BioSimSpace.Metadynamics.CollectiveVariable

The CollectiveVariable package contains tools configuring collective variables for use in metadynamics simulations.

Functions

list()

Return a list of the supported collective variables.

makeFunnel(system[, protein, ligand, …])

Calculate the two sets of atom indices, atoms0 and atoms1, that are used to define the funnel collective variable.

viewFunnel(system, collective_variable[, …])

Visualise the shape of the funnel defined by the collective variable.

Classes

Distance(atom0, atom1[, hill_width, …])

A class for distance based collective variables.

Funnel(atoms0, atoms1[, hill_width, width, …])

A class for a funnel collective variable.

Torsion(atoms[, hill_width, lower_bound, …])

A class for torsion based collective variables.