Aah yes of course. Thanks James.
On Mon, Oct 28, 2013 at 3:16 PM, <jkrie...@mrc-lmb.cam.ac.uk> wrote: > No this isn't a problem. You can use job names under the -hold_jid flag. > As long as you change the job name in the submit script between > submissions this isn't a problem. You could have a submit script for job 4 > with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and > -hold_jid md_job4 for the next job. Then you can submit job 5 as soon as > you have made this change which will be within seconds of submitting job > 4. > > > 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? Read http://www.gromacs.org/**Support/Mailing_Lists< > >> > http://www.gromacs.org/Support/Mailing_Lists> > >> > > > >> > -- > >> > 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 > >> > > >> -- > >> 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 > >> > > -- > > 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 > > > > > -- > 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 > -- 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