[gmx-users] gromacs.org_gmx-users Digest, Vol 132, Issue 117

[Justin Lemkul]

Please use a real subject line rather than generically replying to the digest.

On 4/24/15 1:32 PM, Simon Longela wrote:
> Hi
>
> I am trying to launch a simulation of ameloblastin (421 amino acids).
>
> This will take long time.
>
> But can you help me to estimate how much time I must put as wall time on
> the script below?
>

Run a short benchmark.  Even a few thousand steps would be enough.


> I used 500hours, it run then the simulation stopped after that time, when I

This is what checkpointing is for.  It doesn't matter if the job stops because 
of a wallclock limit, mdrun -cpi will pick up from where it left off.

-Justin

> increased at 1700hours, then the simulation never start!!!
>
> I have 68 000CPU hours remain on my account.
>
> Please advise.
>
> Thanks.
>
> SCRIPT:
>
>> #!/bin/bash
>
>> #PBS -lnodes=2:ppn=16
>
>> #PBS -lwalltime=500:00:00
>
>> #PSB -lpmem=5500MB
>
>> workdir=/global/work/$USER/$PBS_JOBID
>
>> mkdir -p $workdir
>
>> cd $PBS_O_WORKDIR
>
>> cp md.mdp nvt.gro nvt.cpt topol.top $workdir cd $workdir module load
>
>> gromacs/4.5.5 grompp -f md.mdp -c nvt.gro -t nvt.cpt -p topol.top -o
>
>> md_0_1.tpr -maxwarn 10 -zero mdrun -deffnm md_0_1 -nt 8 echo Info from
>
>> the system echo PDW  ls -la $PWD echo Workdir ls -la $workdir echo DIR
>
>> ls -la echo PBS_O_WORKDIR  ls -la $PBS_O_WORKDIR
>
>> echo Start copy data ...
>
>> cp * $PBS_O_WORKDIR
>
>> echo Check your data and do not forget remove $workdir #rm -rf $workdir
>
>
>
> Simon
>

-- 
==================================================

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

==================================================