cvpack 0.3.0

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 configurational space, including regions that are otherwise difficult to access. 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. As such, they can be directly added to a CustomCVForce object or used to define a BiasVariable object for Metadynamics, for example.

The CVs currently implemented in CVPack are:

• Angle: The angle formed by three atoms.
• Atomic Function: A user-defined function of the coordinates of a group of atoms.
• Centroid Function A user-defined function of the centroids of groups of atoms.
• Distance: The distance between two atoms.
• Helix angle content: The alpha-helix angle content of a sequence of residues.
• Helix H-bond content: The alpha-helix hydrogen-bond content of a sequence of residues.
• Helix RMSD content: The alpha-helix RMSD content of a sequence of residues
• Helix torsion content: The alpha-helix Ramachandran content of a sequence of residues.
• Number of contacts: The number of contacts between two groups of atoms.
• Radius of gyration: The radius of gyration of a group of atoms.
• RMSD: The RMSD of a group of atoms with respect to a reference structure.
• Torsion: The torsion angle formed by four atoms.
• Torsion similarity: The degree of similarity between pairs of torsion angles.

Installation

CVPack is available on PyPI. To install it, simply run:

    pip install cvpack

Documentation

The documentation for CVPack is available at Read the Docs.

Copyright

Copyright (c) 2023, Redesign Science

Acknowledgements

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