#!/bin/bash

TRAJ="../traj_dimers/50ns_noWAT_5000frames_chain_4.nc"
start=1
stop=2000
offset=2

MASK[1]=":525-1048@N,CA,C"
MASK[2]=":1-524@N,CA,C"
MASK[3]=":1-1048@N,CA,C"


avg_pdb="avg_pdb"
ptraj_file_suff="tmp.ptraj"
ptraj_thermo_out="thermo.out"
ptraj_avg_out="ptraj.avg.out"

PRMTOP="1XCK_chainAB_noWAT.prmtop"
results="ptraj.out"
grep_file="totals.dat"






for index in 1 2 3;
do
	ptraj_file=${index}_${ptraj_file_suff}

	## Averaging ##
	echo 'trajin '${TRAJ} ${start} ${stop} ${offset}  >> ${ptraj_file}
	echo 'rms mass first '${MASK} >> ${ptraj_file}
	echo 'average '${index}_${avg_pdb}' pdb'  >> ${ptraj_file}
	ptraj ${PRMTOP} ${ptraj_file} >> ${ptraj_avg_out}
	rm ${ptraj_file}

	## Performing Entropy calculation ##
	echo 'trajin '${TRAJ} ${start} ${stop} ${offset}  >> ${ptraj_file}
	echo 'reference '${index}_${avg_pdb} >> ${ptraj_file}
	echo 'rms mass reference '${MASK}'@N,CA,C' >> ${ptraj_file}
	echo 'strip @H*' >> ${ptraj_file}
	echo 'matrix mwcovar name rec-var '${MASK} >> ${ptraj_file}
	echo 'analyze matrix rec-var out '${index}_${ptraj_thermo_out}' thermo reduce' >> ${ptraj_file}
	ptraj ${PRMTOP} ${ptraj_file} >> ${index}_${results} &
	#rm ${ptraj_file}

	grep "Total" ${index}_$results >> $grep_file
done