Hi again, I am now running the latest version of OpenMM but i still have problems with running calculations on multiple gpus. My input file: from __future__ import print_function from simtk.openmm.app import * from simtk.openmm import * from simtk.unit import * from sys import stdout import os impor...

Hi Jason,

Seems that i am running 6.0.0. So i will update my version and try again. Thanks for your help

Hi Peter, I still have a problem with running on multiple gpus in one node. Acutally the energies in the calculation are calculated wrong. they are way to high. I checked my inputfiel by running the same calculation on one gpu which worked fine. I copying my inputfile in here so maybe you can give m...

Hi Peter, We have 2gpus per node. Normally you can run 2 diffrent jobs on both gpus. During a job is running on a gpu no other job can access this GPU. We tested the setup of double gpu use already with other programs (e.g. amber) and it worked. It seems to me that the command 'CudaDeviceIndex':'0,1...

Hi Peter, I tried to run an OpenMM calculation on two gpus in one node. The reservation of the whole node in the queueing systems seems to work, but I got an error message after a few seconds. Is my peace of python code to start OpenMM correct: Inputfile: from __future__ import print_function from s...

Hi Peter,

Thanks for the answer. I see now where the problem is. The polarisation groups seems to overlay and probably this is not working. I changed my definition now that every atom is a own polarization group. This works!

Thanks for your help!

Michael

Hi all, I just have another question, which I cannot solve on my own. I have seen that Polarisation groups are somehow definied in the force field file with the pgrp command. I understood that the number after that command is the atom tpye number. Anyway no I have the problem that I have a C60 molec...

Hi Lee Ping, Thanks for the answer. charge*nanometer make totally sense. I just wanted to doublecheck. I was a bit wondered by the results at a first glance and thought something is wrong, but i am now pretty convinced that the results are reasonible. I just wanted to get sure, as this was the only ...

Hi all, I have once more a question related to this topic. I am quite sure but I wanted to double check. The unit of the induced dipol is proton charge * nanometer? And if i read out my induced dipols the first 3 numbers belong to the first atom in my inputfile? And the same is true for coordinates?...

Hi Lee-Ping,

Thanks for your quick response. I started simulations with the new parameters and at first glance it seems to work but it is nearly a magnitude slower.. I will report you in a few hours if the system is still stabile.

Thanks in advance.

Michael