Hi Justin,<br><br>I do not think that the storage space is an issue because I had submitted another job to the queue (system of one molecule) yesterday, and it's almost near completion. My xtc file is ~4700 kB, trr file is ~22MB, and tpr file ~130MB. I've also checked my *.log files and nothing seems alarming.<br>
<br>Is there anything else I should look into to figure out what is causing my system to stall?<br><br>Thanks,<br>L<br><br><div class="gmail_quote">2009/8/20 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
Lili Peng wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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>
</blockquote>
<br></div></div>
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?<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks,<br>
L<br>
<br>
<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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