[gmx-users] PBS script for gromacs Gromacs

JMandumpal jesbman at rediffmail.com
Mon Jul 21 05:33:05 CEST 2008

Dear Manoj,

Here is the script, for running parallel, which I am using. You may need to change it according to your machine-specifications. 
--------------script for GROMACS 3.3.3-------------------------
#PBS  -l vmem=8gb
#PBS  -l jobfs=10GB
#PBS  -l ncpus=4
#PBS  -l software=gromacs
#PBS  -l other=mpi
#PBS  -wd
#PBS  -q express
module load intel-cc/10.0.023
module load intel-fc/10.0.023
module load gromacs/3.3.3
grompp -np $PBS_NCPUS -f em.mdp -p topol.top -c conf.gro -o binary.tpr
mpirun mdrun -s binary.tpr -o traj1.trr -c out1.gro -g sim.log

On Mon, 21 Jul 2008 Manoj Kumar Singh wrote :
>I am new with Gromacs and I don't know how to submit job on cluster. I am
>looking for a PBS script. I am using cluster made of Intel Xeon CPU E5345.
>The mpi Gromacs has already been installed.
>I will be very thankful for any response.
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