This is part of the colvar module

Calculate RMSD distances for different domains and combine them.

This action is largely depracated. In previous versions of PLUMED a more complex version of this method was implemented. We felt, however, that the input syntax for the method was not very transparant. We have thus provided this minimal action that creates the input for calculating the MultiDomain RMSD for simple cases. This action is a shortcut. If you look at the log you can see how we use the various actions that are in PLUMED to calculate the final quantity. If you would like to implement some of the more complicated CVs things that this could do with MULTI_RMSD looking at how this shortcut works will help you start.

Examples

Glossary of keywords and components

Compulsory keywords

REFERENCE	a file in pdb format containing the reference structure and the atoms involved in the CV.
TYPE	( default=SIMPLE ) the manner in which RMSD alignment is performed. Should be MULTI-OPTIMAL, MULTI-OPTIMAL-FAST, MULTI-SIMPLE or MULTI-DRMSD.

Options

SQUARED

( default=off ) This should be set if you want the mean squared displacement instead of the root mean squared displacement

NOPBC

( default=off ) don't use periodic boundary conditions