[gmx-users] Problem with running MD

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 20 17:53:47 CEST 2009

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?


> Thanks,
> L
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list