Thanks for all your comments. I had took them into account.
Regards, Yu
-----Ursprüngliche Nachricht-----
Von: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Gesendet: Thursday, January 23, 2014 4:13 PM
An: AMBER Mailing List
Betreff: Re: [AMBER] checkpoint on Amber within batch job
Hi,
In addition, when restarting your run make sure you set 'irest=1' and 'ntx=5' in your input; this will restart the run using the velocity information present in your input coordinates.
-Dan
On Thu, Jan 23, 2014 at 6:57 AM, Zhuang, Yu <yu.zhuang.tum.de> wrote:
> Hi,
> Thanks for your information. Does this means I just need to re-format
> the sander command for the next run without modification of .in file?
> For example,
> Original:
> srun_ps sander.MPI -O -i 2q2m_wat_md2.in -o 2q2m_wat_md2.out -c
> 2q2m_wat_md1.restrt -p 2q2m_wat.prmtop -r 2q2m_wat_md2.restrt -x
> 2q2m_wat_md2.mdcrd step 2 simulation:
> srun_ps sander.MPI -O -i 2q2m_wat_md2.in -o 2q2m_wat_md2.out -c
> 2q2m_wat_md2.restrt -p 2q2m_wat.prmtop -r 2q2m_wat_md3.restrt -x
> 2q2m_wat_md3.mdcrd once again, thanks. Yu -----Ursprüngliche
> Nachricht-----
> Von: Jason Swails [mailto:jason.swails.gmail.com]
> Gesendet: Thursday, January 23, 2014 2:44 PM
> An: amber.ambermd.org
> Betreff: Re: [AMBER] checkpoint on Amber within batch job
>
> 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/modules.sh
> >
> > module load amber
> >
> > srun_ps sander.MPI -O -i 2q2m_wat_min1.in -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 2q2m_wat_min2.in -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 2q2m_wat_md1.in -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 2q2m_wat_md2.in -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.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jan 23 2014 - 08:00:02 PST
