D+03 IAcc=3 IRadAn= 5 AccDes= 0.00D+00
Harris functional with IExCor= 205 and IRadAn= 5 diagonalized for initial guess.
HarFok: IExCor= 205 AccDes= 0.00D+00 IRadAn= 5 IDoV= 1 UseB2=F ITyADJ=14
ICtDFT= 3500011 ScaDFX= 1.000000 1.000000 1.000000 1.000000
FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0
NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T
wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 200000004 NGrid= 0
NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0
Petite list used in FoFCou.
Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
Requested convergence on MAX density matrix=1.00D-06.
Requested convergence on energy=1.00D-06.
No special actions if energy rises.
Initial convergence to 1.0D-05 achieved. Increase integral accuracy.
SCF Done: E(RHF) = -2180.15958202 A.U. after 12 cycles
NFock= 12 Conv=0.18D-08 -V/T= 2.0003
ExpMin= 2.53D-02 ExpMax= 4.56D+05 ExpMxC= 1.44D+03 IAcc=3 IRadAn= 5 AccDes= 0.00D+00
HarFok: IExCor= 205 AccDes= 0.00D+00 IRadAn= 5 IDoV=-2 UseB2=F ITyADJ=14
ICtDFT= 12500011 ScaDFX= 1.000000 1.000000 1.000000 1.000000
DSYEVD-2 returned Info= 93 IAlg= 4 N= 46 NDim= 46 NE2= 39299865 trying DSYEV.
Range of M.O.s used for correlation: 26 614
NBasis= 614 NAE= 57 NBE= 57 NFC= 25 NFV= 0
NROrb= 589 NOA= 32 NOB= 32 NVA= 557 NVB= 557
**** Warning!!: The largest alpha MO coefficient is 0.49157062D+02
Semi-Direct transformation.
ModeAB= 4 MOrb= 32 LenV= 1957771648
LASXX= 3163437656 LTotXX= 3163437656 LenRXX= 6342778344
LTotAB= 3179340688 MaxLAS= 3445018592 LenRXY= 0
NonZer= 9506216000 LenScr= 19086992384 LnRSAI= 3445018592
LnScr1= 6917057536 LExtra= 0 Total= 35791846856
MaxDsk= -1 SrtSym= T ITran= 4
JobTyp=0 Pass 1: I= 1 to 32.
SymMOI: orbitals are not symmetric.
Spin components of T(2) and E(2):
alpha-alpha T2 = 0.8154115652D-01 E2= -0.2558459117D+00
alpha-beta T2 = 0.4393782477D+00 E2= -0.1523918660D+01
beta-beta T2 = 0.8154115652D-01 E2= -0.2558459117D+00
ANorm= 0.1265883312D+01
E2 = -0.2035610483D+01 EUMP2 = -0.21821951924995D+04
Would need an additional 33861912485 words for in-memory AO integral storage.
Iterations= 50 Convergence= 0.100D-06
Iteration Nr. 1
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
FoFJK: IHMeth= 1 ICntrl= 200 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F
IRaf= 990000000 NMat= 264 IRICut= 330 DoRegI=T DoRafI=T ISym2E= 2.
FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0
NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T
wScrn= 0.000000 ICntrl= 200 IOpCl= 0 I1Cent= 0 NGrid= 0
NMat0= 264 NMatS0= 0 NMatT0= 132 NMatD0= 264 NMtDS0= 0 NMtDT0= 0
Integrals replicated using symmetry in FoFCou.
MP4(R+Q)= 0.45832481D-01
E3= -0.58472822D-01 EUMP3= -0.21822536653D+04
E4(DQ)= 0.69757970D-03 UMP4(DQ)= -0.21822529677D+04
E4(SDQ)= -0.13759976D-01 UMP4(SDQ)= -0.21822674253D+04
DE(Corr)= -2.0477393 E(Corr)= -2182.2073213
NORM(A)= 0.12713530D+01
Iteration Nr. 2
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.0957334 E(CORR)= -2182.2553154 Delta=-4.80D-02
NORM(A)= 0.12877808D+01
Iteration Nr. 3
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.0969684 E(CORR)= -2182.2565504 Delta=-1.24D-03
NORM(A)= 0.12906576D+01
Iteration Nr. 4
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.1003757 E(CORR)= -2182.2599577 Delta=-3.41D-03
NORM(A)= 0.12914343D+01
Iteration Nr. 5
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.1006849 E(CORR)= -2182.2602670 Delta=-3.09D-04
NORM(A)= 0.12916793D+01
Iteration Nr. 6
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.1007203 E(CORR)= -2182.2603023 Delta=-3.54D-05
NORM(A)= 0.12917212D+01
Iteration Nr. 7
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.1007231 E(CORR)= -2182.2603052 Delta=-2.82D-06
NORM(A)= 0.12917192D+01
Iteration Nr. 8
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.1007233 E(CORR)= -2182.2603053 Delta=-1.22D-07
NORM(A)= 0.12917282D+01
Iteration Nr. 9
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.1007202 E(CORR)= -2182.2603022 Delta= 3.07D-06
NORM(A)= 0.12917286D+01
Iteration Nr. 10
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.1007219 E(CORR)= -2182.2603039 Delta=-1.71D-06
NORM(A)= 0.12917291D+01
Iteration Nr. 11
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.1007217 E(CORR)= -2182.2603037 Delta= 2.37D-07
NORM(A)= 0.12917295D+01
Iteration Nr. 12
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.1007219 E(CORR)= -2182.2603040 Delta=-2.82D-07
NORM(A)= 0.12917297D+01
Iteration Nr. 13
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.1007220 E(CORR)= -2182.2603041 Delta=-8.91D-08
NORM(A)= 0.12917297D+01
Iteration Nr. 14
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.1007220 E(CORR)= -2182.2603040 Delta= 5.74D-09
NORM(A)= 0.12917297D+01
Iteration Nr. 15
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.1007220 E(CORR)= -2182.2603041 Delta=-4.51D-09
NORM(A)= 0.12917297D+01
Iteration Nr. 16
**********************
DD1Dir will call FoFJK 4 times, MxPair= 264
NAB= 528 NAA= 0 NBB= 0 NumPrc= 12.
DE(Corr)= -2.1007220 E(CORR)= -2182.2603041 Delta=-2.21D-09
NORM(A)= 0.12917297D+01
Largest amplitude= 1.82D-02
Hello!
I am trying to optimize a geometry of a bimetallic complex with La3 + and Mn2 +. The total load of the system is zero, because the binders have a total load of -5.
The number of electrons at the end is 362. Therefore, the Gaussian 09 only allows multiplicity of singles, triplets, etc.
But Mn2 + has an unpaired electron and in a strong field the ground state is doubled.
But the Gaussian does not allow this calculation. Would anyone know what I can do in this case?
Hi Sir
May I know the best method/software to plot the electron density of porphyrins? Also, it would be of great help if you suggest me some reading on interpreting from density plots.
Thank you
Hi Mr. Barroso, I heard that you are giving wonderful ideas to people here, That’s surely great of you, however you should also update this blog of yours very often
All missing ideas should also be incorporated here in https://joaquinbarroso.com/questions/#comment-86114
Hello sir,
I am optimizing the structure of nanowires at HF/STO-3g*. I have given a key word of SCF(XQC) in the program. Gradient too large for Newton-Raphson — use scaled steepest descent instead- I got a repeated line in the program.
Restarting incremental Fock formation.
>>>>>>>>>> Convergence criterion not met.
SCF Done: E(RHF) = -11475.4265610 A.U. after 65 cycles
Convg = 0.6676D-04 -V/T = 2.0055
Gradient too large for Newton-Raphson — use scaled steepest descent instead.
Gradient too large for Newton-Raphson — use scaled steepest descent instead.
Gradient too large for Newton-Raphson — use scaled steepest descent instead.
Gradient too large for Newton-Raphson — use scaled steepest descent instead.
Gradient too large for Newton-Raphson — use scaled steepest descent instead.
.
.
.
etc
Can you suggest me a solution to solve the problem to optimize the structure. And also can you tell me what are the best basic set and level of theory for optimizing the nanowires arrays in exploring the conformational and conductivity studies.
Thank you sir,
Dear sir, I have to optimise 13 atom transition metal clusters. I have to also study reaction barriers with varying spin multiplicity on that cluster. Most of literature calculations done on Solid state softwares with RPBE/PAW. Which functional should be used for such cluster systems in G16?(I have only 16*4=64 processer, so cost of calculations is another limitation). Thank you.
#convergencefailure
Hi, could you help me with a problem in my calculations?
I am trying to realize Single Point Energy Calculations with Gaussian on relatively large systems. It is not giving an error, and even with the exchange of functional DFT, the calculation does not converge. Now, I’m trying to get the energy analytically, using Newtonian physics, but I’m worried that the description by the mass-spring system (E = 1/2 kx^2), does not include vibrations in the molecule that are beyond displacement in one dimension. Would anyone know how to provide a solution for this problem or show me some references?
Hi Dr. Barroso
I have done geometry optimization at MP2/cc-pvtz level of theory and using this structure, performed excited state calculations at RI-CC2 level. So, should I mention the level of theory as RICC2/cc-pvtz//MP2/cc-pvtz or MP2/cc-pvtz//RICC2/cc-pvtz ?
Thank you, Dr for your great insight into the problem discussed here in your blog and your solution. Am optimizing a zeolite structure using the ONIOM model in Gaussian 09. I assigned the DFT for the high layer and MM-uff for the low layer which was successful after optimization. However, a message an error :
SCUtil_ConnectionGFCHK::Parse_GFCHK()
Missing or bad data: Atom (or Atom Modified) Types
Line Number: 194
appeared on the screen. This prevented the checkpoint file from displaying the result, but the log file displayed the result.
I will appreciate it if you could respond to this problem which I have been trying to solve for a month now.
Hi Dr Barroso,
Thanks for your very interesting blog. I am trying to generate a Franck-Condon spectrum for a fluorophore, but Gaussian is unable to generate the Franck-Condon spectrum in my case. I used TD-DFT to optimize the structure of my molecule in both ground (S0) and excited (S1) states, then I used this syntax for the FC spectrum generation:
%nprocshared=4
%mem=150MW
%chk=molecule_S0.chk
#p geom=AllCheck Freq=(ReadFC,FC,SaveNM) NoSymm
molecule_S1.chk
but I get this error: Data for final state taken from checkpoint file “molecule_S1.chk” Error termination in NtrErr: ntran open failure returned to fopen.
It looks like Gaussian is unable to open the chk file of the excited state. The same error happens if I reverse the ground and excited states (in order to generate an emission spectrum), the second chk file cannot be opened. Do you have any idea how to solve this issue? Thanks a lot in advance!
Have you tried calculating the frequency (with freq=saveNM) seperately from the FC calculation. For example:
1. Optimize ground + freq=savenm
2. Optimize excited + freq = savenm
3.
%chk=molecule_S0.chk
#p geom=AllCheck Freq=(ReadFC,FC,SaveNM) NoSymm
molecule_S1.chk
This has happened to me in the past when I dont seperate each step, that is calculing freq and fc at the same time.
Hi, thanks for your answer! I think that is what I did; more precisely I used:
1- optimization of the ground state: #p opt freq=savenormalmodes b3lyp/6-31g(d)
2- optimization of the excited state: #p opt freq=savenormalmodes td=(nstates=6,root=1) b3lyp/6-31g(d)
Both calculations terminated normally with no imaginary frequencies.
Then I wrote a new input file called absorption spectrum with:
%chk=molecule_S0.chk
#p geom=AllCheck Freq=(ReadFC,FC,SaveNM) NoSymm
molecule_S1.chk
but Gaussian seems to ignore the second chk file…
Hello Sir
i am new on Gaussian 16 Linux version, can you please tell me how to calculate optical absorption spectra of materials using Gaussian
I am trying to calculate absorption spectra for the excited state but I got an error
1. segmentation violation error
2. segmentation fault (core dumped).
can you please help me with how to solve these. please
#p opt=tight freq=(savenm) scf=(xqc maxcyc=200 novaracc tight) int(grid=ultrafine) td=(nstates=10,root=1) Guess=Read Geom=Check b3lyp/6-31++g(d,p) nosymm
……………………………………………………………………………………………………………………..
(Enter /public4/home/sc53688/software/g16/l101.exe)
—–
Title
—–
Atom specifications unexpectedly found in input stream.
Error termination via Lnk1e in /public4/home/sc53688/software/g16/l101.exe
…………………………………………………………………………………………………………………..
Error: segmentation violation
rax 0000000000000000, rbx ffffffffffffffff, rcx ffffffffffffffff
rdx 000000000000e69d, rsp 00007fffa105d3c8, rbp 00007fffa105d940
rsi 000000000000000b, rdi 000000000000e69d, r8 0000000000000020
r9 00002b8ff250bb10, r10 00007fffa105ce20, r11 0000000000000202
r12 00007fffa105d988, r13 0000000000000000, r14 0000000000000000
r15 00000000000003e6
/lib64/libpthread.so.0(+0xf630) [0x2b8ff1ea9630]
/lib64/libc.so.6(kill+0x7) [0x2b8ff23ee657]
/public4/home/sc53688/software/g16/l101.exe() [0x4ac3a5]
/public4/home/sc53688/software/g16/l101.exe() [0x4c811a]
/public4/home/sc53688/software/g16/l101.exe() [0x4f342b]
/public4/home/sc53688/software/g16/l101.exe() [0x4e5abf]
/public4/home/sc53688/software/g16/l101.exe() [0x529376]
/public4/home/sc53688/software/g16/l101.exe() [0x4190d5]
/public4/home/sc53688/software/g16/l101.exe() [0x4138ac]
/public4/home/sc53688/software/g16/l101.exe() [0x410e9b]
/public4/home/sc53688/software/g16/l101.exe() [0x410da4]
I want to compute La-Sr-Co-O cubic structure system using Gaussian09W and want to optimized the structure and generate PDOS spectrum. In this case what will be the IOP term I can use to converge the file??
I am trying to optimize a small molecular structure in S1 state.
I am receiving the following error. “No executable for file l914.exe.”
Can anyone help me to resolve this?
Dear Dr. Barroso,
Thank you for your blog. I have learnt loads and hope to learn more in the future.
I’m just starting out and I came across a copy of “The Molecular Modelling Workbook For Organic Chemistry”. I have been trying to model the molecules from the exercises and I’m stuck on task number 7.
They ask for the delocalised and localised form of the allyl cation. How would I go about to model the localised form of the allyl cation (or radical or anion for that matter)? I sounds like I would have to “break” the conjugation but I cannot find the settings to do so.
Also, any idea if this can be done in Jaguar too?
Any help is greatly appreciated.
Dear Dr. Borroso,
I want to do PIO (principle interacting orbitals) calculations. Is it possible to do it in gaussian or any other packages ? Could you please help me in this.
I am new to pchem.
I am trying to do PE surface between two molecules by placing Li+ ion on top of benzeneze by changing diatance. A new bond is howing after optimization. Then when I chage the distance the lithium atom is moving apet from one of the carbons instead moving apart from the center of benzene. I am using Avagadro to generate inputfile and calculations by Gaussian09.
Answer will be very very helpful.
Hello Dr I just had some questions concerning the poltizman distribution.
On Mon, 26 Apr 2021 at 7:16 AM Dr. Joaquin Barroso’s Blog wrote:
> Purna commented: “I am new to pchem. I am trying to do PE surface between > two molecules by placing Li+ ion on top of benzeneze by changing diatance. > A new bond is howing after optimization. Then when I chage the distance the > lithium atom is moving apet from one of the ca” >
Hello Dr. Barroso,
I am studying the adsorption of CO2 on a cluster surface. I calculated already the adsor[ption energy as Eads= E(cl+CO2)- Ecl- ECO2 (1). I would like to consider the BSSE and, therefore, I performed a counterpoise calculation using Gaussian. The adsorption energy calculated as in (1) is ~ -50 kcal/mol. However, when I perform the Counterpoise calculations (specifying one fragment as the cluster and the other one as the CO2), I get these results:
Counterpoise corrected energy = -2037.605253108439
BSSE energy = 0.013895245552
sum of fragments = -2037.401610987182
complexation energy = -136.51 kcal/mole (raw)
complexation energy = -127.79 kcal/mole (corrected)
As far as I could understand, the corrected complexation energy should be equal to EabAB – EaAB– EbAB (2), where EabAB is the energy of the full system with the full basis sets, EaAB and EbAB are the energy of the a and b fragments, respectively, calculated using the full AB basis set. Do I have to compare this complexation energy (-127.79 kcal/mol) to the ~ -50kcal I have calculated as in (1)? Or should I compare this corrected complexation energy with the raw complexation energy in the above table (136.51)?
Or do I have simply to correct the energy of the fragments calculated using the fragment basis sets by the computed BSSE correction?
I have done this calculation earlier for another system using Orca but the approach seem to me different and I am honestly quite confused.
Thanks in advance for your help.
My best regards,
Valeria
This is a new question. I am trying to model sodium carboxylate ion pairs using g09. I can model the carboxylate ion up to high level. When sodium is added – one or multiple bonds form between carboxylate and sodium. I have tried running job with CPM solvent model for water and including a few water molecules near the ion pair. I am able to successfully model ammonium compounds with a bromide counter ion but the carboxylate is frustrating me.
Dear Bill,
Sorry for the lateness of my response. Try scanning the O…Na distance and plot the energy curve; this might be indicative of what the correct distance for the formation of the ion pair is.
I hope this helps
Hello Sir,
how to open log file of nwchem with gausswiev5 or 6?
You can’t. You may open wfx or wfn files in nwchem. Maybe also fchk files
Hola Dr. Joaquín, hay forma de mostrar el momento de transición dipolar (TDM) en gaussian? O forma de calcularlo a partir del output de gaussian?
Saludos
Hola Adin, el momento de transición dipolar se puede calcular asi:
https://joaquinbarroso.com/tag/transition-dipole-moment/
Asimismo, el output provee el vector en sus componentes x,y,z que se pueden utilizar para visualizarlo con algún programa de visualización o plotting.
Dear Dr,
I have been trying to do a qst2 calculation for the complex involving FAD,retinol and ARG amino resdues But I have got a frequent error like most of the others got,
New curvilinear step not converged.
***** Convergence failure in GTrans *****
The reason behind this is not having the proper atomic order for both reactant and product and in my case, the total number of atoms for both Reactant and product are not equal.Since I am testing a saturation reaction, of course there is a one atom additionally added and I can’t manually fix the atom order either because it won’t help to solve the problem.Is there anyway to solve this error sir?
Thanks
VH
Dear Virangi,
This is a common conceptual problem. Lets say you have a molecule A with 10 atoms (reagent) and upon addition your product is made of 13 atoms. Those three additional atoms (B) should be optimized in the reagent section without A + B interacting. This means you should consider ALL molecules involved in your reaction but if you put A and B 20 Angstroms apart, the algorithm will have problems linking them together, on the other hand if they are only 2 Angstroms apart the optimization of the reagent section might link them together bypassing the TS. So, it’s all a matter of balance
I hope this helps
Dear Dr Joaquin,
How do I convince a friend to communicate effectively with his peers?
Dear Dr. Jaoquin,
#gaussianerror
I am trying to compute magnetic vectors (AICD) by NMR calculations using
#p B3LYP/6-31G* scf=tight nmr=csgt iop(10/93=1)
to get output file for AICD (current density).
But the program is giving an error termination as
Error termination via Lnk1e in /home/macrocycliclab/154034004/gaussian09/g09/l1002.exe
I had already optimised the original structure using the same basis set functions.
Could you help me out in this regard.
Thank you in advance
Laxman Vamshi
Hi Laxmanvamshi,
Please copy more of the final lines of your output so I may understad what went wrong.
Have a nice day
Dear Dr. Jaoquin,
#NBO(orbital-interaction)
I am working on radical cyclization reactions and I am trying to compare orbital interactions from NBO of transition states. My target is to look at n->n* interactions (radical stabilization by lone pair of electrons), and/or n->σ* of the forming bond. My issue is that running NBO doesn’t always show desired interactions.
Is there a keyword or a way to consistently obtain the desired interactions of lone pairs?
would you recommend another way of estimating energies of such interactions?
Many thanks for having such very nice blog.
Cheers,
Abdulkader
Thank you Abdulkader,
There is a keyword but it’s only available in NBO7, not in NBO3.1 which is the one provided with Gaussian. The keyword is CHOOSE and it allows you to choose which NBOs are to be followed.
I hope this helps
Thanks for the valuable video for the blog commenting tips Thanks for a heplful post,
Dear Sir,
I’m trying to manually modify the amount of HF in Minnesota global hybrid functionals such as M06-2X in Gaussian09.
XC energy of M06-2X is expressed as Exc=(x/100)Ex,hf + (1-x/100)Ex,dft + Ec,dft (where x=0.54)
Is the IOP keyword “m062x IOP(3/76=100006500)” right to only increase the HF in M06-2X(default Hf 54%) to 65% with other part of XC energy remain same as M06-2X?
Thank you very much for the useful blog.
I would really appreciate if you could help me.
Thanks.
I’m afraid I don’t have the answer for this one. I understand the IOp is correct but it needs to be used at your risk. I think in principle it should work (whether it’s meaningful or not, thats a whole different question) but I have never tried. Please try it and share your results with us.
Have a nice day
Dear Dr. Jaoquin,
I am trying to calculate Fukui coefficient.
In my folder I have the original optimization .log file that was computed with pop=NBO and I have two .log files for single point calculations named filename_minus.log (the N-1 electrons state) and filename_plus.log (the N+1 electrons state).
The error that I got is:
Traceback (most recent call last):
File “/fukui.py”, line 104, in
salida [indice1]=salida[indice1]+”(1)”; #(f+)=fP-fo
IndexError: list index out of range
Dear Dr. Jaoquin,
I am facing a problem in optimizing a cation using iefpcm model. The job is getting terminated after 270 iterations without converging (Error termination request processed by link 9999). Similar calculations on the neutral molecule are giving normal termination without any trouble. Hence, I think the convergence error is happening due to the charged molecule. Please suggest a solution for the same.
Thanks and regards
Rini
Input file is
%chk=bi.chk
%mem=10GB
%nprocshared=15
#p opt freq b3lyp/gen pseudo=read scrf(iefpcm,read)
opt freq
2 1
H 2.93549900 0.00285100 0.00295400
.
.
.
.
.
.
radii=uff
Eps=8.93
Output error
Error termination request processed by link 9999.
Error termination via Lnk1e in /opt/apps/gaussian/g16/l9999.exe at Thu Sep 2 11:32:26 2021.
Job cpu time: 32 days 11 hours 18 minutes 43.0 seconds.
Elapsed time: 2 days 10 hours 17 minutes 21.3 seconds.
File lengths (MBytes): RWF= 757 Int= 0 D2E= 0 Chk= 58 Scr= 1
Hello Rini,
If you don’t need to optimize it inside the cavity, try optimizing it first in a vacuum and then optimize the result inside the iefpcm cavity. Sometimes, the cavity becomes to restrictive for some molecules if their geometries change too much.
I hope this helps.
Similar calculations on the neutral molecule are giving normal termination without any trouble. Hence, I think the convergence error is happening due to the charged molecule. Please suggest a solution for the same.
Hi sir,
How to simulate emission spectra – fluorescence & phosphorescence spectra of organic compounds in gaussian using gaussview interface. It would be great if you could provide detailed steps.
Looking at the keywords from gaussian scrf & researchgate sites, I understand that the following steps need to be done.
L.O.T. used – DFT B3LYP 6-31G+(d,p)
1. Geometry optimisation of Ground state with any PCM solvent model (noting down E1)
2. Using the output file, TDDFT – Energy TDSCF calculation with any PCM solvent model with nstates = 6. (UV spectrum can be simulated)
3. Geometry optimisation of 1st excited singlet state (root=1, nstates=6) for fluorescence with any PCM solvent model. (noting down E2)
(which file to be taken as input file for this calculation?- GS optimsation or TDDFT UV file? chk or log file?)
4. Frequency calculation for output (or chk) file of optimised structure of excited state
Job – Frequency,
Method – TDSCF, nstates=6, root=1
5. Emission energy = E1-E2.
what is the purpose of equilibrium & non-eqm calculation using solvent. pls tell me how to do all these procedures to simulate fluorescence spectrum, note down emission energies, lambda max of fluorescence & assignment of transition (if it is from LUMO to HOMO, or HOMO-1 ,etc with % contribution) using gaussview.
also, can we use different functionals for Ground state & excited state energy calculations for the same compound.
Please clarify my doubts.
Kind regards
Pearl
Hola Joaquín, vi que tú manejas el programa NBO. Sabes si las versiones más nuevas (NBO7) funcionan con ONIOM? Así decido comprarlo.
Saludos
Hola Bonanata,
No, lamentablemente NBO y ONIOM son incompatibles.
Saludos
Thank you so much for your posts. They are very helpful in my research. Can you please guide me how can we calculate spin orbit coupling matrix element (SOCME) in gaussian? I dont have access of other packages like ADF and BDF.
Thank you.
Dear Kavita,
Thank you for reading, I’m glad you’ve found the blog helpful.
That requires a CASSCF calculation, very expensive even for small molecules with moderate basis sets, be mindful of your computational resources. You need to use the CASSCF=(n,m,spinorbit) which calculates the spin orbit coupling between states n and m, but for that you need a previous calculation to know exactly what the n and m states of interest are.
I hope this helps. Have a nice day
Respected sir,
Thank you for your kind reply. I will forward my work on your suggested path. Your posts have saved my so much time. I will be grateful to you forever thank you so much.
Kavita Narang
Hellow Sir,
Hope you are doing well!
Sir I have a problem while optimizing the antheracene molecule via Software Gamess (US).
A error is shown in their output file that is
“there are atoms less than 0.100 Apart ,QUITTING…..”
while I visualize the input file via Molden and wxmacmolplt ,it is too good and no atoms overlap ,please let me know how can I resolve this error.
Thanking you.
Dear Nayab,
These atoms are so close that you won’t see them in any visualizer, that is, they overlap almost perfectly. Anthracene has 14 C atoms and 10 H atoms, you should edit the input with a text editor and find the extra-atom. You may also start again from scratch because anthracene is a very small and simple molecule; this is what I’d do.
I hope this helps, have a nice day
Hello,
Hope you doing well!
I have a problem while optimising a transition state structure. I tried both QST 2, QST3 as well as TS Berny method.
But all the time I got an
Linear angle in Bend.
Error termination via Lnk1e in C:\G16W\l716.exe at Tue Sep 21 13:44:19 2021.
Please let me know how can I resolve this issue.
Thanks
Dear Meenu,
Handling linear angles (180°) is always a problem. You could try one of two things:
1) Try using a different geometry guess for the TS in the case of QST3 and TSBerny methods, so as to avert the passing via that linear angle.
2) Re-define the Z-matrix numbering scheme. Probably, the numbering scheme leads gaussian to find a linear angle between atoms that aren’t necessarily connected.
I hope this helps
Thank you so much!
Hello Sir, I need to ask that 2-Chloro alpha alpha alpha trifluoro 3,5-dinitrotoluene is the name of my chemical. It says there is a “Input conversion mistake in IntKMC” when submitting this molecule for frequency computation. I’m not sure how to get rid of that mistake. I’m writing to ask for your help in order to continue my job.
Caro Prof, Dr. Joaquin. Aqui escribe Claudio Téllez. Estoy muy grato por sus éxitos e imagino que aun está en la UNAM. Espero que se encuentre bien sin el fantasma del Covid 19 que tanto nos ha afectado. Tengo una pregunta simples: B3lyp/6-311G(d, p) para calculo de números de onda no acepta al Cd, pero creo que puede usarse como base el LANL2DZ individualmente para ese átomo. Cual sería elcomando para ese calculo? Coloqué de esta forma y no rodó elprograma:
# p B3LYP/GEN opt freq=Ramajn test
0 3 coordenadas cartesianas una línea en blanco S C O H 0 6-311G(d, p) ************* linea en blanco Cd 0 LANL2DZ
Por supuesto que dio error
Si usted me puede ayudar le agradeceria muchísimo
Saludos desde Brasil!
Claudio Téllez
Em qua., 29 de set. de 2021 às 06:36, Dr. Joaquin Barroso’s Blog escreveu:
> Chris Jordan commented: “Hello Sir, I need to ask that 2-Chloro alpha > alpha alpha trifluoro 3,5-dinitrotoluene is the name of my chemical. It > says there is a “Input conversion mistake in IntKMC” when submitting this > molecule for frequency computation. I’m not sure how to get rid ” >
Hola Claudio, hace muchos años que no escribías! Estamos bien ahora, gracias, tuve COVID junto con toda mi familia hace un par de meses. Todos bien ahora, gracias.
El input parece correcto, salvo que falta la parte del pseudopotencial asociado a LANL2DZ para el Cd. Añade la keyword pseudo=read en tu route section (la línea que empieza con #). La parte de la base debe ser en renglones separados y parece que te faltan una línea de ****:
S C O H 0
6-311G(d,p)
****
Cd 0
LANL2DZ
****
–blank line–
Cd LANL2DZ
–blank line–
Sorry, but I need like a lot of far more information to help you with your problem.
Hi Sir, I am getting a error while doing a enzyme substrate complex optimization by oniom method.
Read MM Parameter file
Define OM 1
Define FE 2
#B3LYP / Gen Ifunc -1
Function name note recognized in RdPar.
Kindly help me to resolve it. Thanks in advance.
Hola Dr. Barroso, coordial saludo desde Colombia.
Estoy interesado en realizar una optimización de la geometría del compuesto 2-nitrobenzoyl chloride. Ya he efectudado los calculos con Gaussian 09 usando el método Opt+freq y DFT-B3LPY (631G (d,p)) pero se me generó un problema. Propuse dos estructuras iniciales para realizar el calculo: i) el grupo acilo con el cloro apuntando hacia el grupo nitro y ii) con el grupo cloro apuntando hacia el lado opuesto del grupo nitro. Los dos cálculos me dieron estructuras diferentes, y la verdad no se cual elegir. Una de las soluciones que encontré para este problema fue comparar las energías totales (total energy) de cada compuesto y resultó que una es más grande que la otra, entonces la más pequeña indica que es la estructura más estable.
Sin embargo, no veo que sea un método muy eficaz para realizar la optimización de los otros compuestos ya que me demoraria mucho tiempo proponiendo las estructuras iniciales. Espero que me pueda dar un consejo sobre como realizar una buena proposición de estructura inicial y otro sobre como darme cuenta que va a ser la de mínima energía.
PD: también he consultado en la literatura pero no he encontrado resultados que me ayuden a solucionar este problema.
Muchas gracias.
Hola Alejandro,
Entre más grados de libertad tiene una molécula, más complicada será la superficie de energía potencial sobre la cual tendrás más de un solo mínimo. Encontrar el mínimo global de una molécula es algo muy complicado, requiere de mucho insight químico, realmente el proceso que utilizaste de prueba y error es lo mejor que puedes hacer.
Hay algunos códigos para automatizar la búsqueda (PLAMS, RDKit) que funcionan bien para moléculas pequeñas a primera aproximación, ya después debes hacer cálculos cuánticos sobre ellas si quieres algo más cuantitativo, ahí ya depende de que sea lo que necesitas estudiar.
Espero que sea de ayuda
Hola Dr. Barroso, espero se encuentre bien, saludos desde Puebla , México.
Estoy interesada en realizar un análisis a distintos niveles de teoría sobre el etanol. Sin embargo al usar la función de base 6-311++g(d,p) en el programa Gaussian me aparece este error, espero pueda ayudarme a ver cuál es el problema, por favor.
%Mem=800Mb
%Nproc=3
Will use up to 3 processors via shared memory.
———————————————————————-
#p HF/6-311++g(d,p) opt scf=(xqc,maxcylce=10000) gfinput gfprint pop=(
full,NBO)
———————————————————————-
QPErr — A syntax error was detected in the input line.
+g(d,p) opt scf=(xqc,maxcylce=10000) gfi
‘
Last state= “SCF2”
TCursr= 160842 LCursr= 33
De antemano le agradezco mucho su atención y ayuda.
Saludos.
Hola Daniela,
Tu problema no está en la base sino en las opciones del SCF, la opción MaxCycle está mal escrita (dice MaxCylce).
Ahora bien, si estás usando G16 y vas a usar XQC y quieres modificar el número de ciclos tienes que usar la opción MaxConventionalCycles=10000 en vez de MaxCycle; de cualquier forma puedes tratar ambas opciones pero por lo pronto tienes un error de dedo en la definición del número de ciclos.
Saludos hasta Puebla
Muchas gracias Dr.! Su respuesta fue de mucha ayuda
Sir, Please suggest me some solution to the below error in gaussian 16
“Error termination request processed by link 9999”
before this message
“Optimization stopped. — Number of steps exceeded, NStep= 257 — Flag reset to prevent archiving.”
I solved this issue by submitting the error output file again. i,e the step where the optimization is stopped.
Your approach sounds correct, but please don’t let it happen again! Try checking your optimizations periodically just to know if the structure isn’t getting wrecked somehow. Usually when an optimization reaches these many steps, the structure goes awry.
I hope this helps
Sure, sir. Thank you.
Another doubt strikes when you answered this question, was
when I’ve opened my input file in Gaussian, some bonds in the structure looks broken but when i opened the output file of the same molecule after optimization it looks fine.
why is that so?
Thanks in advance.
The optimization algorithm tries to find a structure corresponding to a minimum on the PES but you have to help it because Gaussian does not perform simulated annealing. So try to build your molecules as close to what you might think the minimum looks like and then optimize them from there.
I hope this helps
Good evening sir
I am using Gaussian 09W I have a doubt regarding what type of bond is present in my molecule so how can I find out from my output file
Then for ion pair what type of basis set want to use and to avoid interaction what type of functional want to use?
Thanks in advance
Hi,
I am trying to run a calculation on metal complex where I intend to use 6-31d basis set for C,H,O but lanl2dz basis set for metal ion but I am getting an error message gain and gain despite making many changes. Can you pls point out the mistake. The input file is as NTED AN INTEGER AS INPUT. FOUND A FLOATING POINT NUMBER AS INPUT. 1 2 2.0 6 1.5 8 1.0 ?
#p opt ub3lyp/gen pseudo=read geom=connectivity
After molecular specifications
C H O N S 0
6-31G+(5d,7f)
****
Cd 0
lanl2dz
****
Cd 0
lanl2dz
****
Hello Prerna,
You may want to delete the connectivity matrix, the geom=connectivity keyword, and the final **** line in the pseudopotential section; i.e. keep that line for the basis set but delete the one in the last section:
C H O N S 0
6-31G+(5d,7f)
****
Cd 0
LANL2DZ
****
Cd 0
LANL2DZ
I hope this helps
Hello Sir,
I wish to calculate emission spectra of a molecule using Gaussian. Could you please comment on the steps and keywords involved in calculating emission spectra of a system using Gaussian? I am using Gaussian 16.
Thanks,
Kaushik
Maximum Force 0.000009 0.000015 YES
RMS Force 0.000003 0.000010 YES
Maximum Displacement 0.001364 0.000060 NO
RMS Displacement 0.000273 0.000040 NO
Predicted change in Energy=-1.259397D-09
Optimization stopped.
— Number of steps exceeded, NStep= 100
— Flag reset to prevent archiving.
How to address this problem, I have even tried opt=(calcfc,noeigentest,maxcycles=500)
and i even tried of optimization maxcycles till 1000.
Please do suggest me to correct this 9999 error..
Thanks in advance.
@mdhmohan786
Are you optimizing a transition state or a local minimum? In the case of a local minimum, “noeigentest” is the default so it is not needed.
Have you checked the optimization curves (i.e. Total Energy = f(stepnumber)) in GaussView ? There are usually two easy-to-spot issues:
a) The algorithm took one “bad” decision, and is stuck oscillating (very) slowly going down in an exponential way. The energy usually oscillates around what would be expected as the exponential decay function after it took that “bad decision” which is indicated by a peak at step #n. In that case, you can simply restart the job at step #(n-10).
b) The Berny algorithm gets stuck oscillating around the actual minimum because at each optimization step the gradients predict the next step to be very close to twice its distance from the actual minimum… One way I got around that issue is to reduce the maximum displacement/step size allowed at each optimization step (without requiring an ultrafine integration grid). For instance, add “maxstep=10” (the default is 30) and see where it goes.. if that is not enough, you might have to go to opt=vtight and int=ultrafine or even change the optimization algorithm.
Either way, I think that calcfc is useless in most cases. If you’re trying to locate a TS, instead of going calcall (which is extremely resource-consuming), you can try recalcfc=5 (it calcultes the force constants at the first step and then every 5 steps afterwards). But I would only do that after seeing how it goes reducing maxstep.
@Imangin
Thank you very much for the clarification and I am trying to optimize a van der Waals complex . It’s not TS. only a local minimum I am searching for.
I have taken the optimized coordinates from a published paper and trying to get the best-optimized geometry by rerunning the calculation with the same basis set.
With only ‘opt’ keyword the calculation converged and reproduced the same coordinates.
But I am wondering when I increase the max cycles, why this is not converging and terminated with a 9999 error.
As you suggested i will try to increase the step size and submit the job and will get back to you once this is done.
Thank you very much for your detailed expalnation.
Very interesting, we need article like this, very useful, thank you
Sir, Is there any way i can know the elapsed time of my calculation?
The output file shows the job CPU time, but my CPU will be turned on since 3 days. I need to know the time took to perform the calculation.
Hello Sir,
How can I calculate emission spectra of a system using Gaussian?
Many thanks,
Kaushik
Hello, First of all I found your post really helpfull thank you for all the work you put in ! Then I’m new with the uses of gaussian and their is few parameters I don’t understand like calcfc I understood it was calculation of force constant but I don’t see where it comes from, also I don’t understand opt=noeigentest I found that it was to prevent gaussian from stopping if no negative hessian value was found but that also doesn’t make much sense to me. If you could explain this to me it would be wonderfull or maybe reoriented me to blog or post that I didn’t see.
Thank you for your time !
#gview5 #gaussian16
I want to generate electrostatic potential maps with gview 5 from gaussian 16 output.
I do opt freq population=full, generate fchk and cube files that I load into gview but once I new mapped surface I get the following error:
Surface map failed!
Executing Gaussian cubegen job
Thank you in advance
Matteo
Hola Dr. Joaquin Barroso. Soy un seguidor asiduo de su blog que brinda gran ayuda a la comunidad de quimicos teoricos. Por supuesto soy un quimico teorico que trabajo en Canada. He realizado algunos calculos de opt freq usando m052x pero sigo teniendo el error:
“Optimization stopped.
— Number of steps exceeded, NStep= 114
— Flag reset to prevent archiving. ”
incluso cuando incluyo la palabras claves opt=maxcycles=400. Alguna idea de como pudiera arreglar esto?
Muchas gracias por adelantado
Lazaro
Hola Lázaro,
No hay más que arreglar la geometría de inicio, son demasiados pasos y seguramente está oscilando la estructura alrededor de algún mínimo local. Intenta tomar alguna de las geometrías de menor energía y reinicia el cálculo desde ahí.
Saludos
I am trying to optimize a dictation of NDI with bromide as counter anion bound to it through anion-pi interactions, the job terminates midway without showing error cause in log file. Help me out.
Is it possible to graph NBO analysis (or line chart)?
Gaussian software is generating the Coriolis zeta couplings from the anharmonic frequency calculation.
Please do clarify/guide me on obtaining zeta values from this.
I could share the OUTPUT file if it is required.
Looking forward.
Thanks in advance.
Hello Sir, How can I optimize metal fluoride “KF, CsF, AgF etc.” and Phase transfer catalysts in gaussian?
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Hello sir,
I’m a beginner to Gaussian, I want some ideas regarding spin states,how can we perform spin polarized and unpolarized spin states and how can we calculate magnetic moment and spin polarization of that particular spin state? what keyword we have to use to get spin densities in Gaussian?
Respected Sir, I hope you are fine in this covid era. I always follow you for your valuable suggestion on your blog. I am also user of Gaussian software. I have some queries related to my research work. I want to know that how to build nanoparticles using gauss view 5. If we choose from periodic table as provided in gauss view it is taken as metals but i want nano-size particles. One other queries that whether it is possible to search transition states in presence of gold or silver particle, if possible then please suggest me how to construct input file for transition states in presence of silver nanoparticles? Thanks in advances
sir. I have a work on gaussian with central linux system. I get chk files but because of the problem of linux-windows , ı cant open my chk files when ı want to calculate frontier molecule orbital. ı tried to change chk files as a fchk file on system . but fchk file ı got is 0 KB. and gaussian does not open it. why this problem occurs? how can ı overcome this problem
Hi,
Could you please uide methrough how to calculate the interaction energies between metal surface and same molecule at different states. For example gold 100 surface interating with amino acid neutral form, cation form and anion form. I found that ionic forms have higher interaction energy compared to neutral form though in reality they are far away from the surfac of the gold. I mean, physically there is no interaction but interaction energy is higher for ionic forms. Thanks
Maybe there is a strong electrostatic component to your interaction energy, but it’s hard to say with so little information.
Hello,
I am working on qst2 calculation to find out TS through gaussian. But I’m ending with an error mentioning “Add virtual bond connecting atoms ATOM1 and ATOM2”. I tried to change the distance/angle but still the error was same. I would be grateful if you could explain me to figure this out.
Thanks
You’re probably defining your structure in Z-matrix format, this makes it easier to find the TS but you have to be careful how you define each degree of freedom. Try changing to cartesian coordinates and switch on and off the geom=connectivity keyword.
I hope this helps
Hello sir! I hope you are doing well. Sir I’m using gaussian 09 at DFT level of theory and the basis set 6-31G d at the B3lyp function. When I’m optimising my geometry it these levels of theory it will give me the following error that here I’m gonna be posting,
Tors failed for dihedral 10 – 14- 18 -20
Tors failed for dihedral 13 – 10 – 18 – 20
Sir can you please help me to sort out this problem and also tell me that how to see these problematic angle in gaussian output file
how can we rerun calculation from checkpoint file in ONIOM model? I tried doing it but all the atoms are getting assigned to the high layer. I could not figure out what to do and so copied the last step of optimisation and ran the opt+freq calculation ( manually assigning the high and low layer again). Do you have any way of using the checkpoint file?
#visualization, #molecular orbitals #electronic wavefunction
hello,
I am not sure if this is a question of technical problem or a point of Scientific discussion. When we visualize the cubes (Molecular orbitals) in gaussian 16, there are different energy levels corresponding to different canonical orbitals separated by a green line which separates the occupied and unoccupied levels. I checked this by generating the MOs for several molecule, there I have noticed that green line doesn’t shift when you go from singlet/ doublet to singlet / doublet transition, however it does shift when we go from a triplet to singlet and quartet to doublet transition. So when you do an optimization for an excited state (single/doublet) then green line does not go up (shift to upper orbitals) as compared to ground state calculations though a change in the energies of orbitals is clearly observed. In principle one electron from ground sate should jump to an excited state so the green line should shift to one of the orbital that is higher in energy. At the same time, when we do an optimization for an excited state for triplet/ quartet then this green line does clearly shift to the orbitals those are higher in energy as compared to ground state optimization calculations (besides the changes in the energy of the orbitals), which makes sense. I am confused about this ambiguity for singlet to singlet or doublet to doublet transitions. Any clarification is much appreciated.
Beside this, Is there any physical meaning of two colours (red, green) represented in these cubes (MOs)?
Additionally, how to get/ calculate mathematically represented electronic wave function for these molecular orbitals by using gaussian 16 software.
thanks
sincerely waiting
Hello Mohan,
Very interesting observation. I’m not sure exactly what you mean, perhaps if you send me pictures I could help you better understand this issue. If you move a single electron from a singlet multiplicity towards a vacant orbital you still have a singlet if the spins are still anti-parallel (up-down), if you experience some spin flip (up up) you now have a triplet, not a doublet; a doublet requires a single unpaired electron so I’m not sure how you go from singlet to doublet. Send me an email with more details because this sounds interesting to discuss, I just need to better visualize it.
There is no physical meaning to wave functions so there is no physical meaning to orbitals 🙂 but the red-green colors only represent the phase change between orbitals (positive or negative, it doesn’t matter which is which)
To obtain the wave function you have to use the keyword output=wfx or output=wfn depending on the format you want it, some programs such as MultiWFN can then process it. Check this link: https://joaquinbarroso.com/2016/06/28/quick-note-on-wfnx-files-and-mp2-calculations-g09-compchem/
I hope this helps
thank you so much, i will share the details soon with you for more information and visualization. how can i have your email to share the details.
Hello sir,
I am interested in calculating charge/electron transfer, for give a quantitative view to my actual study but I am not able to follow the texts. Can you help me through Gaussian or quantum espresso any on how to attain such. For short comment i attach a paper … if possible please read the section “Electronic structure of LiCr_yMn_2À_yO_4” in
“First-principles studies of cation-doped spinel LiMn2O4 for lithium ion batteries Siqi Shi, Ding-sheng Wang, Sheng Meng, Liquan Chen, and Xuejie Huang Phys. Rev. B 67, 115130”.
They performed something like integration of the local DOS and then concluded about the no. of electrons.
Waiting eagerly for your reply.
Regards.
Very interesting and insightful review
Hello Sir,
I am doing computational calculations on Covalent organic Frameworks using Schrodinger software. I am using PBEO-D3 theory with basis set 6-311G*. I am getting an error message. What I have to change ?
**Aborting SCF (increased accuracy is needed)
consider setting nops=1 or nofail=1
in the gen section of the input file.
ERROR 7009: fatal error
Aborting SCF due to very large DIIS error: 1.15E+01
Error: jaguar died in program scf
Sorry, I don’t use Schrodinger so I have no idea. Try changing the initial geometry perhaps.
#failure reading molecular structure
Sir, While trying to optimize my molecule it terminated successfully.
But while trying to open it shows “Failure reading molecular structure”
I assume you’re trying to open it with GaussView. I’m not sure why, but if you search for the line that says “Dipole orientation” and replace it for any other text, it will open without problems.
I hope this helps
Hello Sir,
I am computing reaction Mechnism of Photochemical reaction. Do you elaborate, how to start work on gaussian? And also some tips to regarding jobs for conical interaction.
Hello Sir,
I seen your BSSE correction blog.
My question is how do I do Dannenberg’s counterpoised geometry optimization for the water dimer trimer etc. please share the input file for better understanding.
Thank you
Hello Sir,
I seen your BSSE correction blog.
My question is how do I do Dannenberg’s counterpoised geometry optimization for the water dimer trimer etc. please share the input file for better understanding.
Thank you
Hi there,
I am doing excited state calculations with TD-DFT method in G09 for small organic molecules. I want to calculate vibrationally resolved spectra. However, the software is showing link718 error for many molecules. It has become a regular phenomenon when performing vibrationally resolved spectra calculations. I understand the initial and the final geometries overlap is not suitable here. But how to get rid of it? Many of my work is stuck for it. Please give a solution. I have not found any solution online. Waiting for your kind reply.
Thank You
it has also happened to me several times, but changing the basis sets and DFT methods has worked pretty well, besides that mind any space/special character in between the file names of excited state/ground state etc. I hope it would be helpful.
Dear Dr. Barroso,
I have calculated binding energy between the Metal and ligand using B3LYP/def2tzvp basis set. Now I want to incorporate the BSSE correction in the energy. But when I am optimizing using counterpoise = 2 keyword with same level of theory, the system is not converging. Can I calculate BSSE value from single point calculation using the already optimized structures?
Hi. I am heaving error number 2066 and CConnectionGLOG:Count Geometries() No valid data found in file. Can you please help me fix this
Hi,
I would like to ask you about the way to calculate the surface area of a given molecule . Could you tell me how to get it using Gaussian, please?
Regards,
Benoit
Hi,
I have another question about HOMO and LUMO for openshell molecules. Let say I am interested to calculate the gap, what HOMO and LUMO would I take into consideration to do so since in the output we have the alpha and beta results?
Thank you
Benoit
Hello sir,
I tried to obtain NTOs using the method you mentioned and my calculation ran successfully. The obtained log file also contains the occupation number of occupied and unoccupied orbitals in ascending order but when I visualise any of the HOMO and LUMO i am still getting the energy in fron of them and not their occupation number. So i am not able to find out that the maximum occupation no. given in log file belongs which HOMO/LUMO. Please tell me what to do.
Hi, I have a query on how to observe the “Effect of Applied Electric Field” using Gaussian as it is discussed here in this article (https://doi.org/10.1016/j.comptc.2022.113606 ). Kindly guide me step by step. I will wait for your quick response.
Regards
Hello Sir,
Using tddft gaussian, I am investigating the photochemical reactions. The aromatic compound is created through isomerization, cyclization, and finally oxidation. I started out by using the DFT approach to investigate the mechanism at the m062x/6311g (d,p) level of theory. I now want to use tddft to verify the same result. Please advise me on how to draw an energy profile diagram that includes conical intersections as well as how to locate the conical intersection and transition state.
dear Professor,
I would appreciate it if you could explain to me how to define a 1.2 M hydrochloric solution in the scrf framework of gaussian16.
wait for your kind response.
Regards
Dear Professor,
Greetings to you. I did the TS search in the gas phase using the b3lyp/6-311++g(d,p) level of theory along with opt=(ts,Calcfc,noeigen) keyword and got one imaginary frequency. Now the same geometry runs with the solvent phase using the scrf=(solvent=water) keyword the activation energy is 2 k/cal higher than the gas phase. Can you please help me to sort out this problem? or please suggest using any specific keyword to reduce the energy barrier in the solvent phase. Looking forward to your valuable response. Thanks in advance.
My query is:
How can I perform energy decomposition analysis (partitioning into kinetic, electron-electron repulsion, nuclear-nuclear repulsion and the nuclear-electron attraction energy terms) using Gaussian 09?
Shall remain deeply grateful for any valuable input.
Dear professor,
In Gaussian09, I tried to optimize a iodine containing species with aug-cc-pvdz-pp basis set where small-core energy consistent relativistic pseudo-potential was implemented. I took CPCM as a solvation model. But only first two convergence criterion(Maximum Force and RMS Force) out of four were fulfilled. After that job was terminated with an error.
(Error on total polarization charges = 0.01418>>>> Convergence criterion not met)
Also note, here I have started with an geometry that was already optimized with lower basis set. How can I fix it? Is it fine to proceed with the final energy because two major criterion are fulfilled.
Waiting for your kind response.
In general its not a good idea to use the obtained geometry if those two criteria haven’t converged. Try using a different model of cavity, such as radii=bondi with the SCRF=read option. this might diminish the polarization charges at the surface.
I hope this helps
In analyzing NBO output, sometimes lone pairs on heteroatoms of conjugated systems are not printed, instead π-bond with adjacent atom is printed probably due to strong delocalization. Is there a way to force gaussian to print those lone pairs? The objective is to compare interactions like n–>π* or n–>n* with those present (and printed!) in other systems..
Yes, there is. You need to invoke the CHOOSE option (similar to DEL), but I think its not fully available in NBO3.1 as provided with Gaussian. I’ll check and write a post if possible.
Dear Prof,
I am trying to use Yamaguchi equation to understand the diradical character of an organic molecule. After optimizing the broken symmetry singlet structure, how to I find out the HOMO(/HONO) and LUMO(/LONO) occupancy. I read I have to use Natural orbital occupation number. How do I get the values… what command I need to use in the route section? Any help would be greatly appreciated.
This is a rather old post but it’s still valid. I hope it helps
Hola Joaquin! I am doing calculations on singlet fission materials. My professor asked me to incorporate spin-orbit-coupling after I substituted Silicon on one of the Carbons in the original system. Do you have a tutorial related to this? I am also using Gaussian16. Gracias!
Hola Kirby,
Unfortunately I don’t have a tutorial yet, maybe it’s a good topic, thanks for bringing it to my attention. SO coupling can be calculated within the CASSCF method (which needs a whole different blog post on its own) by invoking the SpinOrbit option in the route section, as in CASSCF=SpinOrbit
Now, bear in mind that you first need to make a thorough evaluation of the orbitals to be involved if you need to set a specific one for a given excited state (I guess I do need to write something about it.)
I hope this helps
Plz help me to understand the meaning of A’ and A” in the Orbital Symmetries part of the Gaussian 09 output file. For example
Occupied (A’) (A’) (A’) (A’) (A’) (A’) (A’) (A’) (A’) (A’)
No lower point found — run aborted. I have tried all varients of scf qc, xqc but each time this error arise and i always get convergence error. please help get out of this.
Sir: Can you please explain the details of DFT calculations using the Broken Symmetry approach in Gaussian 09 package, and how to read the output files so as to calculate the magnetic coupling constants?
Regards
Hi Professor,
could you please help me to plot humo-lumo with quantum espresso. I calculate it through SCF but I cannot plot it!
#maximum replacement convergence failure
Hello Dr. Barroso, I hope you are doing great!
I am running some DFT optimization for large Pt NHC complexes where fluorene moiety is the ligand. I am getting maximum replacement convergence failure each time. I have changed basis sets/functionals several times, starting with even semi-empirical or HF methods. Still, I am getting the same issue. Would you please give me some suggestions on what I should do to resolve this issue?
Thank you.
#problemswithgaussview2Dscan plots
Hello Dr. Barroso
I am wanting to make 3D potential (z) surface plots with 2 scan variables (x,y). But when I open the .log file in Gaussview, I just get a 2D plot of the potential (z) vs the cumulative scan number rather than an actual 3D plot of z vs (x,y) scan coordinates. This keeps me from saving the data in a (x,y,z) column format, which is what I really want. This should be an automatic ability in Gaussview. Any thoughts on why this isn’t working?
Thx
David Nesbitt JILA, U Colorado Boulder
Dear Dr. Barroso,
#deepeutecticsolvents #chargedspecies
My question has to do with the optimization of a deep eutectic solvent (DES) unit, specifically with the one formed by choline chloride (fragment 1, ammonium salt+Cl-) and other neutral species such as urea (fragment 2). I am not entirely sure how to define charges and multiplicities in the gaussian input file for such a case with different fragments and charges; I found some input files in the supplementary material of papers in which the authors defined those two fragments and set their charge and multiplicity as 0 1, also defining charge and multiplicity of the supermolecule as 0 1 (Gaussian requires to be provided with charge and multiplicity of the whole molecular entity and each fragment separately, i.e. 0 1 01 01). However, doing so one would miss the extra electron of the Cl anion and specific charges would not be accounted in the calculation. Are you familiar with this kind of calculations? Thank you very much
Hola Manuel
You may define as many fragments as you want or need depending on what you want to calculate. If you want, you can calculate the ammonium cation as one fragment (charge and multiplicity, 1 1), chlorine as the second fragment (-1 1) and your third fragment would be your neutral molecule (0 1). The input section would look like
0 1 -1 1 1 1 0 1
Cl(fragment=1) x.xx y.yy z.zz
N(fragment=2) x.xx y.yy z.zz
…
C(fragment=3) x.xx y.yy z.zz
H(fragment=3) x.xx y.yy z.zz
…
Where the first 0 1 pair denotes the whole charge and multiplicity of the entire complex.
Now, having said all that, I usually don’t care much about specifying the charge of each fragment unless it is strictly necessary because, if all things go right, the electronic structure will give you the right charges naturally, i.e. in the ammonium chloride fragment, the optimized charge of Cl will be close to -1 after the calculation. In fact, it would be interesting if you ran both calculations and compare them.
I hope this helps
Hola, Joaquin,
Thank you very much for taking the time to address my question. Initially, I also considered (and tried) the charge/multiplicity pairs -1 1 and 1 1 for the Cl anion and ammonium cation, respectively. However, I realized that the number of electrons included in the calculation by Gaussian is not the right one since the software would remove one electron from the system (I guess this is due to the defined positive charge) and would add one more electron to the Cl anion (which is correct); to my understanding, the ammonium cation should not miss any electron since it has just a tetravalent N atom (positive charge but intact number of electrons) and also one unpaired electron from the initial lone pair of the N atom, and thus multiplicity would be 2. Therefore, I tried -1 2 -1 1 0 2 0 1 for the supermolecule, Cl anion, ammonium cation, and neutral singlet molecule fragments, respectively, and was able to find a minimum on the PES (after many geometry optimization failed runs); do you think the charge and multiplicity of that optimized and characterized minimum, which basically result from the charge and multiplicity of the Cl anion and N cation, are the right ones?
Gracias 🙂
Dear CCLers,
I would like to do some solvent calculations in nitric acid (HNO3),
hydrochloric acid (HCl) and sulfuric acid (H2SO4) using Gaussian program. Can
anyone help me?
Regards,
Benoit
Hi Benoit,
As such it isn’t possible to request pure acids as solvents under the implicit solvent or continuum polarizable medium methods. I would suggest you use water as a solvent in any of the continuum solvation models of your choosing, protonate your molecule accordingly to the low pH you’re thinking of, and maybe include a few acid molecules surrounding your molecule.
As always it all depends on what property are you trying to calculate.
I hope this helps.
Hello Dr. Barroso,
I have begun using Gaussian 09 and Gauss View 16 for my projects.
So far, I have successfully optimized a few small structures using these software tools. However, I encountered a persistent issue when attempting to optimize a larger structure, specifically, “transition metal doped graphene.” Despite my efforts, the optimization job always fails.
I have learnt that I can use different basic sets for different in case of large structures, to address the problem, I have experimented with various basic sets and tried to find solutions by researching and exploring different resources online. Unfortunately, my attempts did not yield positive results.
Currently, I am trying to work with the GEN basic set, and to ensure accurate input, I obtained information about the basic set from a website called Basis Set Exchange. I provided this information in the additional input section, but the optimization still remains unsuccessful.
I would greatly appreciate your guidance on this matter.
Thanks in advance !!
Hi Shivam,
Please google GEN external basis set to get the post in this same blog about it. There you will find detailed instructions to achieve just that.
I hope this helps
Dear Dr. Barroso,
I am trying to optimize a #cytochrome #prophyrin system for camphor hydroxylation. The product of the hydrogen abstraction from camphor is (Por)(SMe)Fe(IV)-OH, which can be obtained as a doublet or quartet. I am trying to obtain this complex in Fe(III) form. I tried fragment scheme in Gaussian16 program and also the excited state optimization of the excited sate for Por –> Fe electron transfer obtained from TDDFT but neither of them worked. The work has been done by Shaik and coworkers and can be found at [J. Phys. Chem. Lett., 2011, 2, 2229-2235]. Could you please comment on the right approach to obtain the Fe(III) complex.
I shall be thankful.
Dear Dr. Barrosa,
I wondered if I could print out one- and two-electron integrals from the Gaussian16 package. If yes, what keyword or iop do I have to use? Could you please help?
Hi Pratanphorn
I think the IOp(3/33=N) should work, depending on what you want. You can substitute N with 1 for printing one electron integrals, 3 for two electron integrals, or 5 to get both. According to the manual, these would be printed in regular format, whereas 2,4, and 6 would be printed in debug mode.
Also, check the “output” keyword in the manual and the available options for it, in case you need to interface those values with other programs; I remember using something about it to link to Gaussum for DOS calculations.
I hope this helps
Hello sir, I am facing problem with an error like “Error termination via lnk1e in c:\g09w\1101”
please let me know the solution
That doesn’t actually say anything. That’s just the message of Gaussian quitting, you need to copy the last few lines.
Hi Dr. Barroso,
I am trying to divide my system into 2 fragments and making both of them radicals. I get the following error message and I do not know how to proceed:
CPIOFr: IOpCl= 1 IRwI=-1 IRwCP= 731 ICalc= 2 LCPTot= 66319 Len1MO= 122056 IndFrg= 432487
CPIOFr: IOpCl= 1 IRwI= 2 IRwCP= 731 ICalc= 0 LCPTot= 66319 Len1MO= 122056 IndFrg= 188375
CPIOFr: IOpCl= 1 IRwI= 1 IRwCP= 731 ICalc= 0 LCPTot= 66319 Len1MO= 122056 IndFrg= 188375
CPIOFr: IOpCl= 1 IRwI= 2 IRwCP= 731 ICalc= -1 LCPTot= 66319 Len1MO= 122056 IndFrg= 66319
CPIOFr: IOpCl= 1 IRwI= 2 IRwCP= 731 ICalc= 0 LCPTot= 66319 Len1MO= 122056 IndFrg= 188375
FinFrg: NACore= 12 NAVal2= 28 NAVal1= 1 NBCore= 12 NBVal2= 28 NBVal1= 1
Alpha deviation from unit magnitude is 1.28D-13 for orbital 197.
Alpha deviation from orthogonality is 1.27D-13 for orbitals 200 196.
Beta deviation from unit magnitude is 3.07D-13 for orbital 200.
Beta deviation from orthogonality is 1.03D-13 for orbitals 200 194.
Leave Link 122 at Tue Oct 24 18:07:36 2023, MaxMem= 8589934592 cpu: 1.9 elap: 0.1
(Enter /opt/Gaussian/gaussian16c01/g16/l9999.exe)
This type of calculation cannot be archived.
Any advice would be greatly appreciated.
Thank you.
Hi Dr. Barroso,
Every time I submit a Gaussian job on the cluster, the calculation used to be successful, and the log file opens nicely in GaussView for result analysis. However, the problem is that my .chk file always contains corrupted content. Could you please tell me why this problem is occurring? I have pasted my input file below for you to review.”
%nprocs=4
%mem=6GB
%Chk=fur_ground.chk
#P opt Freq=SaveNM cam-b3lyp/6-31+g(d) geom=connectivity
0 1
C -3.96977339 0.57119042 0.00000000
C -2.59019139 0.57119042 0.00000000
C -2.17545739 1.95855742 0.00000000
C -3.32952339 2.71465642 -0.00008900
O -4.44902539 1.88186742 -0.00022200
H -4.74341939 -0.19001458 -0.00001100
H -1.92567339 -0.28750558 0.00010500
H -1.14887039 2.31205542 -0.00000400
H -3.55897939 3.77551842 -0.00013900
1 2 2.0 5 1.0 6 1.0
2 3 1.0 7 1.0
3 4 2.0 8 1.0
4 5 1.0 9 1.0
5
6
7
8
9
Dear Sir,
I am trying to draw the energy landscape for proton transfer between RCOO-_Tyrosine using g16 calculation. But when I try to optimize the structure setting the distance between O-H 0.95A it shows error termination. It worked for the distance greater than 0.95A but less than that It is not working. Can you help me. Here I am sharing the error message.
Error termination request processed by link 9999.
Error termination via Lnk1e in /opt/gaussian/g16/prebuilt-avx2/g16/l9999.exe at Thu Nov 16 17:51:55 2023.
Hello Sir,
I am trying to calculate ab initio molecular dynamics in Gaussian. I preferred an onium method since the system is an ice grain model. The input is
‘# oniom (uwb97xd/6-311++g(2d,2p):upm6) admp (maxpoints=1000, stepsize=10000,NKE=12825,fullSCF) SCF=QC IOP(1/44=0,1/82=298,1/81=1,1/80=1000000)’
I am facing an error given below.
Search did not lower the energy significantly.
No lower point found — run aborted.
Error termination via Lnk1e in C:\G16W\l508.exe
Any suggestions greatly appreciated.
What is the error limit allowed in molecular dipole moment calculation in Debye units.
Consider, there are two molecules A and B and they are non-covalently interacting with each other and that there is a possibility for several configurations (orientations). Now say, there are two configurations which are much similar but they have different electric dipole moment (static). What is the allowed error bar. Is it 0.1D or is it 5% difference. So that I can consider these two orientations as entirely different ones due to large dipole difference (i.e. being more than the allowed/ threshold value). Is there any research article that discusses about this.
Thank you
I have generating TDDFT output for ions and wanted to know what the number next to the transition means. I know for neutral systems we can get the coefficient from this info (2*(xx)^2) but am not sure what these numbers mean for ions. I am trying to identify which transition possesses the largest contribution for the first 3 excited states of a set of anions.
How to study charge state effect for drug delivery study using Guassion 09. Input preparation ?
Hello Sir,
I am trying to relax scan the bond in alkene and heteroatom but this error resulted
No minimum found in polynomial.The polynomial fit failed. Using point 2.An expanding polynomial of degree 16 produced 1.0000Search did not lower the energy significantly.No lower point found — run aborted.Error termination via Lnk1e in /opt/soft/g16/l508.exe
Hello!
Recently I got this message at the end of my calculation of optimization using Gaussian 09: “The archive entry for this job was punched” but I’d want to know what it means. This is the first time that I perform an layered calculation using the ONIOM tool. The combined method was (PBE1PBE/def2svp:UFF)
Thank you in advance
#convergencefailure
My gaussian job converged for structure optimization but not for frequency calculation. how reliable is the structure and can the geometric parameters of this structure be used? I just need to calculate the pore size of this structure. Can I use this geometry?
Thanks in advance!