Hi MY,
actually you lose continuity of your simulation in both cases. The cpt file stores full precision coordinates and velocities (unlike gro/xtc). In addition, it stores state information about the simulation itself, such as the themostat and barostat. Whether this is an issue is up to you of course ;) Peter On 04-10-17 16:24, Myunggi Yi wrote: > 1. In principle, MD can be restarted if there are coordinates and > velocities on the snapshot. > > 2. Even if you don't have velocity, you can assign random velocity with the > specific temperature. > In this case, you lose continuity of simulation. Don't worry. > If you run same simulation with the exactly same inputs (including the same > random seed), you won't get exactly same trajectory in most cases > (depending on simulation types and hardware, etc). > > MY > > > On Wed, Oct 4, 2017 at 9:16 AM, tarak karmakar <tarak20...@gmail.com> wrote: > >> In that case, I think I do not have any option. The gmx_mpi_d check has >> only the last frame. :( >> >> Command line: >> gmx_mpi_d check -f ../state.cpt >> >> Checking file ../state.cpt >> >> # Atoms 10703 >> Last frame -1 time 190772.080 >> >> >> Item #frames Timestep (ps) >> Step 1 >> Time 1 >> Lambda 1 >> Coords 1 >> Velocities 1 >> Forces 0 >> Box 1 >> >> Thanks for your replies. I appreciate it. >> >> >> On Wed, Oct 4, 2017 at 3:07 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >>> >>> On 10/4/17 9:06 AM, tarak karmakar wrote: >>> >>>> Hi Justin, >>>> Thanks for the quick reply. >>>> >>>> Is there any way to check if the frame is there in .cpt file or not? >>>> >>>> I did the following exercise at difference 'time=' values, >>>> gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr -time >>>> 40000 -o topol.tpr >>>> >>>> It seems in all the cases, the trajectory gets restarted from the last >>>> frame. >>>> >>>> >>> The .cpt files are always overwritten unless you tell mdrun to keep them. >>> You can inspect the contents of any given .cpt file with gmx check. >>> >>> -Justin >>> >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> ================================================== >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >> >> >> -- >> Regards, >> Tarak >> -- >> Gromacs Users mailing list >> >> * Please search the archive at http://www.gromacs.org/ >> Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >>
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