#!/bin/bash
######################################################################################

# MIO SUBMISSION SCRIPT :: SCR = /tmp

######################################################################################
#PBS -l walltime=120:00:00,nodes=4:ppn=8:compute
#PBS -N 25_FA+TOL_mmpbsa
#PBS -e stderr
#PBS -o stdout
#added this line Exports all environment variables from the submitting shell into the \batch shell
#PBS -V

set echo

######################################################################################

# Set environment variables

######################################################################################

export WORKDIR=/panfs/storage/scratch/vbharadw/RUN2/mmpbsa/dielec25

#added this line so that I did not overwrite your directory
#export WORKDIR=$PBS_O_WORKDIR

# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

#  Create scratch directory & copy data files there & execute & copy back when done

# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

cd $WORKDIR

cat $PBS_NODEFILE > $WORKDIR/NODELIST

set NPRCS = `wc -l < $WORKDIR/NODELIST`

echo E $NPRCS
set success = 0
#mpiexec should be used instead of mpirun
#TI job
#mpiexec -np 8 sander.MPI -ng -groupfile TIgroupfile && set success = 1

#standard MD

mpiexec -np 32 MMPBSA.py.MPI -O -i mmpbsa.in -sp fa.tol.bssa.top -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y ../../nvt4/fa.tol.bssa.mdcrd, ../../nvt5/fa.tol.bssa.mdcrd, ../../nvt6/fa.tol.bssa.mdcrd, ../../nvt7/fa.tol.bssa.mdcrd, ../../nvt8/fa.tol.bssa.mdcrd > progress.log

#This is for a serial AMBER 11 job
#sander -O -i md.in -o md.out -p bssa_model1_solv.top -c bssa_model1_solv.rst -r bssa_model1_solv_md_cut12.rst -x bssa_model1_solv_md_cut12.mdcrd2

unset echo