[gmx-users] HELP::Running Gromacs in parellel

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 21 15:49:49 CEST 2008

vivek sharma wrote:
> Hi There,
> I am running gromacs on parellel system using the submit command. 
> Commands are running fine, but the .trr file I got is not matching with 
> the trr file I got while running command in serial.

Based on what analysis?  Have you done gmxcheck -f1 -f2 on these .trr files?

> Also, I am getting a number of log files(equal to number of nodes I am 
> choosing).
> How should I analyze them or check whether results with parellel run are 
> consistent with the serial run, to validate my procedure.

The md0.log contains the most detailed information.  Have a look at the contents 
with a text editor.


> Anybody having experience in related topic, please suggest me the proper 
> way of sorting it out. I am using submit command for submitting my job 
> in parellel run.
> With Thanks,
> Vivek
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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