Non-scalar components

When one of the following components are used, the defined colvar returns a value that is not a scalar number:

• distanceVec: 3-dimensional vector of the distance between two groups;
• distanceDir: 3-dimensional unit vector of the distance between two groups;
• orientation: 4-dimensional unit quaternion representing the best-fit rotation from a set of reference coordinates.

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:

• Calculation of total forces (outputTotalForce option) is currently not implemented.
• Each colvar can only contain one non-scalar component.
• Binning on a grid (abf, histogram and metadynamics with useGrids enabled) is currently not implemented for colvars based on such components.

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.