#!/bin/bash

OUT="0-1000ns_thermo_apo_rmsAvg"
ptraj_file="_"${OUT}"_tmp.ptraj"
avg_pdb="_"${OUT}"_tmp.pdb"
ptraj_avg_out="_"${OUT}"_avg.out"
ptraj_thermo_out="_"${OUT}"_thermo.out"
results="_"${OUT}"_entropy.out"

offset=5
start_a=1
stop_a=5000
start_b=1
stop_b=5000


REF="121_1XCK_chainA_apo/1XCK_chainA_sol.inpcrd"

DIR_PREFIX="/net/lutefisk/slars/groel_md/1XCK_chainA/"
#DIR_PREFIX="/home/slars/lutefisk/groel_md/1XCK_chainA/"



PRMTOP[1]=${DIR_PREFIX}"121_1XCK_chainA_apo/1XCK_chainA_sol.prmtop"

TRAJIN[1]="1-50ns_imposedOnStart.nc"
TRAJIN[2]="51-100ns_imposedOnStart.nc"


#TRAJIN[2]="1-50ns_imposedOnStart.nc"
#TRAJIN[3]="1-50ns_imposedOnStart.nc"
#TRAJIN[4]="1-50ns_imposedOnStart.nc"
#TRAJIN[5]="1-40ns_imposedOnStart.nc"
#TRAJIN[6]="1-40ns_imposedOnStart.nc"

DIR[1]=${DIR_PREFIX}121_1XCK_chainA_apo/results/traj/
DIR[2]=${DIR_PREFIX}121_1XCK_chainA_apo_p1/results/traj/
DIR[3]=${DIR_PREFIX}121_1XCK_chainA_apo_p2/results/traj/
DIR[4]=${DIR_PREFIX}121_1XCK_chainA_apo_p3/results/traj/
#DIR[5]=${DIR_PREFIX}121_1XCK_chainA_apo_p4/results/traj/
#DIR[6]=${DIR_PREFIX}121_1XCK_chainA_apo_p5/results/traj/


rm ${ptraj_file}

for index in 1 2 3 4; 
do

        #TRAJIN[0]=${DIR[index]}${TRAJIN[index]}

	## Performing Averags structure calculation ##
        echo 'trajin '${DIR[index]}${TRAJIN[1]} ${start_a} ${stop_a} ${offset}  >> ${ptraj_file}
	echo 'trajin '${DIR[index]}${TRAJIN[2]} ${start_b} ${stop_b} ${offset} >> ${ptraj_file}

        echo 'rms mass first :8-134,410-517@N,CA,C' >> ${ptraj_file}
        echo 'average '${avg_pdb}' pdb'  >> ${ptraj_file}
        ptraj ${PRMTOP[1]} ${ptraj_file} >> ${ptraj_avg_out}
        rm ${ptraj_file}



	## Performing Entropy calculation ##
	echo 'trajin '${DIR[index]}${TRAJIN[1]} ${start_a} ${stop_a} ${offset} >> ${ptraj_file}
        echo 'trajin '${DIR[index]}${TRAJIN[2]} ${start_b} ${stop_b} ${offset} >> ${ptraj_file}
	echo 'reference '${avg_pdb} >> ${ptraj_file}
	echo 'rms mass reference :8-134,410-517@N,CA,C' >> ${ptraj_file}
	echo 'matrix mwcovar name rec-var :8-134,410-517' >> ${ptraj_file}
	echo 'analyze matrix rec-var out '${ptraj_thermo_out}' thermo reduce' >> ${ptraj_file}
        ptraj ${PRMTOP[1]} ${ptraj_file} >> ${results} 
	rm ${ptraj_file}
done