#!/bin/tcsh

if ( $# != 2 ) then
  echo "This script requires two arguments:"
  echo "  NAMD input file"
  echo "  NAMD log file"
  exit -1
endif

setenv CONFFILE $1
setenv LOGFILE $2

if ( ! -f $CONFFILE) then
  echo "NAMD input file $CONFFILE does not exist!"
  exit -1
endif

if ( -f $LOGFILE) then
  echo "NAMD input file $LOGFILE already exists!"
  exit -1
endif

setenv RUNDIR `pwd`

echo "Submitting NAMD run to batch queue..."
echo ""

# Run in a batch queue
qsub -q summertcb -V -j oe -N runbatch -l walltime=03:00:00,nodes=4:ppn=2:prod -A nle << ENDINPUT

cd $RUNDIR

~jphillip/SS03/vmirun "/u/ac/jphillip/SS03/namd2 $CONFFILE >& $LOGFILE"

ENDINPUT

echo ""
echo "NAMD is submitted to the queue, to check on your job use this command:"
echo ""
echo "    qstat -u $USER"
echo ""
echo "Your job is running if there is an R (running) in the S (state) column."
echo "Once the job has started you may monitor progress with this command:"
echo ""
echo "    tail -f $LOGFILE"
echo ""
echo "You will need to press Control-C to exit the tail command."
echo ""