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

[Simon Longela]

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?

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