collective variable package

This module provides access to CVPack, an external library of useful collective variables.

Some examples of collective variables implemented in CVPack are:

• Angle:

  angle formed by three atoms

• Atomic Function:

  a user-defined function of the coordinates of a group of atoms

• Attraction Strength:

  strength of the attraction between two groups of atoms

• Centroid Function:

  a user-defined function of the centroids of groups of atoms

• Distance:

  distance between two atoms

• Helix angle content:

  alpha-helix angle content of a sequence of residues

• Helix H-bond content:

  alpha-helix hydrogen-bond content of a sequence of residues

• Helix RMSD content:

  alpha-helix RMSD content of a sequence of residues

• Helix torsion content:

  alpha-helix Ramachandran content of a sequence of residues

• Number of contacts:

  number of contacts between two groups of atoms

• Radius of gyration:

  radius of gyration of a group of atoms

• RMSD:

  root-mean-square deviation of atoms with respect to a reference structure

• Torsion:

  torsion angle formed by four atoms

• Torsion similarity:

  degree of similarity between pairs of torsion angles