To get started with RMS fitting and alignment, source the script (kindly provided by Alexander Balaeff from the Theoretical Biophysics Group) called rmsd.tcl, which should be located in the scripts subdirectory of your VMD installation. For example, if VMD is installed in /usr/local/lib/vmd, type the following from the command line: source /usr/local/lib/vmd/rmsd.tcl. You should now have two new menus, titled RMSD calculator and RMS Alignment. We'll describe the RMSD calculator first.