The rmsd command evaluates the root-mean-square deviation (RMSD) between specified sets of atoms. It differs from match in that no least-squares fit is performed (no model is moved). Atom-spec1 and atom-spec2 should contain equal numbers of atoms from two different models, respectively. The atoms need not be connected. Atoms are paired according to the order in which they are specified, i.e., the first atom of the first model is paired with the first atom of the second model, the second atom to the second atom, and so on.
The RMSD in angstroms is reported in the status line and Reply Log. The RMSD value is only for the specified atoms.
An ordered specification should be used, for example
rmsd #1:3@C1@C2@P@O2 #2:3@C1@C2@P@O2rather than
rmsd #1:3@C1,C2,P,O2 #2:3@C1,C2,P,O2Unordered specifications can be used, but the results may not be as expected.
All of the atoms (from both models) can be specified collectively using the word selected, sel, or picked if the current selection contains equal numbers of atoms from each model. The atoms should have been selected (most likely picked) in the proper order, first the desired atoms from one model, then the corresponding atoms in the corresponding order from the other model. When order information is lacking (for example, the atoms were selected simultaneously), the measurement may not be the one intended.
See also: match, matchmaker, Ensemble Match, MD Movie (see RMSD analysis)