search

TinkerTools / poltype2

Poltype 2: Automated Parameterization and Free Energy Prediction for AMOEBA
Other
41 stars 11 forks source link

running separate qm calculations #50

Open scinikhil opened 4 months ago

scinikhil commented 4 months ago

Hi, I wanted to paramterise a molecule of 64 atoms, i wanted to use gaussian for QM calculations, is it possible to get the input files from pltype2 and i can run gaussian separetly on cluster, then add the output from the gaussian to polypep for the further calculations? At the moment where the poltype2 installed not having gaussian installed as well as enoigh compuational cores.

leucinw commented 4 months ago

It is probably easier to install Poltype on the computer that has Gaussian.

scinikhil commented 4 months ago

Thanks for the response.

scinikhil commented 3 months ago

Hi, I have a follow-up question. I installed it on a computer, and it is running fine. However, the Gaussian calculations are taking time. Our cluster, which runs Gaussian faster, uses SLURM scripts. Is it possible to automate the submission of Gaussian jobs to the cluster for each calculation? Alternatively, if I edit the Poltype.py code and run the gaussian calculations separately on the cluster, feeding it as input to the script, would that work? What would you suggest?

pren commented 3 months ago

It is possible. If you “restart” poltype with all the Gaussian files in the right folder, Poltype will detect/skip them and continue.

From: Nikhil Maroli @.> Date: Tuesday, August 6, 2024 at 12:23 AM To: TinkerTools/poltype2 @.> Cc: Subscribed @.***> Subject: Re: [TinkerTools/poltype2] running separate qm calculations (Issue #50)

Hi, I have a follow-up question. I installed it on a computer, and it is running fine. However, the Gaussian calculations are taking time. Our cluster, which runs Gaussian faster, uses SLURM scripts. Is it possible to automate the submission of Gaussian jobs to the cluster for each calculation? Alternatively, if I edit the Poltype.py code and run the gaussian calculations separately on the cluster, feeding it as input to the script, would that work? What would you suggest?

— Reply to this email directly, view it on GitHubhttps://github.com/TinkerTools/poltype2/issues/50#issuecomment-2270408430, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABNC6XTVPELTHGX6JBCK2CTZQBMU7AVCNFSM6AAAAABLBZKVDGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZQGQYDQNBTGA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

scinikhil commented 2 months ago

HI, Thanks, it worked. Though, the program is running for few weeks with :+1: Calling: analyze.x /home/nmaroli/programs/poltype/VersionFiles/water.xyz -k /home/nmaroli/programs/poltype/VersionFiles/water.key e> version.out

For help, use: python dimorphite_dl.py --help

If you use Dimorphite-DL in your research, please cite: Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD (2019) Dimorphite-DL: An open-source program for enumerating the ionization states of drug-like small molecules. J Cheminform 11:14. doi:10.1186/s13321-019-0336-9.

[14:11:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 6 7 [14:11:55] Can't kekulize mol. Unkekulized atoms: 0 1 3 4 5 6 7

Do you suggest any way to speed up the calculations? i tried to add multiprocessing the calculations, since it is very long code end up with several errors. Do you have any suggestions to improve the performance of the whole calculations? other than gaussian or xtb.