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

[Mark Abraham]

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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