Polarizable Continuum Model (PCM) in G03
This is my first post on a series I have in mind regarding frequent questions on the CCL regarding the use of some computational chemistry software, mostly Gaussian. Readers are still encouraged to contact the Gaussian Help Desk for further (and more accurate) help.
Gaussian 03, the popular electronic structure calculation suite of programs, includes the necessary modules for performing calculations in a solvated environment using the continuum models approximations. Among such models, the Polarizable Continuum Model (PCM) is one of the most widely used methods since it meets a good compromise between accuracy and computation time. Nevertheless, Gaussian may not be the best option for performing such calculations (as opposed to other programs as COSMO) but it still can be very useful when used properly. Unfortunately there is a lack of specific info in the literature regarding the usage of the different variables involved in the cavity generation for G03; the newest version, G09, includes some improvements on the corresponding codes making PCM calculations more achievable. While browsing the CCL archives, it is common to find more questions than answers and usually the same questions are posted over and over by different users over time. This post will get updated as needed.
I hope with this post I can summarize most of the common problems found in Gaussian regarding implicit solvation calculations as well as their respective solutions. Some of the solutions come from Gaussian technical support itself, so my best advise is always to address your questions directly to them. Keywords are typed in capital letters, variables in italics.
Brief background
Implicit solvent calculations imply the generation of a vacuum cavity inside a continuous and homogeneous dielectric field. The simplest model to do this is Onsager’s in which the molecule is treated as a dipole inside a spherical cavity (SCRF=DIPOLE in Gaussian use along the VOLUME keyword to generate the optimum radius for such cavity.) PCM calculations generate a cavity that relates more closely to the molecule’s shape by placing spheres on each atom or groups of atoms. Check the Gaussian link at the bottom of this post for further info; this is a troubleshooting post, not a tutorial on PCM.
Some common errors and their solutions
In order to get a better definition of a cavity it has been recommended to use the option SCRF=(READ,model,SOLVENT=solvent) with the following parameters to be read at the end of the input file:
OFac=0.8
RMin=0.5
Additionally we may include a third line indicating the kind of radii to be used on each atom to generate a sphere around it, the default option is Radii=UA0 (Topological United Atoms model) which treats functional groups as a single sphere. Including this line with Radii=UFF; Radii=Pauling or Radii=Bondi will treat each atom independently, which is very useful to use when some H atoms lye outside the UAKS sphere. The error message associated with this problem is: “Error message, treat H atom explicitly” see below
-> BldSpC: Error generating genealogic tree for sphere 309 at level 15
According to Gaussian’s Help Desk, this is a numerical error in the generation of the cavity. The use of fewer spheres (implicit H atoms for instance) is recomended, so if you are using RADII=PAULING or BONDI, delete that line. It is also recommended to use the NOSYMM keyword on the route section. This problem seems to have been addressed in G09.
-> Too many tesserae. Increase the MxTs.
Try using the TSNUM keyword in the route section as SCRF=(TSNUM=num,…) This will modify the number of tiles to describe each sphere that makes the cavity.
-> AdVTs1: ISph= 500 is engulfed by JSph= 501 but Ae( 500) is not yet zero! Error in link301
Generation of cavity fails. Try using a different radii model (RADII=…) and/or the NOSYMMCAV keyword at the end of the file, via the SCRF=(Read,…) option. Also using the NOSYMM keyword in the route section can work. Once again using the OFAC=0.8 and RMIN=0.5 parameters is useful.
-> UA0: Hydrogen 40 is unbound. Keep it explicit at all point on the …
-> UA0: potential energy surface to get meaningful results.
The location of a certain H atom (number 40 in this case) lies outside the cavity placed on a functional group, so it must be treated explicitly by either changing the RADII= model or by placing a sphere on that particular atom alone through the SPHEREONH=40 (40 for this example) option via SCRF=(Read,…)
Additional remarks and suggestions
- The use of spheres on functional groups is suggested for calculating energies, but for geometry optimization the use of a more sophisticated model in generating the cavity is encouraged.
- Always pay attention to the value of the density lying outside the cavity, i.e. inside the dielectric. In G03 this value is labeled as “error on total polarization charges”. As a rule of thumb this value should be less than 0.05 for the calculation to be acceptable.
- Just in case you are using a very old version of Gaussian, be aware that the keyword COSMORS doesn’t launch a COSMO-RS calculation (thermodynamics of solutes and solvents) but a CPCM calculation in a format that can be post-processed by COSMO software.
- PCM calculations are highly parametrized so it’s useful to always have an experimental reference to which you can validate your choices in each calculation.
If you found interesting or helpful information in this post, please leave a comment however short. This will encourage me to keep gathering and posting this kind of information which in turn may be of help for other users, thanks.
References
http://www.ccl.net
http://www.gaussian.com/g_tech/g_ur/k_scrf.htm
http://www.cosmologic.de
Posted on September 7, 2009, in Computational Chemistry, Gaussian, White papers and tagged Computational Chemistry, Gaussian, PCM, Solvation. Bookmark the permalink. 81 Comments.
This is great work. It is of great help to many especially beginners in solvent related calculations. A number of issues have been clarified and I am indeed happy my jobs will be faster.
Thanks and keep it up.
muhavini
Thanks for your comment Muhavini! I’m glad you found it helpful. Stay tuned!
Joaquin
Thanks.It helps me a lot.
I reiterate Muhavini’s comment. Thank you!
Thanks Kathy, I’m glad it helped you.
Dear Joaquin, many thanks for the very helpful comments on the use of SCRF with g03. Otherwise it would have been rather difficult to get hold of some of the information you provided.
Best wishes
Jevgenij
Thank you Jevgenij!
I am always glad to know this thing is helping others. My best wishes to you too.
dear joaquin your work is very good and you help me a very concise manner.
Many thanks from Italy!
Luca
Thank you very much for your kind words Luca! Hopefully this blog will continue to be a useful place for more people interested in computational chemistry such as yourself.
Greetings from Mexico
Thank you for the helpful information!
You are welcome Sema! Thanks for commenting and stopping by.
Greetings from Mexico
Hi Joaquin
Thank you for that highly useful post on the PCM
implementation in G03.Optimisations with PCM can be difficult:I wonder if you have any experience with the PCM variant in G09 which incorporates the SMD model of Cramer et al?The G09 manual is not too helpful on this.
Hi Emrys
I’m glad you found this post useful. I do not have any experience with the model you mention on G09 but I do have the program available. Maybe if you tell me a little bit more about the problem you are facing I can help you work it out. I share your opinion about Gaussian’s manuals not being all that helpful, however their help desk always gets in touch very quickly when contacted, so maybe you can approach your doubts on two fronts: here and with Gaussian Inc. itself.
Cheers!
Dear Dr.Joaquin:
many thanks for your blog, you have good topics in it. Now I am working with DNA sequence, but I am using Gaussian 03 and 09, I am doing calculations using PCM with B3PW91/6-31g**, but the jobs failed, I am looking for help, but I could not find it. The error is:
Model : PCM.
Atomic radii : UA0 (Simple United Atom Topological Model).
Polarization charges : Total charges.
Charge compensation : None.
Solution method : Matrix inversion.
Cavity : GePol (RMin=0.200 OFac=0.890).
Default sphere list used, NSphG= 63.
Tesserae with average area of 0.200 Ang**2.
1st derivatives : Analytical V*U(x)*V algorithm (CHGder, D1EAlg=0).
Cavity 1st derivative terms included.
Solvent : Water, Eps = 78.390000
Eps(inf)= 1.776000
RSolv = 1.385000 Ang.
——————————————————————————
AdVTs1: ISph= 3601 is engulfed by JSph= 3609 but Ae( 3601) is not yet zero!
Error termination via Lnk1e in /opt/g03-e01-linda/g03/l301.exe at Tue May 11 07:17:15 2010.
Job cpu time: 0 days 0 hours 8 minutes 54.0 seconds.
File lengths (MBytes): RWF= 3881 Int= 0 D2E= 0 Chk= 96 Scr= 1
Could you help me? because I restart the job changing the geometry but It was the same, I think the problem is with SCRF=solvent=water
and the other error is:
Analytical V*U(x)*V algorithm (CHOWder, D1Eg=0). Cavity 1st derivative terms included. Solvent : Water, Eps = 78.390000 Eps(inf)= 1.776000 RSolv = 1.385000 Ang. —————————————————————————— AdVTs1: ISph= 3601 is engulfed by JSph= 3609 but Ae( 3601) is not yet zero! Error termination via Lnk1e in /opt/g03-e01-linda/g03/l301.exe at Tue May 11 07:17:15 2010. Job cpu time: 0 days 0 hours 8 minutes 54.0 seconds. File lengths (MBytes): RWF= 3881 Int= 0 D2E= 0 Chk= 96 Scr= 1
What can I do?
Thanks for your help
Ivonne
Hi Ivonne!
Thanks for your comment, I’m glad you find this blog useful.
About your two errors, unless I’m missing something here, are the same. One of the spheres surrounding an atom is overlapping incorrectly to another leading to an ill-defined cavity. Now for the solution: Keep using the SCRF=(read,…,…) option (the solvent choice is irrelevant at this point) and try some of the following options, you might even mix them and find out the best conditions for your calculations.
- Use the so called “magic numbers” OFac=0.8 RMin=0.5. This redifines the way each sphere is broke down into smaller surfaces altering in turn the way they interconnect.
- Use the NOSYMMCAV keyword. For computing reasons having a symmetrical cavity is more effective, however they tend to be unrealistic and not necessarily suitable to some systems.
- Use the NOSYMM keyword in the route section. Same reason as before but this time applied to the molecule itself and not the cavity which contains it.
- Change the radii model which defines these spheres (Default is UA0, you might change it for UAKS, BONDI or PAULING). This tends to surpass overlaping issues
As I said you might want to take a small molecule (say a nucleotide since you are working with DNA sequences) and try to run it again just the way you’ve been doing it so far, if it crashes (hopefully!) then try running it again trying these options, mix them if you need to.
I don’t know how long your sequences are but whether they are strands or bundles, I’d try to run an Onsager calculation depending on the depth of insight you need on your systems.
I hope this was helpful. Thanks again for reading and submitting your questions.
Joaquín
Dear joaquin
I want to optimize a modified dipeptide structure (CH3-lysine-serinephosphate-NH2) in solvent water using G 03. “# b3lyp/6-31+g* fopt=(maxcycle=10000) SCRF=(DIPOLE,a0=5.40,solvent=water) scf=tight”
This structure has a positive charge in lysine and a negative charge in phosphate. but it has error termination as blow:
“Error termination via Lnk1e in /home/computation/g03/l502.exe” and seeing in GAUSSVIEW the output structure was fragmented.
Can you help me?
Hello Emran
The error you mention is related to the SCF procedure. Your input seems correct. How many steps did the calculation took before the error? It would be easier for me to help you if you send me by email both your input and output for this calculation. My email is joaco_barroso/a\yahoo.com (the /a\ must be replaced by the @ symbol)
I wait for your files!
Have a nice day!
Dear joaquin
Special thanks for your attention. I will send you as soom as possible.
Best regards
Emran
Dear Joaquin
I sent the files last week. Did you receive it?
Yes Emran I got them. Sorry for not replying sooner but now you have your answers in your inbox
Cheers!
Dear Joaquin
I sent the right files.
special thanks for your help.
Emran
Hi Emran, I’m finally back from Texas! The hurricane Alex made the trip back home quite interesting.
I have seen your files and I don’t see anything wrong with them, other than the convergence is not met in the solvated structure. I see you are using SCF=tight, why don’t you try opt=tight (along with Int=UltraFine since you are using DFT). I still believe Onsager’s model is the best way for you to go because of the nature of your molecule, you just have to play a bit with the convergence criterion. Other than that I think you are doing things right. Try my suggestion and let me know how it went ok? Im very interested in this case.
I hope I can be of help
Have a nice day and keep me posted!
dear Joaquin
Finally I solved the problem using Int=UltraFine keyword I guess. Special thanks to you for your kindly help.
Emran Heshmati
Hello Joaquin, thanks so much for your blog.
Working with G03, I got an error “BldSpC: Error generating genealogic tree [..]”
Your suggestions helped me to solve the problem.
Alfredo Douglas
You are welcome Alfredo! I’m always glad to know the blog is helpful
Have a nice day
Dear Dr Joaquin,
many thanks for the helpful informations on the use of SCRF with g03.
I want to simulate implicit hydrochloric acid HCl solvent effects in G03 but I don’t know how to do it;
Any form of information will be greatly appreciated.
Thank You,
Zineb
Hi Zineb
Since I chose today to reply to blog commenters and also to catch up with my email, I couldn’t help but notice you already posted this question to the CCL.
What exactly is it that you want to calculate about HCl in solvent (I presume water)? Now if you want to simulate how does HCl becomes ionized then implicit solvent methods are NOT the way to go. Plus you should use a different model which allows you to follow a change in multiplicity from one species to another (what basis set could you use for an H+ since it has no electrons!?!?!) In order to help you I need more information on what you want to do. If you only want to calculate the properties on the molecular form of HCl then you are ok and I would suggest comparing two different models: Onsager’s (SCRF=dipole) and maybe PCM; since it is a very small molecule you could also use SCIPCM which generates an isosurface in a self consistent way (modifies the geometry and recalculates the surface, this is by far the most realistic one but of course is rather time consuming for large molecules).
I hope this helps you, I also encourage you to read those articles that were already suggested to you on the CCL. Have a nice day!
hi
thanks for the fast reply;
actually I’m studing corrosion inhibition efficiency of some organic molecules in acidic media HCl 1M;
so the solvant is HCl; in G03 I couldn’t find a way to simulate implicite HCL effect;
regards;
Zineb El Adnani
Now I get it! I’m affraid you are out of luck. This cannot be done through Gaussian and in fact it is not trivial at all! you are going to have to develop most of the science for this question since I don’t think you are going to find some tool that would allow you to just calculate it. Molecular Dynamics are imperative if you want to extract some bulk properties which are necessary to develop a model for implicit HCl.
Best regards
hi
thanks a lot for your help I was completely lost for the last few days;
one last question: can you give me some references that can help me to understand how to do it?
regards
Zineb El Adnani
Dear Joaquin,
Thank you very much for the great job you made instead of Gaussian Inc.
I try to understand what is the difference between “After PCM corrections, the SCF energy is …” and “Total free energy in solution: with all non electrostatic terms” printed by Gaussian 03. How they are calculated and why “Total free energy” is not printed by G09?
Hope to get your answer soon.
Thanks in advance,
Irena
Hi Irena
Thanks for your comment, I don’t think I am doing a better job than Gaussian INC but I do thank you for your lovely words.
When you read “After PCM corrections, the SCF energy is…” this means the energy of the molecule under the field exerted by the continuous medium over the cavity (where the molecule is located) This is a quantum quantity, just like the SCF energy you calculate with Hartree Fock, only that now is calculated under a field and not in the vacuum. “Total free enery in solution…” refers to the energy of the compound if you were to synthesize it under solution. This is a thermodynamic quantity.
“How are they calculated?” That is too long to fit in this reply but maybe I can write about it soon. In the mean time I encourage you to read the references contained in Gaussian’s manual regarding the particular model you are using:
http://gaussian.com/g_tech/g_ur/k_scrf.htm
Now for the third and final question, I don’t know if they just changed the format or if they aren’t printing it at all. I’ll tell you what you can do: run a job in G09 and the same one on G03, you should get the same results (if the new algorithm for PCM convergence in G09 isn’t doing funny things); look for your wanted section in G03 and notice the number, then look for that same number string in the file produced by G09 (maybe not using every single last digit of it). That’s what I would do! Sometimes things get labeled differently from one version to another and they wont let you know about it. I will take a look into it and see if I can find out more about it, ok?
Take care and thanks for reading!
Dear Joaquin:
I am calculating the enthalpy and free energy for complexation reaction between transition metal with chelate ligand (has four N-atoms for coordination) in both gas phase and solvent (COSMO-RS). In both cases I used tetrasolvated cluster of water molecules around the transition metal (i.e. bare metal is not used). So the reaction will be:
L + [M(H2O)4]2+ —- [ML]2+ + 4H2O (either in gas or in solvent).
I have two questions; the first: is this scenario is right? If yes please confirm me by a reference if possible. The second question, is I need to do geometry optimization for reactants and products again in solvent or single point calculations is enough for calculating the enthalpy and free energy for complexation?
Thanks in advance
Sayed
Hello Sayed!
First of all let me point out that if you are using Gaussian, asking for a COSMO-RS job actually generates a PCM job in a format that can be read by COSMO but it is not a COSMO-RS job, you know what I mean?
I’m not sure your approach is right because you need to establish the presence of a tetracoordinated metal which becomes uncoordinated upon the entrance of the ligand. I would recommend an IRC calculation (for which you need to find a suitable transition state) I ignore if IRC and PCM are compatible but since the introduction of “state-specific” PCM in G09 you might be able to make it with a low model like Onsager’s (PCM=DIPOLE). Assuming the approach was right then you would NEED to re-optimize your products and reactants in the continuous model to account for their solvation. Probably you wont find any significant diferences but this is the right procedure.
Thanks for reading the blog! Best wishes
Sir
3.Can I calculate third order permissibility by using G09,if so what is the key word used.
2.How can calculate the the thermodynamical parameters by changing temperature.What is the corresponding key word
I just realized I didn’t reply to you, I’m awfully sorry. You can do thermochemical analysis at a different from 298K temperature by adding TEMPERATURE=n (where n = the temperature in Kelvin you want to use) in the route section of the input file.
As for your first question I’m afraid it lies outside the scope of my research and therefore I have no quick answer for it.
Hope this semi-helped.
Have a nice day!
Dear sir,
I have posted two questions two days before.But unfortunately there was a mistake in the question.So I would like to repeat the same question.
1. Can I calculate third order polarizability by using G09,if so what is the key word has to use for this calculation.
2.How can calculate the thermodynamical parameters by changing temperature.What is the corresponding key word used.
Hi Xavier!
Sorry for not replying sooner.
About your first question I’m afraid I don’t know. About the second, this is very easy to accomplish: You just have to add the keyword TEMPERATURE=300 in your input file, of course here 300 is just an example you can choose whatever value (IN KELVIN!) you want, the default is 298.15K
Take a look at G09 list of keywords:
http://gaussian.com/g_tech/g_ur/l_keywords09.htm
Hope this helps!
Hey, I was just looking for info on general PCM theory and I came across your blog: I found this post very useful and I’ll be sure to have a thorough look at the rest of your blog in the near future. Keep up the good work!
I’m glad you found it useful, I’m even more glad you will become a regular reader, thank you for your kind words!
Have a nice day
I am Debasish Mandal a graduate student in Indian
Association For The Cultivation Of Science,India.I am now
try to modelling a reaction in water medium.For this at
first we use the IEFPCM solvation model,and radii=UFF
condition. But we get an error of the type “consistency
failure # sepera”.and in some cases we get ‘PCMQM-DMIVC
allocation faliure’.What could these error be due to, and
what can I do to avoid this error?
again please let me Know The basic difference between the model PCM and
IEFPCM and the condition used ‘Radii=UAHF or UFF or UAO’.
In my system H,C,O,P,S,N atoms are present. please suggest the method and
condition for get accurate result.
I shall Looking forward for your kind response
Thanking you
Debasish Mandal
Hi Debasish
Wow, I hope I can go to India next year, it is a country I really want to get to know.
Now about your questions: I’ve never seen the first error, but the second (allocation failure) means you run out of disk space. I don’t know what level of theory are you using but try using a smaller basis set. Another solution is to use %rwf in the link0 section of your input file. Take a look here to know how to use it.
PCM and IEFPCM are the same thing, well actually IEFPCM is the algorithm (which by the way is the default in SCRF calculations) by which PCM is calculated in Gaussian. As a matter of fact PCM and IEFPCM are both synonyms in Gaussian so no matter which one you use you will end up with the same calculation
About Radii:
Every model that begins with UA means “United Atoms” this means that the sphere on each atom will enclose all Hydrogen atoms bonded to it, if this fails you will see an error like “H atom unbound keep it explicit at all times”. UFF, Bondi, Pauling and others will place an independent sphere on H atoms, the radii of the spheres will differ on their definition (Pauling atomic radii, Bondi atomic radii, UFF molecular mechanics hard radii, Van der Waals radii, etc.!)
Conditions to get accurate results? Well, I’m afraid it depends on what you want to calculate and the available computers you have, so I would need more info to help you on it.
I hope this helps!
Dear Joaquin,
Thank you very much for your interest about our country. you are most welcome in India in anytime.
again thanks for your kind attention.
I am now studied a nucleophilic reaction by anion. in some of my system when UFF radii is used that gives the error of the type “consistency failure # sepera”. but when we used the radii=UA0 the job terminates normally.now I want to know what is the basic difference of the two different radii condition.Is the energy value determined from different Radii condition change dramatically?
Guassian
Dear Joaquin
am Desikan, writing this email to clarify the PCM or COSMO model.
am working in the interaction of DNA bases in solvent phase using the following key words in gaussina 09
Key word: B3LYP/6-31+G* opt SCRF=(CPCM, read)
end of the input file: Radii=UAKS
My doubt is; the above input file is PCM model or COSMO model
Pleasae clarify the same. Thanks for your help in advance.
Regards,
Desikan.
Hi Desikan
You are asking for a PCM job in your input file. In fact Gaussian CANNOT run COSMO jobs, if you ask for it the program will run a PCM job for which the output file looks like a file that can be read by COSMORS (Andreas Klamt original software)
Have a nice day
Dear joaquin
Thank you for your reply. Now i got it, my input file is PCM model calculation implemented in G09.
Hello Joaquín,
I have this error in a G03 sp calculation in water:
Error on total polarization charges = NaN
You’ve mentioned this error would be less than 0.05 to be acceptable. In my case, how can I solve this error?
Thanks for your response!
Hi Jorge!
NaN means “Not a Number” which means something went terribly wrong during your calculation. Probably the SCRF method you chose wasn’t good enough to describe the solvation cavity, but I don’t know, I need more info to help you.
Have a nice day!
Hello Joaquín:
I have this error in a G09, I use B3LYP/LANL2DZ ECP
Error on total polarization charges = 0.02039
>>>>>>>>>> Convergence criterion not met.
SCF Done: E(RB3LYP) = -2224.17498965 A.U. after 501 cycles
Convg = 0.9015D-06 -V/T = 2.0451
Convergence failure — run terminated.
how can I solve this error?
Thanks for your response!
Hi Abril!
It’s hard to say, obviously you have a convergence failure which might be caused by a bad input geometry or a bad cavity definition (you are using SCRF methods, right? I mean PCM and such). Is this a single point or an optimization? Send me your input file to take a better look and be able to help you, ok?
Have a nice day!
Please, Joaquin, could you help me?
I want to do a calculation with a different solvent from ones of the Gaussian list. The dielectric constant is 3.0, and I am using the IEFPCM, but I have not success to define this new solvent. What can I do, what are the keywords? Thanks!
Hola Flavia!
Having a dielectric constant is not enough to define a new solvent, there are many things to be considered such as the molar volume and such. Even then, there aren’t keywords -to the best of my knowledge- in Gaussian to just introduce the new solvent, it would require some editing in the source code of the program
Take care and thanks for reading!
Dear Jaquiin,
When i do the CCSD(T)/6-311++G**//B3LYP/6-31+G* single poind energy calculation using G09, after long time the out put file shows the following error. i.e.,
Warning!!: The largest alpha MO coefficient is 0.12759641D+03
How can i solve this?. Please help me. Thank You!
Regards,
Desikan.
Hi Desikan
Sorry for my late response. This is due to a colinearity or near colinearity in your basis set. Try using a smaller basis set.
I hope this helps
Hi Jaquiin,
Its indeed a very useful post. While browsing the CCL archives,I also found find more questions than answers. I am using g03 and had the error :
BldSpC: Error generating genealogic tree for sphere 1562 at level 15.
Your post was useful
as i was unable to find that answer in CCL archives. I am rerunning the jobs with the solution you suggested. Hope to get my work done. 
Hi Ankita!
I’m very glad to know you found it useful!
Thanks for reading!
hi, friends,
I want to optimize a polymer at different pH levels. like 2.5 then 2.8, 3.4 and so on. Can I do it in Gaussian. if yes then how to do this and if no then what should I do for this calculations. it is important for my project work.
Hi
Do you know the degree of deprotonation of your polymer at each pH value? if not, then Gaussian can’t predict it for you. You must somehow, probably experimentally with a titration curve, determine the ratio of your carboxylic groups which will become deprotonated at each pH value and then take a guess on which of them will remain as COO- in the actual molecule, define the total charge of the molecule (the multiplicity wont change) and then optimize it with Gaussian.
We used to do this back at my old job all the time with polyacrilic acid and we always had good results when combining the study with molecular dynamics for geometries -radius of gyration.
I hope this helps and thanks for reading!
Dear Dr. Barroso, I spend a lot of time dealing with PCM calculation a I often have failure problems. As you said, in the CCL website you find more questions tahn answers. I find your post very useful and easy to understand. Thank you!!
Gracias Matias! I’m glad to know you have found it useful.
Have a nice day!
Thanks for the website.
Thank you for reading Matt! I’m glad to know the site’s been helpful
Cheers!
Dear Dr Barroso,
I have a very simple (and dumb) question.
I need to do a single point energy calculation #p HF SCF=CONVER=12 6-311g* SCRF
and it keeps giving me an error which says Consistency failure #1 in Separa.
And after adding in SCRF=(READ,PCM,SOLVENT=WATER), OFac=0.8 and RMin=0.5 the same error was still given. May I know how do I rectify this?
Thank you so much for your help!
Ashley
Hi Ashley!
Your question is not dumb at all! In fact I had never seen this problem before. According to the first paragraph of your message you ran a single point calculation in a vacuum, then you try to fix it by simulating a water medium surrounding your molecule. Am I right?
I think I need more information to solve your question but I would start trying the following:
1) Use another basis set. Try using a smaller one, say 3-21G**. If this works you might try to fix the energy value by launching an MP2 calculation on the resulting wavefuntion.
2) Change the SCRF model. If your system has a net dipole moment (larger than zero) use the Onsager model by changing the PCM keyword by Dipole this will generate a spherical cavity around your system, instead of trying to define a more neat, accessible and physically realistic cavity, it is a first approach but it just might work.
I hope this helps but if it doesn’t please let me know, ok?
Have a nice day and thanks for stopping by!
Dear Dr Barroso,
Thank you for your prompt reply! I have learnt so much from you web. I will try the methods you have suggested.
The following is the input file for my gaussian calculations:
%chk=001298
%nproc=1
%mem=2gb
#p HF SCF=Conver=12 6-311g* SCRF
1.000000000000 Nonbonded frag 1298 = 23 26
0 1
7 -8.956096000 -1.494101000 -1.435722000
6 -9.807413000 -2.658919000 -1.147287000
1 -7.960251000 -1.549003000 -1.224367000
1 -10.398438000 -2.896867000 -2.040642000
6 -8.998589000 -3.866795000 -0.747318000
1 -9.693745000 -4.714102000 -0.527537000
1 -8.308095000 -4.171196000 -1.571661000
1 -8.382622000 -3.661540000 0.163457000
1 -9.299284381 -0.759722442 -1.891027252
1 -10.566002747 -2.479356364 -0.369470786
7 -11.948153000 0.957776000 0.905991000
6 -12.659790000 2.229517000 0.723569000
1 -10.983488000 0.920131000 0.582042000
1 -13.560595000 2.170053000 1.346986000
6 -11.855710000 3.436675000 1.143184000
1 -12.424651000 4.364177000 0.885984000
1 -11.673566000 3.421609000 2.245101000
1 -10.864857000 3.465027000 0.624227000
1 -12.243202170 0.322143837 1.529824027
1 -13.021085364 2.407957078 -0.298910455
I have done the exact calculations for many other systems and they all worked. This is the only system that keeps giving the same error. And I can’t figure out the source of this error. Thanks once again!
Regards,
Ashley
Hi Dr Barroso,
I have managed to solve the problem by just simply rearranging the order of the atoms. Thanks so much for your help.
Regards,
Ashley
Very useful post! I have found a great explanation on some issues related to PCM that I hardly could handle!!
Thanks for sharing your experience!
Dear Dr. Joaquin Barroso,
I have found your post recently.I hope that you will solve my problem.I calculated the optimization of several structure,but when the simple structure was repeating and become bigger optimization lead to error termination link 502 (convergence failure).I try to change the input file but it is not succeeded.Somtimes I use the scf=qc on the route section,but it doesnot work too.I am looking forward to hearing from you soon.
Sincerely,
Mehri
Hi Mehri,
I’m not so sure what your problem is. I need to know more about your system and the calculation you are running.
Have a nice day
Dear Dr. Joaquin Barroso,
Thank you for your attention.I work on polymer in g03 and try to optimize some structure like as P3HT.It can be succeeded until 7 monomer , but I stopped with 8 monomer with the error termination such as Link 502 or 508.It can be happened because of the structure became big.What am I doing with that?Do you have any suggestion dear Dr?
Best Wishes,
Mehri
P.S:I was so pleasure that you are in love with your wife.I hope its continuing for a millione years.
Dear Dr. Joaquin Barroso
i have found your post recently, its very interesting and helpfull,,
i have a problem with my calculation. i try to optimize p-hidroxychalcone in gas and aqueous solution(solvent=water and methanol). i try to use C-PCM with this following input
%mem=70MB
———————————————————————-
# opt rb3lyp/6-31+g(d,p) scrf=(cpcm,solvent=water,read) geom=connectiv
ity scf=(xqc,maxcycle=512,vshift=100)
i success run my calculation without error, but i found this on my logfile
Requested convergence on MAX density matrix=1.00D-06.
Requested convergence on energy=1.00D-06.
Virtual orbitals will be shifted by 0.100 hartree.
No special actions if energy rises.
Restarting incremental Fock formation.
Error on total polarization charges = 0.03843
SCF Done: E(RB+HF-LYP) = -729.331123241 A.U. after 20 cycles
Convg = 0.3677D-08 -V/T = 2.0100
S**2 = 0.0000
but the calculation still run until its finished
Do you have any suggestions for my problem Dr.Joaquin?
Best Regards and Thank you very much
Dear Dr. Joaquin Barroso,
Please help me~
Input file:
pt freq b3lyp/6-311++g(2df,2p) scrf=(iefpcm,solvent=dmso,read)
geom=connectivity
..
Icomp=3
TSNUM=60
TSARE=0.4
radii=bondi
alpha=1.20
Output file:
Polarizable Continuum Model (PCM)
=================================
Model : PCM.
Atomic radii : UA0 (Simple United Atom Topological Model).
Polarization charges : Total charges.
Charge compensation : None.
Solution method : Matrix inversion.
Cavity : GePol (RMin= .200 OFac= .890).
Default sphere list used, NSphG= 230.
Tesserae with average area of .200 Ang**2.
1st derivatives : Analytical V*U(x)*V algorithm (CHGder, D1EAlg=0).
Cavity 1st derivative terms included.
Solvent : DMSO, Eps = 46.700000
Eps(inf)= 2.179000
RSolv = 2.455000 Ang.
——————————————————————————
BldSpC: Error generating genealogic tree for sphere10463 at level 15
I don’t know how to fix this error~
Please help me~
My moleculer is quite big~ maybe d=1.6nm
Hi doctor,
I am interested in the pH discussion.
I want to calulate the effect of pH on the chemical shifts of molecules. Can you give me please a tip about the determination of the deprotonation degree, and is it always called deprotonation in the case of acid or base (i.e why we do not consider that the molecule may gain a proton).
Hint; the molecule I am studyng is found in a mixture of other molecules with a given pH each time.
Hola Dr Joaquin,
Estoy tratando de optimizar complejos unidos por puentes de hidrógeno, entre el 4F-PhOH…Base. Las bases son Acetona, Imidazol, ciclohexeno, N-oxidotrimetilamina. el método y conjunto base utilizado es:
____________________________
%chk=complex_oxido.chk
%mem=20GB
%nproc=12
# maxdisk=400gb
#P Opt freq=(NoRaman) MP2(full)/aug-cc-pvdz scf(xqc,vshift=150,tight) output=wfx GFInput IOP(6/7=3) IOP(8/6=30) density=current test
/*complejo_oxido*/
0 1
coord
complex_oxido.wfx
__________________________________
Sin embargo he tenido problemas al calcular las frecuencias para el complejo formado entre el 4F-PhOH y el N-oxidotrimetilamina. El fichero de salida marca un error en las frecuencias el cual es:
_________________________________
LinEq1: Iter= 16 NonCon= 1 RMS=6.34D-11 Max=1.37D-09
LinEq1: Iter= 17 NonCon= 1 RMS=2.60D-11 Max=1.27D-09
LinEq1: Iter= 18 NonCon= 0 RMS=9.35D-12 Max=2.54D-10
Linear equations converged to 1.000D-10 1.000D-09 after 18 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 28 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.
___________________________________
He leido que al parecer es un problema de dependencia lineal.
Quisiera saber su comentario y ver si me podria ayudar?
Att,
Yazmin Carrasco
Jacinto Sandoval
FC Quimicas-Posgrado
BUAP
Thank you for this helpful post! Several calculations were failing while generating the cavity, and your suggestions here have allowed those calculations to proceed.
Is possible ask a question on to PCM program GAMESS.11 ?
I’m sorry Alexandr, I have no experience whatsoever in working with any version of GAMESS.
Have a nice day
Dear Joaquin,
Thank you for your reply.
I still do not leave hope to solve my project.
I want to gradually increase the number of spheres of PCM and monitor changes in the vertical transition energies (absorption spectrum).
In a series of programs GAMESS, I would not succeed.
Can I do this in the G03 or 09?
With regards
Alexandr
Dr. Borasso,
This blog is really helpful to get things clear and understand conceptually….thanks:)
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