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

Keywords

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]