#!/bin/bash

ptraj_file="tmp.ptraj"
OUT="50ns_noWAT_1000frames_noH"

REF="../../1SX4_noWAT.inpcrd"

PRMTOP="../../1SX4_noWAT.prmtop"

TRAJIN[1]="../traj/1-25ns_imposedOnStart.nc"
TRAJIN[2]="../traj/26-50ns_imposedOnStart.nc"


MASK[1]=":1-1048"
MASK[2]=":525-1572"
MASK[3]=":1049-2096"
MASK[4]=":1573-2620"
MASK[5]=":2097-3144"
MASK[6]=":2621-3668"
MASK[7]=":3145-3668,1-524"

#MASK[5]=":2097-2620"
#MASK[6]=":2621-3144"
#MASK[7]=":3145-3668"
#MASK[8]=":3669-4192"
#MASK[9]=":4193-4716"
#MASK[10]=":4717-5240"
#MASK[11]=":5241-5764"
#MASK[12]=":5765-6288"
#MASK[13]=":6289-6812"
#MASK[14]=":6813-7336"




rm ${ptraj_file}

for index in 1 2 3 4 5 6;
do
        echo 'trajin '${DIR[index]}${TRAJIN[1]} 1 2500 5 >> ${ptraj_file}
        echo 'trajin '${DIR[index]}${TRAJIN[2]} 1 2500 5 >> ${ptraj_file}

        echo "strip '* & !"${MASK[index]}"'" >> ${ptraj_file}
        echo "strip @H*" >> ${ptraj_file}

	echo 'rms first mass :8-27,52-58-133,416-456,496-514@N,CA,C' >> $ptraj_file
	#echo 'rms first mass @N,CA,C' >> $ptraj_file
        echo 'trajout '${OUT}"_chain_"${index}".nc netcdf nobox" >> ${ptraj_file}
        ptraj ${PRMTOP} ${ptraj_file}

        rm ${ptraj_file}
done