There might be relevant to walltime settings. There might be a default limit.
try qsub -l walltime=1000:00:00 yourjob adjust the time or google further to meet your need. On Fri, Jul 15, 2011 at 2:27 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Sayan Bagchi wrote: >> >> Hello All, >> I am having a weird problem and I do not know whether it has to do >> anything with Gromacs or the cluster setting I am using. >> When I run a MD simulation (on any protein), the job automatically >> terminates overnight without an error message. I mean if I start the job >> early in the morning it runs longer than if I start the job later in the >> day. But it never runs to the desired length mentioned in the .mdp file. >> > > If you are not receiving any error messages from Gromacs, then it is > something your system is doing that is unrelated to mdrun. Contact your > system administrators. Some queues employ systems to purge jobs after a > certain amount of time or even stop all jobs at a certain time of day to > allow other jobs to start. > > -Justin > >> I am copying the .mdp file: >> >> ----------------------------------------------------- >> >> integrator = md >> nsteps = 5000000 >> dt = 0.002 >> nstlist = 10 >> nstcomm = 1 >> rlist = 1.0 >> coulombtype = pme >> rcoulomb = 1.0 >> vdw-type = cut-off >> rvdw = 1.0 >> tcoupl = Nose-Hoover >> tc-grps = protein non-protein >> tau-t = 0.5 0.5 >> ref-t = 298 298 >> Pcoupl = Parrinello-Rahman >> pcoupltype = isotropic >> tau_p = 1.0 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> nstxout = 100 >> nstvout = 100 >> nstxtcout = 100 >> nstenergy = 100 >> userint1 = 123 >> userint2 = 124 >> userint3 = 247 >> ----------------------------------------------------------- >> >> Any thoughts? >> >> Sayan. >> >> >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- Best Regards, lina -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
