CV:MDIS: Difference between revisions
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Latest revision as of 13:38, 9 June 2015
Navigation: Documentation / Collective Variables / CV:MDIS
Distance
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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.