Hi all,<br><br>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.<br><br>Does anyone have any insight on what the problem could be? My mdrun input is:<br><br>$MPIRUN -np $NSLOTS $MDRUN -v -nice 0 -np $NSLOTS -s all.tpr -o all.trr -c confout.gro -g all.log -x all.xtc<br>
<br>Thanks,<br>L<br>