[gmx-users] Gromacs-5.1.2 Checkpoint/restart example

[Mark Abraham]

Yes

On Tue, 26 Apr 2016 08:12 Husen R <hus3nr at 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.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > On Tue, 26 Apr 2016 06:19 Husen R <hus3nr at 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=hus3nr at 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 <hus3nr at gmail.com> wrote:
> > >
> > > > Hi,
> > > >
> > > > Thanks a lot !
> > > > I'll try it,..
> > > >
> > > > Regards,
> > > >
> > > >
> > > > Husen
> > > >
> > > > On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul <jalemkul at 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
> > > >>
> > > >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > > >> http://mackerell.umaryland.edu/~jalemkul
> > > >>
> > > >> ==================================================
> > > >> --
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