This is part of the colvar module

Calculate the RMSD distance between the instaneous configuration and multiple reference configurations

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	a vector containing the RMSD between the instantaneous structure and each of the reference structures that were input

In addition the following quantities can be calculated by employing the keywords listed below

Quantity	Keyword	Description
disp	DISPLACEMENT	the vector of displacements for the atoms
dist	DISPLACEMENT	the RMSD distance the atoms have moved

Compulsory keywords

ARG	the labels of two actions that you are calculating the RMSD between
TYPE	( default=SIMPLE ) the manner in which RMSD alignment is performed. Should be OPTIMAL or SIMPLE.
ALIGN	( default=1.0 ) the weights to use when aligning to the reference structure
DISPLACE	( default=1.0 ) the weights to use when calculating the displacement from the reference structure

Options

SERIAL	( default=off ) do the calculation in serial. Do not parallelize
SQUARED	( default=off ) This should be set if you want mean squared displacement instead of RMSD
UNORMALIZED	( default=off ) by default the mean sequare deviation or root mean square deviation is calculated. If this option is given no averaging is done
DISPLACEMENT	( default=off ) Calculate the vector of displacements instead of the length of this vector