Collective Variables

Overview

Collective Variables available in PySAGES

pysages.colvars.angles.Angle(indices)	Angle between 3 points in space.
pysages.colvars.angles.DihedralAngle(indices)	Computes the dihedral angle spanned by four points in space (usually atom positions).
pysages.colvars.shape.RadiusOfGyration(indices)	Collective Variable that calculates the unweighted radius of gyration as CV.
pysages.colvars.shape.PrincipalMoment(...[, ...])	Calculate the principal moment as collective variable.
pysages.colvars.shape.Asphericity(indices[, ...])	Collective Variable that calculates the Asphericity.
pysages.colvars.shape.Acylindricity(indices)	Collective Variable that calculates the Acylindricity CV.
pysages.colvars.shape.ShapeAnisotropy(indices)	Collective Variable that calculates the Shape Anisotropy CV.
pysages.colvars.coordinates.Component(...[, ...])	Use a specific Cartesian component of the center of mass of the group of atom selected via the indices.
pysages.colvars.coordinates.Distance(indices)	Use the distance of atom groups selected via the indices as collective variable.
pysages.colvars.orientation.ERMSD(indices, ...)	Use a reference to calculate the eRMSD of a set of RNA structures.
pysages.colvars.orientation.ERMSDCG(indices, ...)	Use a reference to calculate the eRMSD of a set of Coarse-grained RNA structures.

Abstract base classes

pysages.colvars.core.CollectiveVariable(indices)	Abstract base class for defining collective variables
pysages.colvars.core.AxisCV(indices, axis[, ...])	Collective variable that specifies a Cartesian Axis in addition.
pysages.colvars.core.TwoPointCV(indices)	Collective variable that takes group of length 2.
pysages.colvars.core.ThreePointCV(indices)	Collective variable that takes group of length 3.
pysages.colvars.core.FourPointCV(indices)	Collective variable that takes group of length 4.

Contents:

• Angles as collective variables
  • Angle
  • angle()
  • DihedralAngle
  • dihedral_angle()
  • RingPuckeringCoordinates
  • ring_puckering_coordinates()
  • RingPhaseAngle
  • ring_phase_angle()
  • RingAmplitude
  • ring_amplitude()
• Shapes as collective Variables
  • RadiusOfGyration
  • radius_of_gyration()
  • weighted_radius_of_gyration()
  • PrincipalMoment
  • gyration_tensor()
  • weighted_gyration_tensor()
  • principal_moments()
  • Asphericity
  • asphericity()
  • Acylindricity
  • acylindricity()
  • ShapeAnisotropy
  • shape_anisotropy()
• Cartesian Coordinate Collective Variables
  • barycenter()
  • weighted_barycenter()
  • Component
  • Distance
  • distance()
  • Displacement
  • displacement()
• Abstract Collective Variables
  • CollectiveVariable
  • AxisCV
  • TwoPointCV
  • ThreePointCV
  • FourPointCV
  • multicomponent()
  • build()
• Orientation as collective variables
  • kabsch()
  • rmsd()
  • RMSD
  • ERMSD
  • calc_local_reference_systems()
  • g_vector()
  • reshape_coordinates()
  • ermsd_core()
  • ermsd()
  • ERMSDCG
  • infer_base_coordinates()
  • ermsd_cg()

Collective variables describe a macro state with many possible micro state realizations. PySAGES tries to support a variety common collective variables, but it is easy to extend PySAGES with your own.