To get started with RMS fitting and alignment, type vmdrmsd from the command line. Alternatively, you can source the script called rmsd.tcl, which should be located in the scripts/vmd 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/scripts/vmd/rmsd.tcl. You should now have two new menus, titled RMSD calculator and RMS Alignment (kindly provided by Alexander Balaeff from the Theoretical Biophysics Group). We'll describe the RMSD calculator first.