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

[Husen R]

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)

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 ?

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.

#!/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
>>
>> ==================================================
>> --
>> 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-request at gromacs.org.
>>
>
>