#!/bin/bash

PRMTOP="../1SVT_chainA_sol.prmtop"
REF="../1SVT_chainA_sol.inpcrd"
#TRAJ_FILE="2ns_imposedOnStart.nc"
TRAJ_FILE="10ns_imposedOnStart_offset10.nc"
ptraj_file="temp.ptraj"

INC_INT=500
SIZE=0
START=1
STOP=10000
OFFSET=1

while [ $SIZE -lt $STOP ]; do
        rm $ptraj_file
        let SIZE=${INC_INT}+${SIZE}
	let END=${START}+${SIZE}-1
	let END_PS=${END}

	echo 'trajin '${TRAJ_FILE} ${START} ${END} ${OFFSET} >> $ptraj_file 
	echo 'reference' ${REF} >> $ptraj_file 
	echo 'strip :WAT' >> $ptraj_file
	echo 'rms reference mass @N,CA,C' >> $ptraj_file
	echo 'matrix covar @CA name mwcvmat' >> $ptraj_file
	echo 'analyze matrix mwcvmat out evecs_pca_'${START}-${END_PS}ps'.dat vecs 50' >> $ptraj_file

	ptraj $PRMTOP $ptraj_file
done