cvpack 0.11.3

Useful Collective Variables for OpenMM

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, for instance.

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 predefined path in CV 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
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

Acknowledgements

Initial project based on the CMS Cookiecutter version 1.1.