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
