This is part of the colvar module

Calculate the RMSD with respect to a reference structure.

Examples

Glossary of keywords and components

Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
.#!value	the RMSD between the instantaneous structure and the reference structure that was input

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 OPTIMAL or SIMPLE.

Options

NUMERICAL_DERIVATIVES

( default=off ) calculate the derivatives for these quantities numerically

NOPBC

( default=off ) ignore the periodic boundary conditions when calculating distances

SQUARED

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