#!/bin/bash

ptraj_file="tmp.ptraj"
OUT="500ns_noWAT_5000frames"

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

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

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



MASK[1]=":1-524"
MASK[2]=":525-1048"
MASK[3]=":1049-1572"
MASK[4]=":1573-2096"
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 7 8 9 10 11 12 13 14;
do
        echo 'trajin '${DIR[index]}${TRAJIN[1]} 1 2500 1 >> ${ptraj_file}
        echo 'trajin '${DIR[index]}${TRAJIN[2]} 1 2500 1 >> ${ptraj_file}


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

	echo 'rms reference 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 nobox netcdf" >> ${ptraj_file}

        ptraj ${PRMTOP} ${ptraj_file}

        rm ${ptraj_file}
done