[gmx-users] Problem with running MD
lpeng at ucsd.edu
Thu Aug 20 19:25:07 CEST 2009
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?
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
>> $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?
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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
> gmx-users mailing list gmx-users at gromacs.org
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