This is part of the colvar module

Create a vector that holds the components of the position of a set of atoms.

Examples

Glossary of keywords and components

Description of components

By default this Action calculates the following quantities. 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
x	the x-component of the atom position
y	the y-component of the atom position
z	the z-component of the atom position

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

Quantity	Keyword	Description
a	SCALED_COMPONENTS	the normalized projection on the first lattice vector of the atom position
b	SCALED_COMPONENTS	the normalized projection on the second lattice vector of the atom position
c	SCALED_COMPONENTS	the normalized projection on the third lattice vector of the atom position

The atoms involved can be specified using

ATOM	the atom number. For more information on how to specify lists of atoms see Groups and Virtual Atoms
ATOMS	the atom numbers that you would like to use the positions of. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
WHOLEMOLECULES	( default=off ) if this is a vector of positions do you want to make the positions into a whole before
SCALED_COMPONENTS	( default=off ) calculate the a, b and c scaled components of the position separately and store them as label.a, label.b and label.c