XYZ_DIAG

Section to define the distance of an atom from its starting position ((X-X(0))^2+(Y-Y(0))^2+(Z-Z(0))^2) or part of its components as a collective variable. If absolute_position is specified, instead the CV is represented by the instantaneous position of the atom (only available for X, Y or Z components). [Edit on GitHub]

Subsections

• POINT

Keywords

• ABSOLUTE_POSITION

• ATOM

• COMPONENT

• PBC

Keyword descriptions

ABSOLUTE_POSITION: logical = F

Lone keyword: T

Usage: ABSOLUTE_POSITION

If enabled, the absolute position of the atoms will be used. [Edit on GitHub]

ATOM: integer

Aliases: POINT

Usage: ATOM {integer}

Specifies the index of the atom/point. [Edit on GitHub]

COMPONENT: enum = XYZ

Usage: AXIS (XYZ | X | Y | Z | XY| XZ | YZ)

Valid values:

• XYZ

• X

• Y

• Z

• XY

• XZ

• YZ

Define the component of the position vector which will be used as a colvar. [Edit on GitHub]

PBC: logical = T

Lone keyword: T

Usage: PBC

Whether periodic boundary conditions should be applied on the atomic position before computing the colvar or not. [Edit on GitHub]