CV:MDIS: Difference between revisions

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Navigation: [[Documentation]] / [[Collective variables]] / [[CV:MDIS]]
Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:MDIS]]
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Latest revision as of 13:38, 9 June 2015

Navigation: Documentation / Collective Variables / CV:MDIS


Distance

Angle

Coordination

Shape

Nucleic Acids

Puckering

Special

Energy

Algebra

Definition

The minimum value of atom pair distances. To ensure that the collective variable is a continuous function a probabilistic definition is used. This is an approximation providing good estimate of minimal distance. In most cases it provides a value slighter higher than a real minimum distance. However for degenerate situations, where more than one atom pair distance is very close to a minimum value, the value of collective variable will be lower than this minimum value.

Non-degenerate case:

Degenerate case (ng is degree of degeneracy):

PBC note: The minimum-image convention is apllied to all atom pair distances if the fenable_pbc option is activated.


Specification

Section name: MDIS

Key Type Default Description




name string unique CV name
beta real 1.0 factor β
pair mask mask two masks specifying the atom pair. Each mask can hold only one atom. This line is repeating until all atom pairs are specified.

Keys in bold are mandatory.