#!/bin/bash

PRMTOP="../1SVT_chainA_MGADP_sol.prmtop"
REF="../1SVT_chainA_MGADP_sol.inpcrd"
TRAJ_FILE="heile_driten.nc"
ptraj_file="temp.ptraj"

INT=500
C=1
STOP=10000
OFFSET=1

while [ $C -lt $STOP ]; do
        rm $ptraj_file
	let END=${C}+${INT}-1

	echo 'trajin '${TRAJ_FILE} ${C} ${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' >> $ptraj_file
	echo 'analyze matrix mwcvmat out evecs_pca_'${C}-${END}'.dat vecs 50' >> $ptraj_file

	ptraj $PRMTOP $ptraj_file
	let C=${C}+${INT}
done