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

[Husen R]

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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