Pittsburgh Supercomputing Center 

Advancing the state-of-the-art in high-performance computing,
communications and data analytics.

#!/bin/bash
#PBS -l ncpus=16
#PBS -l walltime=30:00
#PBS -o alanin.out
#PBS -j oe 
#PBS -q	debug 

set -x

# move to directory containing input files
cd  ~/namd

source /usr/share/modules/init/bash

module load namd/2.7


mpirun -np $PBS_NCPUS dplace -s1  namd2 alanin.namd > alanin.log