submitbd.sub

#!/bin/bash
#PBS -q home-mccammon #as a McCammon user, leave this
#PBS -N glycans #job name
#PBS -l nodes=1:ppn=3:gpu #use GPUs in multiples of 3, and CPU in multiples of 12
#PBS -l walltime=192:00:00 #use maximum walltime, if the job ends before the time runs out, the remaining time will be released for other users
#PBS -o glycans_nam_simulation-out.txt #give any name for the output text file
#PBS -e glycans_nam_simulation-err.txt #give any name for the error text file
#PBS -V #leave this blank
#PBS -M #if you want to receive an email when a job is started and finished, put your email here
#PBS -m abe #leave this as is
#PBS -A mccammon-gpu #leave this as is

export MODULEPATH=/projects/builder-group/jpg/modulefiles/applications:$MODULEPATH
module load browndye #these two commands must be run to use Browndye in TSCC

INITDIR=/home/cseitz/run #the directory where your run files are

cd $INITDIR

nam_simulation /home/cseitz/run/2hty-oseltamivir-simulation.xml #the command you would normally use for Browndye