#!/bin/bash

length=$1
type=$2
index=$3

OUT="1-"$length"ns_thermo_"${type}"_rmsAvg_"${index}
ptraj_file="_"${OUT}"_tmp.ptraj"
avg_pdb="_"${OUT}"_tmp.pdb"
ptraj_avg_out="_"${OUT}"_avg.out"
ptraj_thermo_out="_"${OUT}"_thermo.out"
#grep_file=${OUT}"_Total.dat" 
grep_file=${length}"ns_"${type}"_Total.dat"


let frames=${length}*100

let offset=${frames}/2000
start=1
stop=${frames}

FIT_MASK=":8-517"
MASK=":8-517"

#TRAJ_DIR="/net/lutefisk/slars/groel_md/1XCK_chainA/auto_calcs/trajs/"
TRAJ_DIR="trajs/"
PRMTOP="1XCK_chainA_noWAT.prmtop"


rm ${ptraj_file}

	if [ $type = "holo" ]; then
		let index=${index}+6
	fi	

	results="_"${OUT}"_entropy_p"$index".out"
	TRAJ=${TRAJ_DIR}"100ns_noWAT_noATP_10000frames_p"${index}".nc"

	## Averaging ##
        echo 'trajin '${TRAJ} ${start} ${stop} ${offset}  >> ${ptraj_file}
        echo 'rms mass first '${FIT_MASK}'@N,CA,C' >> ${ptraj_file}
        echo 'average '${avg_pdb}' pdb'  >> ${ptraj_file}
        ptraj ${PRMTOP} ${ptraj_file} >> ${ptraj_avg_out}
        rm ${ptraj_file}

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

	grep "Total" $results >> $grep_file