Peter, (ignoring full precision) Are the thermostat and barostat computed by coordinates and velocities, in principle ?
Myunggi Yi (이명기, Ph. D.), Professor Department of Biomedical Engineering (의공학과 bme.pknu.ac.kr), College of Engineering Interdisciplinary Program of Biomedical Mechanical & Electrical Engineering Center for Marine-Integrated Biomedical Technology (BK21+) College of Engineering Pukyong National University (부경대학교 www.pknu.ac.kr) 45 Yongso-ro, Nam-gu (남구 용소로 45) Busan, 48513, South Korea Phone: +82 51 629 5773 Fax: +82 51 629 5779 On Wed, Oct 4, 2017 at 11:07 AM, Peter Kroon <p.c.kr...@rug.nl> wrote: > 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. > >> > > > > -- > 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. > -- 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.