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.
RMSD(system, reference, rmsd_indices[, …])	A class for a root-mean-square deviation (RMSD) collective variable.
Torsion(atoms[, hill_width, lower_bound, …])	A class for torsion based collective variables.