Periodic components

The following components returns real numbers that lie in a periodic interval:

• dihedral: torsional angle between four groups;
• spinAngle: angle of rotation around a predefined axis in the best-fit from a set of reference coordinates.

In certain conditions, distanceZ can also be periodic, namely when periodic boundary conditions (PBCs) are defined in the simulation and distanceZ's axis is parallel to a unit cell vector.

In addition, a custom or scripted scalar colvar may be periodic depending on its user-defined expression. It will only be treated as such by the Colvars module if the period is specified using the period keyword, while wrapAround is optional.

The following keywords can be used within periodic components, or wthin scripted variables ).

• period $\langle\,$ Period of the component$\,\rangle$
  Context: distanceZ, custom colvars
  Acceptable values: positive decimal
  Default value: 0.0
  Description: Setting this number enables the treatment of distanceZ as a periodic component: by default, distanceZ is not considered periodic. The keyword is supported, but irrelevant within dihedral or spinAngle, because their period is always 360 degrees.

• wrapAround $\langle\,$ Center of the wrapping interval for periodic variables$\,\rangle$
  Context: distanceZ, dihedral, spinAngle, custom colvars
  Acceptable values: decimal
  Default value: 0.0
  Description: By default, values of the periodic components are centered around zero, ranging from $-P/2$ to $P/2$ , where $P$ is the period. Setting this number centers the interval around this value. This can be useful for convenience of output, or to set the walls for a harmonicWalls in an order that would not otherwise be allowed.

Internally, all differences between two values of a periodic colvar follow the minimum image convention: they are calculated based on the two periodic images that are closest to each other.

Note: linear or polynomial combinations of periodic components (see ) may become meaningless when components cross the periodic boundary. Use such combinations carefully: estimate the range of possible values of each component in a given simulation, and make use of wrapAround to limit this problem whenever possible.