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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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Run gmx_MMPBSA in background #204

Closed marioernestovaldes closed 2 years ago

marioernestovaldes commented 2 years ago

I was running this command, nohup mpirun -np 8 gmx_MMPBSA MPI -O -i mmgbsa_5frames.in -cs sys.pdb -ci prot_rna_dna.ndx -cg 1 15 -ct fnrna-dna_0-500ns_norest-350-400_nopbc_compact_fit_dt1ns.xtc -cp topol.top & it was running fine earlier, not the process stops after closing the terminal.

On Wed, Mar 23, 2022 at 5:31 AM Mario Sergio Valdés Tresanco < @.***> wrote:

My error appears to be related to a second install of Qt5, so not a problem with gmx_MMPBSA_ana.

@wrmartin https://github.com/wrmartin Did you solve it or are you still having problems?

@gayatripanda5 https://github.com/gayatripanda5 Please be careful when defining the PYTHONPATH variable. This variable overrides the path where the python interpreter looks for modules/packages. The current definition you have points to a python interpreter, not to the python library folder, which can generate errors.

— Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/176#issuecomment-1075766649, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQSH3UZEZVJU7JOBJUTLIADVBJNNTANCNFSM5P5FICFA . You are receiving this because you were mentioned.Message ID: @.***>

-- Gayatri Panda PhD19206 (Computational Biology)

_Originally posted by @gayatripanda5 in https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/176#issuecomment-1077916567_

marioernestovaldes commented 2 years ago

fundamentally, nothing has changed in the way gmx_MMPBSA runs... As a matter of fact, I tried using nohup and it works fine...

gayatripanda5 commented 2 years ago

The gmx_MMPBSA run that I am performing is for 700 frames. It takes about 4-4 hrs to complete a run with 100 frames. Since I am accessing my server remotely, I often set up my jobs using "nohup" and "&" signs to push the job in the background, so that the job keeps running even after closing the terminal or after getting disconnected from the server. I rerun this same command, nohup mpirun -np 8 gmx_MMPBSA MPI -O -i mmgbsa_5frames.in -cs sys.pdb -ci prot_rna_dna.ndx -cg 1 15 -ct fnrna-dna_0-500ns_norest-350-400_nopbc_compact_fit_dt1ns.xtc -cp topol.top & but it terminated when the terminal was closed.

Valdes-Tresanco-MS commented 2 years ago

This seems to be a very common problem. As you were told earlier, gmx_MMPBSA did not change its execution mode. You can check if it is this problem and let me know.

marioernestovaldes commented 2 years ago

closing this... feel free to reopen if the problem persists...