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

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About joaquinbarroso

Computational and theoretical chemist in his early forties, in love with life, science, baseball, and literature. Science literacy makes us responsible citizens, it is therefore a scientific duty to talk, write, and engage with the general public; as Feynman said, if you find science boring, your learning from the wrong teacher. "Make like a molecule and react!"

Posted on September 7, 2009, in Computational Chemistry, Gaussian, White papers and tagged , , , . Bookmark the permalink. 208 Comments.

• Comments 206

1. 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

• Kuo

Thanks.It helps me a lot.

2. Kathy

I reiterate Muhavini’s comment. Thank you!

3. Jevgenij A. Raskatov

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.

4. luca basolo

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

5. Sema

Thank you for the helpful information!

• You are welcome Sema! Thanks for commenting and stopping by.

Greetings from Mexico

6. Emrys Thomas

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!

7. ivonne otero

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

8. 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

9. Emran

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!

10. Emran

Dear joaquin
Special thanks for your attention. I will send you as soom as possible.
Best regards
Emran

11. Emran Heshmati

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!

12. Emran

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!

• Emran

dear Joaquin
Finally I solved the problem using Int=UltraFine keyword I guess. Special thanks to you for your kindly help.
Emran Heshmati

• Emran

Dear joaquine
I want to calculate the dipole moment of a part of a big molecule. this part isn’t neutral and has net charge. after much more unsuccessful trying for calculate the dipole moment from the geometry and partial charge of atoms, I decided to use 2 layer ONIOM computation using Gaussian (I define this part as high layer). Now I have 3 dipole moment in Gaussian output. which is the dipole moment of high layer?

• If you want to calculate the dipole moment of only a part of the molecule, then I would run a single point of only that part of the molecule taking care of defining correctly the charge and multiplicity of this fragment. Try optimizing the entire molecule and then delete all atoms except those that form your part of interest and run a single point. That should work

I hope this helps. Have a nice day!

13. Alfredo Douglas

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

14. zineb El Adnani

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!

• zineb El Adnani

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

15. zineb El Adnani

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

16. Irena

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!

17. Sayed Mesa

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

18. xavier

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!

19. xavier

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!

20. 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

21. Debasish Mandal

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

22. 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!

23. Debasish Mandal

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?

24. Desikan

Guassian

25. Desikan

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

• Desikan

Dear joaquin
Thank you for your reply. Now i got it, my input file is PCM model calculation implemented in G09.

26. Jorge

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!

27. Abril Castro

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!

• Hi Joaquin, I find the same error, can you please help? I don’t know the email address to send my input file.
Thanks

• Send it to joaquin.barroso|at|gmail|dot|com
I hope I can give you a useful answer in a proper amount of time

Have a nice day!

28. Flavia

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!

29. Desikan

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

30. Ankita Kumari

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!

31. Arobendo

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!

32. Matias Sancho

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!

33. matt

Thanks for the website.

• Thank you for reading Matt! I’m glad to know the site’s been helpful

Cheers!

34. ashley

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!

• ashley

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

• 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

• anonymous

Hi.
Setting “Volume=Tight” solved it for me.

35. Miguel

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!

36. Mehri

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

• mehri

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.

37. 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

• Hello there,

Sorry for the lateness of my response. You’ll be glad to know you have no problem. This is only normal. The error on polarization charges is only the diference between the number of electrons that are supposed to be inside the cavity and the number that there actually are; if it is below a certain threshold then the calculation continues. This is only a checking point, don’t worry about it.

I hope this helps. Have a nice day!

38. Hieido

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

39. Zeinab ATIEH

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.

40. Yaz

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

41. mickey

Thank you for this helpful post! Several calculations were failing while generating the cavity, and your suggestions here have allowed those calculations to proceed.

• I’m glad I can help!
Thank you for your comments, Mickey!

Have a great day

42. Alexandr

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

43. Alexandr

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

• Hi Alex,

I would do it with SCIPCM that way the cavity becomes recalculated at every step of an optimization (assuming thats what you want to do). Increasing the number of spheres is possible but a bit tricky. Read the following link in order to learn how to do it.

http://www.gaussian.com/g_tech/g_ur/k_scrf.htm

I hope this helps. Have a nice day!

44. prema

Dr. Borasso,
This blog is really helpful to get things clear and understand conceptually….thanks:)

• Thank you Prema! I hope it continues to be useful in the future

45. Padma

Dear. Borasso,

I am trying to optimize the structure of an alkaloid in solvent system using DFT , basis set STO3G. The compound is getting optimized in gas phase. when i try to do it in solvent, after few hours the program gets terminated. The error is 2070 and it says convergence failure.
I am an amateur trying to start my work related to quantum chemistry. It would be really helpful if you could suggest me how I can learn the concepts behind Gaussian program. We have G03 version in our lab.

46. chemdz

Hi Padma,
the problem is due to to the allocated memory you asked in your Gaussian input (
try to decrease the memory size, it will solve the problem

Sincerely;

• adel

thanks alot

47. ALI

Dear Dr. Borasso

I want to run a solution phase with this order;

# HF/6-31+G(d) scf=tight scrf=( IEFPCM, solvent=Acetonitrile, read)

ALPHA=1.35
SCFVAC
RADII=BONDI

Unfortunatedly, when i ran that, i saw this output:

Using the following non-standard input for PCM:
ALPHA=1.35
SCFVAC
RADII=BONDI
— end of non-standard input.
——————————————————————————
Polarizable Continuum Model (PCM)
=================================
Model : PCM.
Atomic radii : Bondi.
Polarization charges : Total charges.
Charge compensation : None.
Solution method : Matrix inversion.
Cavity : GePol (RMin=0.200 OFac=0.890).
Default sphere list used, NSphG= 3.
Tesserae with average area of 0.200 Ang**2.
Solvent : Acetonitrile, Eps = 36.640000
Eps(inf)= 1.806000
RSolv = 2.155000 Ang.
—————————————————————————–

IEFPCM model was replaced with PCM and alpha did not change and only scfvac and radii were applied. also, it should be said that my goal is deltag solvation. I used gaussian 03 version c.01.

• Hello Ali,

No. The Solvation Model was not changed. IEFPCM and PCM are synonyms in Gaussian. IEF stands for Integral Equation Formalism, that is, this is only the computational way in which the PCM model is actually calculated.
Take a look at the Gaussian website, type in google SCRF.

Hope this helps! Have a nice day

• ALI

Thank you for suggestions. My question arises from one paper that used acetonitril solvent with bondi radii, iefpcm solvation model and applied SCFVAC keyword. Its wonderful when i repeat that, unfortunately, the same results don’t obtain.

48. Hi Joaquin,
I`m new in computational chemist. I have been working calculating delta G of solvation in g03 for different molecules. but now i want to calculate the same but for these molecules in complex with another molecule (a pair). but it is not working… the command line i used is this:

#p b3lyp/6-31G* scf=tight int=finegrid SCRF=(PCM,Read,Solvent=Water) geom=connectivity

in g03, but it gives me only this parameters,
——————————————————————–
Variational PCM results
=======================
(a.u.) = -1184.773004
(a.u.) = -1184.812984
Total free energy in solution:
with all non electrostatic terms (a.u.) = -1184.775090
——————————————————————–
(Polarized solute)-Solvent (kcal/mol) = -25.09
——————————————————————–
Cavitation energy (kcal/mol) = 51.64
Dispersion energy (kcal/mol) = -29.85
Repulsion energy (kcal/mol) = 1.98
Total non electrostatic (kcal/mol) = 23.78
——————————————————————–
not as in the molecules by separate where the Delta G of solvation appears at the end.
I dont know if the command line is not ok for a complex, or if in g03 it is not posible to calculate deltaG of solvation for complexes.

I really appreciate your help!
Best!!

thanks
xaviera.

49. devi

Dear sir,
Please explain me, how to write input file for solvation effects were accounted for explicit addition of different number of water molecules (for example n=1 to 7) for hydantoin-5-acetic acid molecule in Guassian 03.
Thanking you,
Ms. Devi.

• If you want to include explicit water molecules in a calculation in G03 you have to do it manually, i.e., build the molecule in gaussview or any other visualization tool and manually add the water molecules.
Gaussian only allows for implicit solvation not explicit.
I hope this helps.

50. ken

hey there Joaquin,
I’m a long time reader, first time poster.
I have a rather strange question and decided to post it here because its the only place I’ve seen similar errors. There have been several other people in this thread posting about “internal consistency” errors but I fear that their solutions have not worked for me.
what I’m trying to do is generate a relaxed potential energy surface (using redundant internal coordinates) at the UB3LP/6-31+G(d,p) level followed by a higher level SP calculation with UCCSD(T)/aug-cc-pVDZ for every scanned point on the surface, all in one input file. I’ve been trying to use something like:

– #CCSD(T)/aug-cc-pVDZ//B3LYP/6-31+G(d,p) opt=modredundant geom=connectivity

but I get the error:

– CompJT: unrecognized IType=13.
– Error termination via Lnk1e in /usr/local/g09/l1.exe

I’m not even sure if it is possible to do that type of calculation… so i decided to simplify the calculation;
However, when I use the normal input:

– #CCSD(T)/aug-cc-pVDZ//ub3lyp/6-31+g(d,p)

I get this error:

– Warning: this job cannot use analytic gradients
and so will do many energy evaluations.
– Internal inconsistency #2 in ROv01.
Error termination via Lnk1e in /usr/local/g09/l1.exe

I haven’t been able to find solutions through conventional means, so at the risk of sounding like noob, in the event that there is a very simple solution to this problem I thought I would ask you. Since your articles have answered so many of my questions in the past.

Thanks so much!

51. I do not even know the way I finished up right here, however
I assumed this put up was once good. I do not recognize who you might be but definitely you are going to a well-known blogger in case you are not already.
Cheers!

52. An outstanding share! I have just forwarded this onto a co-worker who had been doing a little research on
this. And he actually ordered me lunch simply because I stumbled upon it for him.
.. lol. So let me reword this…. Thanks for the meal!

! But yeah, thanx for spending some time to talk about this issue here on your site.

53. kamal

I have a problem in gaussian want to run my molecule with solvent as acetonitrile using DFT (B3LYP, 631G). but i dont know how to start correctly. What are these keywords for? Actually whnvr i start the molecule it give some understandable errors . Thank You

54. abeer

dear sir

what that statement mean( End of G2Drv Frequency-dependent properties file 721 does not exist.) when we use Gaussian 05 to solve high molecule

with best regard

• It means you are making a reference to a file that has not been created or that has been deleted.
I hope this helps

• abeer

how i can solve such problem

55. Hurrah, that’s what I was exploring for, what a data! present here at this webpage, thanks admin of this web page.

56. I always spent my half an hour to read this
blog’s content daily along with a mug of coffee.

57. alejandro piedras

que tal Dr. Joaquin,

estoy haciendo cálculos, con g09, de absorción y emisión, pero en los archivos de salida tengo

” **** Warning!!: The smallest alpha delta epsilon is 0.27187962D-01 ”

ya lei en este blog su respuesta, bajarle al tamaño de base que se esta usando. La base que ocupé fue la 6-31+G. la pregunta ¿hay alguna otra forma de eliminar el warning? estoy pensando en aumentar la tolerancia de un parametro.

saludos y lo felicito por este epsacio tan útil

alejandro

58. jayshree

as u noted above “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.”
I have doubt what if that values goes beyond 0.05???what one should do to kip it less than 0.05?

59. I always used to read piece of writing in news
papers but now as I am a user of web thus from now I am
using net for articles or reviews, thanks to web.

60. Ashley

Hi Joaquin,

I have a rather strange question, I know that IPCM models the cavity using isodensity. But what happens if I include the command (ipcm, read) and radii=UAHF. In this case will the cavity be modeled using isodensity or UAHF?

Thank you!!!!!
Ashley

• Hi Ashley

Strange questions are often the most interesting ones! It would have never occured to me to use both formats at the same time. Have you done it? doesn’t it end on an error?
In order to find out the answer I would launch a test job of a small molecule, lets say methane or CCl4 or something like that. Run it with IPCM (no read) also with PCM read UAHF and a third calculation with IPCM read UAHF, and see to which of the first two does the third one correspond.

I hope this helps and please come back and share your findings!

Have a nice day

• Ashley

Hi Joaquin,

I have done it and it does not end on an error. What do I look for in the log file to see which cavity it corresponds to?

Thank you!

61. emran heahmati

Dear Joaquin
Thanks for your help. now I have another question. Is it possible to run computation on molecule when its net charge isn’t an integer (for example -0.67 esu) in gaussian 03??

• No, charges are defined in integers numbers.

• Emran Heshmati

Dear Joaquin
I am working on a molecule with 2 NH3+ and 1 COO- charged groups. The charge of this molecule in +1, but I am in doubt about its multiplicity. I need your help.
Emran

• Dear Emran,

I’m assuming the rest of your molecule is a normal organic fragment.
Organic molecules (C, H, O, N, S) with neutral charge have always singlet multiplicity. If you deprotonate a residue, like you did when going from RCOOH to RCOO(-), you keep the same multiplicity because you removed a proton while the electron count stays the same.
Same thing if you protonate a basic residue, like you did when going from RNH2 to RNH3(+). You just added a proton, the electron count hasn’t been affected.

In short your multiplicity remains as 1 🙂
your input should read something like this:

#route section keywords

1 1
coordinates

I hope this helps. Have a nice day!

62. Praveen Saini

Dear Joaquin,
while optimizing a structure of nitrone of my interest in Gaussian using CASSCF AND 6-31G basis set i am getting an error massage
“Convergence failure — run terminated.
Error termination via Lnk1e in C:\G09W\l510.exe”
please help

63. elahe

Dear Joaquin
I am interesting in calculation peptides structure in solvent model using GAUSSIAN. Is it possible to geometry optimization using IPCM and SCIPCM solvent model? I used these keywords in rute section: # opt freq pop=nbo b3lyp/D95 SCRF=(SCIPCM,solvent=water), but it terminates erroneously as below: Error termination via Lnk1e in /home/elahe/g09/l502.exe .

• That is only the exiting error, there is no information regarding the status of your calculation in that line. Please provide the last 10 lines so I can help you properly.
SCIPCM is more time and memory consuming, be careful and mind the kind of computational system you are working with. SCIPCM is also the highest quality (more meaningful) model available since the cavity gets recalculated with every optimization step.

Have a nice day

• elahe astani

Hi. what is multiplicity of mercury 2+?

64. mohammad

hi
I have got problem with CPCM model. I would like to calculate freq of a molecule taken in some solvents. I found that dielectric constant for these solvents and my keyword line is
# b3lyp/6-311++g(d,p) scrf=(cpcm, dielectric=1.0005870)
If I use “solvent=water” instead of “dielectric=1.0005870” there is no problem with calculations. If I use dielectric constant of water there is this error :
Raffenetti 2 integral format.
Two-electron integral symmetry is turned on.
50 basis functions, 72 primitive gaussians, 51 cartesian basis functions
5 alpha electrons 5 beta electrons
nuclear repulsion energy 13.6865182256 Hartrees.
NAtoms= 5 NActive= 5 NUniq= 2 SFac= 3.00D+00 NAtFMM= 80 NAOKFM=F Big=F
Illegal ISolv in PCMInp.
Error termination via Lnk1e in E:\G09W\l301.exe at Sun Jul 14 11:15:16 2013.
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
please help me . thank you
by : khavanim@yahoo.com

• Defining a dielectric constant alone wont help you get a meaningful result since other variables are to be expected.
Gaussian offers a wide selection of solvents for SCRF calculations, I suggest you stick to that list; if the solvent you are interested in isn’t listed then try using a similar one from within the list.

Have a nice day!

65. Andy

Hi Joaquin,
I hope you don’t mind me asking a question abut PCM.

I haven’t found a good answer to this elsewhere — COSMO assumes that the gas phase and solvation phase geometries are very close, and so solvation energies are obtained by carrying out single point calculations on the gas phase geometry.

I would have presumed that this is the case with PCM, but e.g. http://www.gaussian.com/g_tech/g_ur/k_scrf.htm even lists an example where a structure is optimised with PCM.

Would you happen to know what the proper approach is here when using PCM? I’m not really after the solvation energy explicitly, but am looking at the reaction enthalpy for simple reaction. In most cases the results are fine, but in cases where there’s a large number of degrees of freedom, the difference in the gas phase and PCM structures can yield differences in reaction enthalpies of around 5 kcal/mol between the gas phase and PCM reactions. For systems where the gas and solvent phase structures are very similar, the differences are typically on the order of 0.5-2 kcal/mol.

Or so it seems.

66. Having read this I believed it was really
enlightening. I appreciate you finding the time and energy to put
this information together. I once again find myself personally
spending a significant amount of time both reading and commenting.
But so what, it was still worthwhile!

67. I was wondering if you ever considered changing the structure of your site?
Its very well written; I love what youve got to say. But
maybe you could a little more in the way of content so people could
connect with it better. Youve got an awful lot of text for only having one or two pictures.

Maybe you could space it out better?

• Well, thank you very much for your comment and thanks for your kind words about my blog. Could you be more specific about the layout proposal?
I don’t use many pictures, maybe I should. About the spacing, I’ll leave some indents or extra blank lines between paragraphs but I don’t think I can change the spacing settings that wordpress provides with this free theme.

Thanks a lot for your observations! Have a nice day!

68. Hi there, yuup this post iis actually good
and I have learned lot of things from itt concerning blogging.
thanks.

69. Philippe

This blog is a virtual treasure trove of computational tips! Many thanks for keeping it updated 🙂

70. elahe astani

Dear joaquin
I have problem with this command in rute section:
MP2/6-31+g* opt SCFR=(dipole, a0=4.33, solvent=water)
it got error as:
error termination via lnk1e in C:/ . . . . . 11.exe
is it possible to help me?

71. Fatemeh

Hi,

Thank you for your useful posts. I am a graduate student and sometimes I solve my Gaussian related problems by reading your weblog. Even your answers to the questions in the comments sometimes help.Thank you!

I actually have a general question about the differences between SCRF=PCM and SCRF=SMD in G09. As far as I know, in theory SMD includes corrections for CDS (cavitation, dispersion and solvent structure effects) while PCM does not. In practice, SMD distorts and reorients the gas optimized structures much more than PCM does and also SMD gives more accurate solvation energies compared to PCM ( though SMD has been parameterized more carefully on a large number of input solvation free energies, so its success over PCM may be just as a result of its optimized parameters for delta G and not because of its more realistic structure !?). So, is the more distorted SMD optimized geometry more reliable than PCM? In fact, I have not seen many papers using SMD??

The other question is that are vibrational IR frequencies calculated with SCRF optimized geometry reliable or preferable over vacuum frequencies? And if yes, since the normal mode vibrational frequencies calculated at SMD differs with those obtained by PCM, which one is more reliable?

I would really appreciate if you could help me with these questions. I saw that you answer the questions on the comments very carefully and I thought that may be I can get blessed and find my answer too.

Best regards
Fatemeh

72. I’m not that much of a online reader to be honest but
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dear dr joaquin

‘m new to the area, and I’m trying to make the example contained in the G09 guide on SCRF ( http://www.gaussian.com/g_tech/g_ur/k_scrf.htm ). I follow all the steps and can not evolve.

please help me in this simple example?

sorry if the question is stupid.

Thanks and continue with your blog, it is very important.

fernando

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Dear Dr. Joaquin sir,
In methanol medium I was doing freq calculation in opt=qst2 route with basis set b3lyp/6-31G* for a TS structure (from its optimised coordinates in gas phase), it was showing the error 21 H is unbound, then I gave SPHEREONH=21, then it was showing 23 H was unbound (actually my molecule has two phenolic H), then I gave SPHEREONH=21,23 (next time SPHEREONH=21 23), but it was showing wrong input 23. So please guide me sir how to give individual sphere on both the H’s and what would be the input for this section?

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I optimized a molecule in a specific concentration of solvent(methanol) with eps=68.0 (from experiment) using G09. But for doing a frequency calculation it require eps(inf) value. I am curious to know how one can obtain the eps(inf) value for a particular concentration of a solvent.

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118. Jonathan

Hi, I have this problem:

>>>>>>>>>> Convergence criterion not met.
SCF Done: E(RPBE-PBE) = -1893.03326259 A.U. after 1026 cycles
Convg = 0.1726D-05 -V/T = 1.9804
Convergence failure — run terminated.
Error termination via Lnk1e in /usr/local/g09/l502.exe at Tue Sep 30 23:12:42 2014.

my original input is this one:

#n pbepbe/gen pseudo=read td=(nstates=20) scrf=(pcm,solvent=water)
SCF=(Direct,Maxcycle=1025)

I´m working with a Zn complex and i already tried different SCF convergence methods like QC an XQC and have the same problem but with XQC i have a different error

NROrb= 842 NOA= 107 NOB= 107 NVA= 735 NVB= 735

**** Warning!!: The largest alpha MO coefficient is 0.10784743D+02

**** Fatal Problem: The smallest alpha delta epsilon is -0.95271819D-03

Error termination via Lnk1e in /usr/local/g09/l801.exe at Wed Oct 1 02:26:48 2014.

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122. Chris

Hi Joaquin,
I’m not sure whether you read the comments left anymore (it looks like some of the spamming has got a little out of hand, but this is just a note to let you know that your blog has been invaluable to me throughout my degree. It has served as an excellent first port of call with any of my computation based problems (even before ccl in most cases). Thanks again for your excellent blog.

As a final note of help to me, I am wondering if you know what the units of the ‘error on total polarisation charges’ are. Is the value presented as a proportion (%?) or does it carry units of charge. Many thanks once again,

Cheers,
Chris

• Hi Chris,

First of all thanks a lot for your kind words about my little blog! It is so rewarding to know that people actually reads my ramblings! I try to keep up with comments and questions but as you can imagine it takes a lot of time, a luxury I seldom have. Its true the spam has gotten out of hand and I thought I was deleting those comments but I guess I’m not doing it efficiently; hopefully this winter break will let me dive into the guts of wordpress and deal with spammers once and (almost) for all. But I will try to keep up with comments, thank you very much!

About your question, I’m almost certain that the error is a percentage but let me check it. If I don’t reply again please REMIND ME with a new comment, ok?

Best wishes!

123. Sara

Dear joaquin

I want to do DFT studies on properties of unit cell of NiTi alloy by Gaussian software, but I have some mistakes in computational methods. First of all, I build inputs by gaussview software and apply periodic boundary conditions (PBC). However, methods are selected using DFT/HSEH1PBE or PBEPBE with the GEN or GENECP basis sets but I get link 302 “error” in my outputs.

I am quietly needful of your help and waiting for your kind and valuable words.

Best regards

• Hi Sara,
links are the programs with which Gaussian works so I need more information about the error you are getting in order to help you.

Have a nice day!

124. lokesh kumar agarwal

Good evening sir, what is the difference b/w SCIPCM and IPCM Model, how can we put dielectric constant of a solvent (which is not in default list)

• Hello

SCIPCM re-calculates the shape of the cavity in a self consistent way (hence SC-IPCM), in other words, the shape of the cavity is also optimized as you procede with your molecular optimization. This procedure is of course more computationally demanding and I would advice to use it carefully.
About introducing a new dielectric constant, I would advice against it since you also need to introduce other features such as molar volume for the solvent and it would be best if the potential is parametrized/fitted and you cannot do that with Gaussian’s code.
If you insist on doing it then use SCRF=Read and after the input place the following information:
Eps=X1
Epsinf=X2
Rsolv=X3
Where Xi refers to static dielectric constant, dynamical dielectric constant and solvent radius in Angstroms, respectively.

I hope this helps

125. alex

Dear Dr. Barroso

I am working naftalimide fluoresence, using G09. I had done two steps, the first is the ground state geometry optimization (and Freq of course), second is td-dft calculation. In order to perform the last step emision), the input file have to indicate the excited state to optimize. What if the first excited state, in the second calculation, have a oscillator strength value les than 0.05 and some other have a higher oscillator strength. Which one is the correct to write in the last input file.

I appreciate your comments, i work in synthesis, but now i am trying to make my first steps in theoretical chemistry

regards

• Definitely you want to go with the one with the higher oscillator strength.
Welcome to CompChem 🙂

126. saf85

Dear Dr. Barroso
Can I study a system of Molecule-surface using G03W software? 🙂
I am studying now the hydrogen molecule adsorbed on some ionic surfaces.

• saf85

Best regards.

• Hi there

In principle you can but beware of the following: 1) Gaussian is not the best option for the large calculation you need, for if you want to get rid of border effects you need a very large surface. 2) you are using a very old version of the software and the fact that you are using the windows version leads me to believe you are trying to run things in a regular PC which won’t support a large calculation in an efficient way.
I recomend using CRYSTAL if you can get a hold of the license which is rather expensive. You could associate with someone who has a more recent version of gaussian and a propper computing facility.

I hope this helps and thanks for stopping by

127. Fatih Yıldız

Dear Dr. Barroso

first question:
i have used gaussian 09 with NBOPro6 for calculation of meral bounded to carbonyl and nitrogen of prymidine system.
firstly, i do geometry optimizations in solvents using PCM using dichloromethane, cyclohexane, etc.
which settings can i do for solvent system in gaussian to take best results.
i have added to end line of my input file for pcm read section as iterative, cav, Dis, Rep keywords. is it true for metal system.
finally, do i add extra sphere to my solvent calculation.

second question:
for above calculation, i use NBOPro 6.0 for describing bonding properties. But, Metal-Nitrogen bond(dative bonds) is not seen as 2-center (BD) and 3C-4e hyperbond for any DFT methods. metal-nitrogen bond(s) is not formed. is the NBOPro 6.0 recommended for this metal-nitrogen bond systems?
or can i find this bond describing with other ways in NBOPro program

Help pls for the best calculation

128. Francesca

Thank you for this very useful post. I learnt a lot from it. I finally have my PCM calculations terminating without errors (at least some of them), but they all give high “error on total polarisation charges’, between 0.05 and 0.1 (sometimes even larger). Do you have any suggestions for how to proceed to reduce this error? The system is a small silica particle terminated by H/OH with organic groups attached to some of the Si.

Best regards,
Francesca

• Hi Francesca!

I’m glad to know you’ve found the blog useful. In order to reduce the error on total polarization charges I would suggest to either increase the size of the cavity by modifying the radii model employed or cheating a little bit by reducing the polarization of your basis set.
I wouldn’t worry about this error (unless its too large) because it is an error on the model not your calculation.

I hope this helps!

129. Abbey Philip

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 Abbey,

You should just delete de SCRF keyword and all the commands for it inside the parentheses. This will eliminate the solvent from your calculations.
I hope this helps

130. Celia

Dear Dr. Barroso,

I was wondering whether you could comment on the difference between radii uff, pauling and bondi. To my understanding, all three use explicit hydrogens, but I don’t know which is the fundamental difference.

Much appreciated if you could reply,

Celia

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132. Hi Dr J. Barroso,

I am trying to locate transition states for each step of a solution phase reaction using:
#n CAM-B3LYP/6-311++G(d,p) Opt=QST3 scrf=(solvent=TetraHydroFuran) Freq

Previously, all steps were successfully found (one imaginary frequency) in vacuum, but I would like to generate a solution phase model for more realistic chemistry. While a few steps seem to work, others give either one of two errors:

(1) – multiple bends and dihedral ‘fails’

Bend failed for angle 5 – 4 – 9
Tors failed for dihedral 9 – 4 – 5 – 2
Tors failed for dihedral 5 – 4 – 9 – 11
FormBX had a problem.

or (2) – convergence failures

Restarting incremental Fock formation.
Restarting incremental Fock formation.
Restarting incremental Fock formation.
>>>>>>>>>> Convergence criterion not met.
Error on total polarization charges = 0.02464
SCF Done: E(RCAM-B3LYP) = -6260.01082537 A.U. after 129 cycles
NFock=128 Conv=0.12D-02 -V/T= 2.0013
Convergence failure — run terminated.

All reagents/transition states/products are highly polar/ionic so I’m finding it difficult. I’ve tried using restarts and SCF=QC but get the same results. May I ask if there is a better long-range correlation functional?

Thanks very much for your informative blog and help.

• Dear Leighton,

I’m very sorry for the delay of my response. There have been many changes to the SCRF module and I should review them here in the blog; that is a post long overdue.
My guess is your problems relate to the cavity, since you are using PCM by default, the size and shape of the cavity is not updated during the optimization, if part of your molecule tries to leave the original cavity you could observe the convergence problems you mention in (2). Try using a larger cavity by defining larger spheres. Use SCRF=(Read,…) in your route section and add a final line in your input file saying Radii=Bondi
you could use also UAKS for a more consistent DFT definition (radii defined from PBEPBE/6-31G**) however I’m not a big fan of using united atoms models but in this case it could work though.
Problem (1) is a bit more rudimentary to solve: Simply slightly twist your molecule around the dihedral in question, that usually works for me.
As for the third part of your question I would suggest (without any knowledge of your system) to use any of Grimme’s functionals, say wB97D along with SMD solvation model. SMD was developed to work along Truhlar’s functionals (Minnesota kind M06, M05 etc.) but it works with empirical dispersion functionals too.
I hope this helps
Have a nice day!

133. Neelam bajarh

Hi Dr J. Barroso,

I am trying to study IEF-PCM model with acetic acid solvent for a dye molecule using gaussian 03. the same study with other solvents which were set as default has been carried out successfully. but i m not able to do the same for an unassigned solvent. How can i include acetic acid in my set of analysis.

134. Dear Joaquin,

I am wandering if it is possible to print the radius of the cavity used in Gaussian. I’m using two different softwares one is Gaussian (for geometry optimisations) and another is DALTON (for multi-photon calculations). I optimised my system using Gaussian in a solvent (say CH2Cl2). Next I want to use the optimised geometry as input in DALTON. In DALTON there are options for defining the cavity (there is no default cavity generation option). For consistency I want to use the save cavity radius as used in Gaussian. For this reason I want to print the cavity radius. It would be great if you give your valuable suggestion on this topic.

Regards,
Mehboob

135. Leila

Dear Joaquin!

I’m using Gaussian and I’m having difficulty with the SVP + sp input base because it gives a command line error. Could you suggest me an input command used to run the base SVP + sp in the Gaussian 03W to optimize a molecule geometry in PCM?

Thankful, Leila.

• Dear Leila,

What exactly is the error in the command line? Please share it so I can help you properly.

Have a nice day.

136. Corrado

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