Yes On Tue, 26 Apr 2016 08:12 Husen R <hus...@gmail.com> wrote:
> Hi, > > > Thanks for your reply. > > There is no state.cpt or state_prev.cpt file. > > In equilibration part 1 the resulting checkpoint files : nvt.cpt and > nvt_prev.cpt > In equilibration part 2 the resulting checkpoint files : npt.cpt and > npt_prev.cpt > In Production MD the resulting checkpoint files : md_0_1.cpt and > md_0_1_prev.cpt > > is this because of -deffnm option ? > I just want to make sure. > > Regards, > > > Husen > > > On Tue, Apr 26, 2016 at 11:45 AM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > On Tue, 26 Apr 2016 06:19 Husen R <hus...@gmail.com> wrote: > > > > > Hi all, > > > > > > I tried to run this gromacs tutorial ( > > > > > > > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html > > > ) > > > in order to understand how checkpoint/restart works in Gromacs-5.1.2. > > > > > > Based on running that tutorial I found that mdrun automatically > > checkpoint > > > even though I didn't specify -cpt option (based on mdrun manual page, > by > > > default checkpoint every 15 minutes) > > > > > > > Yes, as that webpage suggests. > > > > 1. What if I specify -cpt option with a value longer than or smaller than > > > 15 minutes ? does -cpt value will automatically override the default ? > > > > > > > Yes, the default is used when you don't supply a value. But usually you > > don't need to think about this. > > > > 2. I run the following command to restart production MD step (using > SLURM) > > > from checkpoint file. md_0_1_prev.cpt is .cpt file resulting from > > previous > > > mdrun execution. is my command right ? I just want to make sure. > > > > > > > Not quite. From that webpage: "Note that mdrun will write state.cpt and > > state_prev.cpt files. As you can see from their time stamps, one was > > written approximately at the checkpoint interval before the other (15 > mins > > by default). Or you can use gmxcheck to see what is in them." You want to > > follow the examples there and do your restart from the most recent file, > > which is state.cpt. The older file is just kept for safety. Your command > > will lead to wasting 15 minutes of simulation. > > > > Mark > > > > #!/bin/bash > > > #SBATCH -J Lysozyme > > > #SBATCH -o md-%j.out > > > #SBATCH -A necis > > > #SBATCH -N 3 > > > #SBATCH -n 24 > > > #SBATCH --time=144:00:00 > > > #SBATCH --mail-user=hus...@gmail.com > > > #SBATCH --mail-type=begin > > > #SBATCH --mail-type=end > > > > > > mpirun gmx_mpi mdrun -cpi md_0_1_prev.cpt -deffnm md_0_1 > > > > > > > > > Thank you in advance > > > > > > Regards, > > > > > > > > > Husen > > > > > > > > > On Sun, Apr 24, 2016 at 7:57 PM, Husen R <hus...@gmail.com> wrote: > > > > > > > Hi, > > > > > > > > Thanks a lot ! > > > > I'll try it,.. > > > > > > > > Regards, > > > > > > > > > > > > Husen > > > > > > > > On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul <jalem...@vt.edu> > > wrote: > > > > > > > >> > > > >> > > > >> On 4/24/16 12:04 AM, Husen R wrote: > > > >> > > > >>> Dear all, > > > >>> > > > >>> is there any complete documentation discussing checkpoint/restart > in > > > >>> Gromacs-5.1.2 ? > > > >>> I found this link that discuss checkpoint ( > > > >>> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations > ) > > > and > > > >>> this link that discuss restart ( > > > >>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but > > these > > > >>> are > > > >>> not specifically for gromacs 5.1.2. > > > >>> > > > >>> > > > >> There are no differences for 5.1.2, so that information is all > > relevant. > > > >> > > > >> -Justin > > > >> > > > >> -- > > > >> ================================================== > > > >> > > > >> Justin A. Lemkul, Ph.D. > > > >> Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > >> > > > >> Department of Pharmaceutical Sciences > > > >> School of Pharmacy > > > >> Health Sciences Facility II, Room 629 > > > >> University of Maryland, Baltimore > > > >> 20 Penn St. > > > >> Baltimore, MD 21201 > > > >> > > > >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > >> http://mackerell.umaryland.edu/~jalemkul > > > >> > > > >> ================================================== > > > >> -- > > > >> 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. > > > -- > 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.
