Mark, The problem with one .tpr file set for 100ns is that when job number (say) 4 hits the wall limit, it crashes and never gets a chance to submit the next job. So it's not really automated.
Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5 till job 4 ends. But the PBS queuing system is sometime weird and takes a bit of time to recognize a job and give back its jobID. So I could submit job 5 but be unable to change its status to /hold/ because PBS does not return its ID. Another problem is that if resources are available, job 5 could start before I ever get a chance to /hold/ it. On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty <pavan.grom...@gmail.com > >wrote: > > > I have need to collect 100ns but I can collect only ~1ns (1000steps) per > > run. Since I dont have .trr files, I rely on .cpt files for restarts. For > > example, > > > > grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 > > > > This runs into a problem when the run gets killed due to walltime > limits. I > > now have a .xtc file which has run (say) 700 steps and a .cpt file which > > was last written at 600th step. > > > > You seem to have no need to use grompp, because you don't need to use a > workflow that generates multiple .tpr files. Do the equivalent of what the > restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a .tpr > for the whole 100ns run, and then keep doing > > mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime > > with or without -append, perhaps with -maxh, keeping whatever manual > backups you feel necessary. Then perhaps concatenate your final trajectory > files, according to your earlier choices. > > - To set up the next run I use the .cpt file from 600th step. > > - Now during analysis if I want to center the protein and such, /trjconv/ > > needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ > know > > to stop at 600th step? > > > trjconv just operates on the contents of the trajectory file, as modified > by things like -b -e and -dt. The .tpr just gives it context, such as atom > names. You could give it a .tpr from any point during the run. > > Mark > > If this has to be put in manually, it becomes > > cumbersome. > > > > Thoughts? > > > > > > > > > > > > On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > > > > On 10/27/13 9:37 AM, Pavan Ghatty wrote: > > > > > >> Hello All, > > >> > > >> Is there a way to make mdrun put out .cpt file with the same frequency > > as > > >> a > > >> .xtc or .trr file. From here > > >> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts< > > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>I see that > we > > >> can choose how often (time in mins) the .cpt file is written. But > > clearly > > >> if the frequency of output of .cpt (frequency in mins) and .xtc > > (frequency > > >> in simulation steps) do not match, it can create problems during > > analysis; > > >> especially in the event of frequent crashes. Also, I am not storing > .trr > > >> file since I dont need that precision. > > >> I am using Gromacs 4.6.1. > > >> > > >> > > > What problems are you experiencing? There is no need for .cpt > frequency > > > to be the same as .xtc frequency, because any duplicate frames should > be > > > handled elegantly when appending. > > > > > > -Justin > > > > > > -- > > > ==============================**==================== > > > > > > Justin A. Lemkul, Ph.D. > > > Postdoctoral Fellow > > > > > > Department of Pharmaceutical Sciences > > > School of Pharmacy > > > Health Sciences Facility II, Room 601 > > > University of Maryland, Baltimore > > > 20 Penn St. > > > Baltimore, MD 21201 > > > > > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu > > > > | (410) > > > 706-7441 > > > > > > ==============================**==================== > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > > * Please search the archive at http://www.gromacs.org/** > > > Support/Mailing_Lists/Search< > > 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? 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