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. - 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? 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
