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

Compulsory keywords

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
ARG	the input for this action is the scalar output from one or more other actions. The particular scalars that you will use are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates a single scalar value. The value of this scalar is thus used as the input to this new action. If * or . appears the scalars calculated by all the proceeding actions in the input file are taken. Some actions have multi-component outputs and each component of the output has a specific label. For example a DISTANCE action labelled dist may have three components x, y and z. To take just the x component you should use dist.x, if you wish to take all three components then use dist.*.More information on the referencing of Actions can be found in the section of the manual on the PLUMED Getting Started. Scalar values can also be referenced using POSIX regular expressions as detailed in the section on Regular Expressions. To use this feature you you must compile PLUMED with the appropriate flag.. You can use multiple instances of this keyword i.e. ARG1, ARG2, ARG3...