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 Thanks, L
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