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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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