GROMACS

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

http://www.gromacs.org/

PBS/Torque submit script

#!/bin/bash

source /usr/modules/init/bash
module load openmpi-apps/1.6.4/gromacs/5.0.4 openmpi

cd $PBS_O_WORKDIR

export PATH=/usr/local/cuda-7.0/lib64:$PATH
echo $PATH
gmx grompp -f 1wq5 -po prod.mdout -c 1wq5 -p 1wq5 -o prod >> gmx_run.log 2>&1

Run it (fortythree)

qsub gromacs.pbs

Slurm submit script

#!/bin/bash

source /usr/modules/init/bash
module load openmpi-apps/1.10.2/gromacs/5.1.2

cd $SLURM_SUBMIT_DIR

export PATH=/usr/local/cuda-7.0/lib64:$PATH
echo $PATH
gmx grompp -f 1wq5 -po prod.mdout -c 1wq5 -p 1wq5 -o prod >> gmx_run.slurm$SLURM_JOBID.log 2>&1

Run it (fortyfour)

sbatch -p cmci-gpu gromacs.slurm

Download example data and scripts here.