Collective Variable Package

Overview

Collective variables (CVs) are functions of the coordinates of a molecular system and provide a means to project its conformational state onto a lower-dimensional space. By stimulating the dynamics of a judiciously chosen set of CVs, one can obtain an enhanced sampling of the configuration space, including regions that are otherwise difficult to access. The system's free energy as a function of these CVs can be used to characterize the relative stability of different states and to identify pathways connecting them.

CVPack is a Python package that provides pre-defined CVs for the powerful molecular dynamics engine OpenMM. All these CVs are subclasses of OpenMM's Force class and, as such, can be directly added to a CustomCVForce or used to define a BiasVariable for Metadynamics.

Collective Variables

The CVs implemented in CVPack are listed in the table below.

Collective Variable	Description
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
Composite RMSD	multibody RMSD with concerted-rotation alignment
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
Meta CV	a function of other collective variables
Number of contacts	number of contacts between two groups of atoms
OpenMM Force wrapper	converts an OpenMM Force object into a CVPack CV
Path in CV space	progress along (or deviation from) a path in CV space
Path in RMSD space	progress along (or deviation from) a path in RMSD space
Radius of gyration	radius of gyration of a group of atoms
(Radius of gyration)^2	square of the radius of gyration of a group of atoms
Residue coordination	number of contacts between two disjoint groups of residues
RMSD	root-mean-square deviation with respect to a reference structure
Sheet RMSD content	beta-sheet RMSD content of a sequence of residues
Shortest Distance	shortest distance between two groups of atoms
Torsion	torsion angle formed by four atoms
Torsion similarity	degree of similarity between pairs of torsion angles

Installation and Usage

CVPack is available as a conda package on the mdtools channel. To install it, run:

    conda install -c conda-forge -c mdtools cvpack

Or:

    mamba install -c mdtools cvpack

To use CVPack in your own Python script or Jupyter notebook, simply import it as follows:

    import cvpack

Documentation

Documentation for the latest CVPack version is available on Github Pages.

Copyright

Copyright (c) 2023-2024 C. Abreu & Redesign Science

Acknowledgments

Initial project based on the CMS Cookiecutter version 1.1.