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

Type: logical
Default: F
Lone keyword: T
Usage: ABSOLUTE_POSITION

Description: If enabled, the absolute position of the atoms will be used.

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ATOM

Type: integer
Aliases: POINT
Usage: ATOM {integer}

Description: Specifies the index of the atom/point.

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COMPONENT

Type: enum
Default: XYZ
Usage: COMPONENT (XYZ | X | Y | Z | XY| XZ | YZ)

Description: Define the component of the position vector which will be used as a colvar.

Valid values:

• XYZ

• X

• Y

• Z

• XY

• XZ

• YZ

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PBC

Type: logical
Default: T
Lone keyword: T
Usage: PBC

Description: Whether periodic boundary conditions should be applied on the atomic position before computing the colvar or not.

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