This is part of the colvar module

Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule multiple times.

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	Description
x	the x-component of the vector that is normal to the plane containing the atoms
y	the y-component of the vector that is normal to the plane containing the atoms
z	the z-component of the vector that is normal to the plane containing the atoms

The atoms involved can be specified using

ATOMS

the three or four atoms whose plane we are computing. 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