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saeed_E

Member

Registered: 2019-12-21

Posts: 311

A question about Molclus

Dear Tian,
The below command is given in the settings.ini of Molclus:
xtb_arg= "--gfn 1 --chrg 0 --uhf 0"  // Additional arguments for xtb, e.g. "vtight --gfn 1 --gbsa h2o --chrg 0" (don't write task keywords such as "--opt" here)

Please suppose one wants to use xtb and employs the gfn2 method, while the structure is also optimized and the implicit solvent such as water is also considered. Please let me know how the above line should be changes to satisfy these expectations.

My own changes:

I changed the "igprog" to 4 and change itask to 3 so that xtb is used as computational code and optimization together with frequency is employed along any xtb execution. In addition, I changed the above line to the: xtb_arg= "--alpb water --gfn 2 --chrg 0 --uhf 0"  // Additional arguments for xtb, e.g. "vtight --gfn 1 --gbsa h2o --chrg 0" (don't write task keywords such as "--opt" here).

Please let me know if all these changes are in line with my goal.

Best regards,
Saeed

Last edited by saeed_E (2025-06-06 01:45:54)

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 2,007

Website

Re: A question about Molclus

Dear Saeed,

Your change is correct.

Tian

saeed_E

Member

Registered: 2019-12-21

Posts: 311

Re: A question about Molclus

Dear Tian,
Thank you very very much.
Please, if possible, let me ask another question:
When the "isostat" is executed, a question "Input the geometry threshold for distinguishing different clusters e.g. 0.25  (in Angstrom)" is asked. Please let me know what is the exact meaning of this question. I always enter 999 for this question. Is it correct?
Please, also let me know if "isuffle=1" in genmer.ini is always better than "ishuffle=0" and, leads to much better results.

Sincerely,
Saeed

Last edited by saeed_E (2025-06-06 20:42:27)

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 2,007

Website

Re: A question about Molclus

If you do now know how to set the thresholds, simply using the default value. If you found the number of resulting clusters is too high, you can double the threshold. The meaning is described in http://bbs.keinsci.com/thread-577-1-1.html. Briefly speaking, in isostat, if the energy deviation and geometric deviation between two structures are less than the thresholds, the two structures will be considered to be the same and one of them will be removed, or in other words, they will be classified into one cluster.

The meaning of isuffle is described in http://bbs.keinsci.com/thread-2369-1-1.html. =1 means disrupting the order of adding monomers, =0 means do not do this. If you don't have special reasons to disrupt the order, just use the default one (=0).

saeed_E

Member

Registered: 2019-12-21

Posts: 311

Re: A question about Molclus

Dear Tian,
Your very kind attention and highly informative comments are deeply appreciated.

In the "genmer.ini" there is an option namely "ngen" associated with the number of configurations expected to be generated. it seems  a high number is better since when number is increased, the chance of finding most stable conformed is also increased. For instanse, suppose I want to put 4 molecules of water around one molecule of HCl. Then, I select 10 for "ngen" indicating that 10 times or ten configurations should randomly be constructed any of which includes one HCl and four H2O. Again, I select 50 for "ngen". This time, 50 configurations will be constructed and undoubtedly the chance of an arrangement corresponding to the most stable conformer increases. Do you agree with me?

Best regards,
Saeed

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 2,007

Website

Re: A question about Molclus

In principle, the larger the ngen, the higher the proability to find the most stable configuration, but evidently, the higher the computational cost, which is linearly proportional to ngen.

saeed_E

Member

Registered: 2019-12-21

Posts: 311

Re: A question about Molclus

Dear Tian,
Thank you very much.

Sincerely,
Saeed