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.