Hi Justin, 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.
Is there anything else I should look into to figure out what is causing my system to stall? Thanks, L 2009/8/20 Justin A. Lemkul <jalem...@vt.edu> > > > 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 >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > 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 > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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