This is part of the colvar module

Calculate a vector containing the distances between various pairs of atoms

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
x	COMPONENTS	the x-component of the vector connecting the two atoms
y	COMPONENTS	the y-component of the vector connecting the two atoms
z	COMPONENTS	the z-component of the vector connecting the two atoms
a	SCALED_COMPONENTS	the normalized projection on the first lattice vector of the vector connecting the two atoms
b	SCALED_COMPONENTS	the normalized projection on the second lattice vector of the vector connecting the two atoms
c	SCALED_COMPONENTS	the normalized projection on the third lattice vector of the vector connecting the two atoms

The atoms involved can be specified using

ATOMS

the pair of atom that we are calculating the distance between. 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
COMPONENTS	( default=off ) calculate the x, y and z components of the distance separately and store them as label.x, label.y and label.z
SCALED_COMPONENTS	( default=off ) calculate the a, b and c scaled components of the distance separately and store them as label.a, label.b and label.c