#!/bin/bash

ptraj_file="tmp2.ptraj"

#MASK=":720@NH* :385@OE*"
#MASK=":800@NZ :385@OE*"
#MASK=":805@CA :180@CA"
#MASK=":182@CB,CG :883@CG,CZ"
#MASK=":35@CZ :637@SD"
#MASK=":46@CD :595@CB"
#MASK=":38@CG* :596@CE"
#MASK=":45@CB :595@CB"
#MASK=":41@CA :1046@CB"
#MASK=":28@CB :1041@CB"
MASK=":42@CB :1046@CB"


OUT="tmp"
#OUT="720-385"
#OUT="805-180"

PRMTOP[1]="../1XCK_chainAB_noWAT.prmtop"


PREFIX[2]="/net/gulrotkake/slars/groel_md/1XCK/129_1XCK_MGATP/results/traj_dimers/"
PREFIX[1]="/net/gulrotkake/slars/groel_md/1XCK/116_1XCK_apo/results/traj_dimers/"

FILE="50ns_noWAT_5000frames_chain"

for index in 1 2;
do
        rm ${ptraj_file}
	
	for j in 1 2 3 4 5 6;
	do 
		echo 'trajin '${PREFIX[index]}${FILE}_${j}.nc 1 5000 10 >> ${ptraj_file}
	done
	echo 'dist dist5 '${MASK} 'out ' ${OUT}_${index}'.out' >> ${ptraj_file}

	ptraj ${PRMTOP[1]} ${ptraj_file}
done