View source for Vmd.rmsd.csh

  ##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
  exit
  EOF
  ## run vmd.
  /nfs/user03/mcgillic/vmd-1.8.6/bin/vmd  -dispdev text -e vmd.rmsd.tcl > vmd.rmsd.log
  exit
  ##end script