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 ##start script
 #! bin/csh
 set psf = "filename.psf"
 set dcd = "filename.dcd"
 cat << EOF > vmd.rmsd.tcl
 mol load psf $psf dcd $dcd
 set outfile [open rmsd.dat w]
 set nf [molinfo top get numframes]
 set frame0 [atomselect top "protein and backbone and noh" frame 0]
 set sel [atomselect top "protein and backbone and noh"]
 # rmsd calculation loop
 for { set i 1 } { \$i <= \$nf } { incr i } {
 \$sel frame \$i
 \$sel move [measure fit \$sel \$frame0]
 puts \$outfile "[measure rmsd \$sel \$frame0]"
 close \$outfile
 ## run vmd.
 /nfs/user03/mcgillic/vmd-1.8.6/bin/vmd  -dispdev text -e vmd.rmsd.tcl > vmd.rmsd.log
 ##end script