To get started with RMS fitting and alignment, open the RMSD item from the Extensions menu. You should now have a new window titled RMSD Tool We'll describe the RMSD calculator function first.
The RMSD calculator button is used to calculate RMS distances between molecules. The upper left corner of the menu is where you specify which atoms are to be used in the calculation. In the input field, type the atom selection text just as you would in the Graphics window. The checkbox below the input field entitled Backbone only restricts whatever atom selection you typed to just the backbone atoms of the selection; in effect, it adds "and backbone" to the atom selection text.
The upper right corner of the menu has a button labeled RMSD. Its effect depends on which of the Top, Average, or Selected radio buttons are selected. If Top is selected, VMD calculates the RMS distance between the top molecule (which is usually the last molecule loaded) and every other molecule. If Average is selected, VMD first computes the average x, y, z coordinates of the selected atoms in each molecule, then computes the RMS distance of each molecule from that average structure.
Results of the RMS calculations for each molecule are shown in the browser in the bottom half of the menu. Note that this list is not updated until you presse the RMSD button, so the effects of loading/deleting molecules will not be immediately reflected. The Total RMSD label at the bottom of the menu shows the average RMSD for all molecules listed.
The RMS Alignment button fits molecules based on selected groups of atoms. Whereas the RMSD calculator button finds the RMS distance between molecules without disturbing their coordinates, the RMS Alignment button actually moves molecules to new positions.
This button is quite simple: Enter an atom selection in the input field, and press Align to align the molecules based on the atoms in that selection. If you recompute the RMSD between molecules with the RMSD calculator button, you will probably find that the values are different; this is because the calculation is made based on the current positions of the atoms.