LAMMPS

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

In order to use this application you will first need to script a submit job. Below is a sample script. Edit it to your specific needs.

#!/bin/bash
#$ -S /bin/bash
#$ -N name_of_your_job
#$ -o /work/abc123/output.log
#$ -cwd
#$ -pe openmpi 8 
. /etc/profile.d/modules.sh
export OMP_NUM_THREADS=8
module load openmpi/gcc/64
module load lammps
mpirun -np 8 /usr/lib64/openmpi/bin/lmp < input_file > out

Now submit your job file using qsub

[abc123@login01 ~]$ qsub job_submit_file.sh
Your job 378 (job_submit_file.sh") has been submitted

-- AdminUser - 25 Aug 2016