#!/bin/csh

cpptraj <<EOF
parm ../../GAAC-ions.topo
trajin ../../GAAC-strip.netcdf 1 9999999999 500
createcrd crd1
rms2d crd1 first time 50 :1-36 rmsout 2drms_full.gnu
rms2d crd1 second time 50 :2-17,:20-35 rmsout 2drms_2-17_20-35.gnu
EOF



