#! /bin/ksh
#PBS -l mppwidth=16
#PBS -l walltime=30:00:00
#PBS -j oe
#PBS -N 1xckApoEnergy
#PBS -A cbu 

CORES=16

export AMBERHOME=/home/cbu/slars/amber11
sander=sander.MPI

OUT="20-50ns_freeEnergy_apo"
ptraj_out="_"${OUT}"_tmp.ptraj.out"
ptraj_file="_"${OUT}"_tmp.ptraj"
MD_IN="gb.mdin"

offset=5
start_a=2001
stop_a=5000


PRMTOP[1]="prmtops/cis.prmtop"
PRMTOP[2]="prmtops/cis.prmtop"
PRMTOP[3]="prmtops/1XCK_apo_noWAT.prmtop"

INPCRD[1]="prmtops/cis.inpcrd"
INPCRD[2]="prmtops/cis.inpcrd"
INPCRD[3]="prmtops/1XCK_apo_noWAT.inpcrd"


TRAJIN[1]="trjs/50ns_noWAT_5000frames_hept_1.nc"
TRAJIN[2]="trjs/50ns_noWAT_5000frames_hept_2.nc"
TRAJIN[3]="trjs/50ns_5000frames_noWAT.nc"

cd $workdir
#rm ${ptraj_file}

for index in 1 2 3;
do
	MD_OUT="_"${OUT}"_energies_"${index}".out"

	## Performing Averags structure calculation ##
        #echo 'trajin '${TRAJIN[1]} ${start_a} ${stop_a} ${offset} >> ${ptraj_file}

        #echo "strip '* & !:1-524'" >> ${ptraj_file}
        #echo 'trajout '${MDCRD}' nobox netcdf' >> ${ptraj_file}
        #ptraj ${PRMTOP[index]} ${ptraj_file} >> ${ptraj_out} 
        #rm ${ptraj_file}


	## Performing Energy calculation ##
        mpirun -np $CORES $sander -O -i $MD_IN -o $MD_OUT -p ${PRMTOP[index]} -c ${INPCRD[index]} -y ${TRAJIN[index]}
done