#!/bin/bash

ptraj_file="tmp.ptraj"
OUT="10-50ns_fluct_fitEQ"

REF="1XCK_chainA_noWAT.inpcrd"
PRMTOP="1XCK_chainA_noWAT.prmtop"

DIR_PREFIX="../traj_monomer/"
TRAJIN_PREFIX="500ns_noWAT_5000frames_chain"


for i in 1; 
do
	rm ${ptraj_file}

	for j in 1 2 3 4 5 6 7; 
	do
		if [ $i -lt 2 ]; then 
			let index=$j
		else
			let index=$j+7
		fi

		tin=${DIR_PREFIX}${TRAJIN_PREFIX}_${index}.nc
		echo 'trajin '${tin} 1001 5000 1 >> ${ptraj_file}
	done

	echo 'reference '${REF} >> ${ptraj_file}
	#echo 'rms reference :10-134,409-516@CA,C,N' >> ${ptraj_file}
        echo 'rms reference :10-28,64-84,88-108,112-131,433-457,461-470,515-496@CA,C,N' >> ${ptraj_file}
	
	#echo 'rms reference :190-375@CA,C,N' >> ${ptraj_file}
	#echo 'rms reference :133-189,376-407@CA,C,N' >> ${ptraj_file}
	#echo 'rms reference :10-515@CA,C,N' >> ${ptraj_file}

	echo 'atomicfluct out '${OUT}'_'${i}'.out byres'  >> ${ptraj_file}
	ptraj ${PRMTOP} ${ptraj_file}

done