Re: [AMBER] checkpoint on Amber within batch job

From: Jason Swails <>
Date: Thu, 23 Jan 2014 08:43:58 -0500

On Thu, 2014-01-23 at 13:33 +0000, Zhuang, Yu wrote:
> Dear all,
> I am wondering how to make a checkpoint on Amber 12 within batch job. I am running Amber on Linux cluster, however, they have a time limit for 48 hours. I would like to continue or restart the simulation after it stopped. The cluster is running under SLURM system. if anyone has a similar experience, it will be highly appreciated if you can share with me.
> Thanks and regards, Yu
> The following is the command I used for sander.MPI.
> #!/bin/bash
> #SBATCH -o /home/.../myjob.%j.%N.out
> #SBATCH -D /home/.../
> #SBATCH -J beta_lg_1
> #SBATCH --get-user-env
> #SBATCH --clusters=MPP1
> #SBATCH --ntasks=32
> #SBATCH --partition=myri_large
> #SBATCH --time=48:00:00
> source /etc/profile.d/
> module load amber
> srun_ps sander.MPI -O -i -o 2q2m_wat_min1.out -c 2q2m_wat.inpcrd -p 2q2m_wat.prmtop -r 2q2m_wat_min1.restrt -ref 2q2m_wat.inpcrd;
> srun_ps sander.MPI -O -i -o 2q2m_wat_min2.out -c 2q2m_wat_min1.restrt -p 2q2m_wat.prmtop -r 2q2m_wat_min2.restrt;
> srun_ps sander.MPI -O -i -o 2q2m_wat_md1.out -c 2q2m_wat_min2.restrt -p 2q2m_wat.prmtop -r 2q2m_wat_md1.restrt -x 2q2m_wat_md1.mdcrd -ref 2q2m_wat_min2.restrt;
> srun_ps sander.MPI -O -i -o 2q2m_wat_md2.out -c 2q2m_wat_md1.restrt -p 2q2m_wat.prmtop -r 2q2m_wat_md2.restrt -x 2q2m_wat_md2.mdcrd

There is no true 'checkpoint' facility in Amber. The solution is to use
the restart file from the previous simulation to start the next
simulation. This is almost always as good as a checkpoint file.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Jan 23 2014 - 06:00:03 PST
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