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? 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