[gmx-users] Problem with running MD

Lili Peng lpeng at ucsd.edu
Thu Aug 20 15:59:28 CEST 2009

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

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