Shortcut: MULTI_RMSD

Module	colvar
Description	Usage
Calculate RMSD distances for different domains and combine them.
output value	type
the sum of the multiple RMSD distances	scalar

Further details and examples

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. You can see an example in example from the plumed nest.

We felt 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 inputs in the egg that is linked above 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.

Syntax

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
REFERENCE	compulsory	none	a file in pdb format containing the reference structure and the atoms involved in the CV
TYPE	compulsory	SIMPLE	the manner in which RMSD alignment is performed
SQUARED	optional	false	This should be set if you want the mean squared displacement instead of the root mean squared displacement
NOPBC	optional	false	don't use periodic boundary conditions