Pittsburgh Supercomputing Center 

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

 
#!/bin/csh
#PBS -l ncpus=16
#PBS -l walltime=20:00
#PBS -o tinker.out
#PBS -j oe
#PBS -q debug

set echo

# move to scratch working directory
cd $SCRATCH

# copy the input files to the working directory
cp ~/tinker/anion.dat .
cp ~/tinker/anion.key .
cp ~/tinker/anion.xyz .

# set up the module command
source /usr/share/modules/init/csh

# load the tinker module
module load tinker

# define OMP_NUM_THREADS to be the number of cpus requested above
setenv OMP_NUM_THREADS $PBS_NCPUS

# run my executable
# here we run the dynamic program
# input files are named anion
# input parameters are: number of steps,
# time interval between steps,
# time interval between coordinate/trajectory saves,
# the type of statistical mechanical ensemble you want (2 = Canonical - NVT)
# and the temperature in Kelvin.
 omplace -nt $OMP_NUM_THREADS dynamic anion 1000 2.0 0.1 2 300.0 # move back to your home directory tree cd ~/tinker # copy the output .dyn file back from $SCRATCH cp $SCRATCH/anion.dyn .