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Subsections


Advanced usage and special considerations


Periodic components.

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

The following keywords can be used within periodic components (and are illegal elsewhere):

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 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.


Non-scalar components.

When one of the following components are used, the defined colvar returns a value that is not a scalar number: The distance between two 3-dimensional unit vectors is computed as the angle between them. The distance between two quaternions is computed as the angle between the two 4-dimensional unit vectors: because the orientation represented by $ \mathsf{q}$ is the same as the one represented by $ -\mathsf{q}$ , distances between two quaternions are computed considering the closest of the two symmetric images.

Non-scalar components carry the following restrictions:

Note: while these restrictions apply to individual colvars based on non-scalar components, no limit is set to the number of scalar colvars. To compute multi-dimensional histograms and PMFs, use sets of scalar colvars of arbitrary size.


Calculating total forces.

In addition to the restrictions due to the type of value computed (scalar or non-scalar), a final restriction can arise when calculating total force (outputTotalForce option or application of a abf bias). total forces are available currently only for the following components: distance, distanceZ, distanceXY, angle, dihedral, rmsd, eigenvector and gyration.


next up previous contents index
Next: Linear and polynomial combinations Up: Collective variable components (basis Previous: Configuration keywords shared by   Contents   Index
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