[gmx-users] Problem with running MD

[Justin A. Lemkul]

Lili Peng wrote:
> 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?
> 

Your one-molecule system is likely to be substantially smaller than an 
11-molecule system in a 50-nm cubic (solvated!) box, so file sizes of 
trajectories from the one-molecule system are meaningless.  If your .tpr file is 
130 MB, then your trajectories are undoubtedly going to be larger, even many GB; 
did grompp warn you about how much data would be output?  How large are the 
files from your 11-molecule system at the time when output stopped?

If there are no signs of a crash whatsoever, then I still strongly suspect 
storage limits might be the problem.

-Justin

> Thanks,
> L
> 
> 2009/8/20 Justin A. Lemkul <jalemkul at vt.edu <mailto: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 <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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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

========================================