[gmx-users] Problem with running MD

[Lili Peng]

Hi Justin,

I do not think that the storage space is an issue because I had submitted
another job to the queue (system of one molecule) yesterday, and it's almost
near completion.  My xtc file is ~4700 kB, trr file is ~22MB, and tpr file
~130MB.  I've also checked my *.log files and nothing seems alarming.

Is there anything else I should look into to figure out what is causing my
system to stall?

Thanks,
L

2009/8/20 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> Lili Peng wrote:
>
>> Hi all,
>>
>> I am having a problem while running an MD simulation on a system of 11
>> identical molecules solvated in a 50nm X  50 nm X 50nm box with Na+ ions.  I
>> submit my job, and it starts to run successfully.  However, after 2500ps,
>> the xtc and trr files do not increase in size anymore, which I presume that
>> the simulation has stalled because the files no longer get updated.
>>  However, the queue still shows that the job is still running.  This problem
>> I only encounter with a system of 11 molecules.  I do not encounter the same
>> problem with simulation of a single  molecule, as they run to completion
>> (200ns).  My submission scripts for the system of multiple molecules and
>> system of single molecule are the same.
>>
>> Does anyone have any insight on what the problem could be?  My mdrun input
>> is:
>>
>> $MPIRUN -np $NSLOTS $MDRUN -v -nice 0 -np $NSLOTS -s all.tpr -o all.trr -c
>> confout.gro -g all.log -x all.xtc
>>
>>
> Well, if the job is running out to 2500 ps, then your command line isn't
> the problem.  Any indication in the .log file of errors or crashing?  How
> large are the files?  Do you have sufficient storage space for these files?
>
> -Justin
>
>  Thanks,
>> L
>>
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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