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https://github.com/redesignscience/cvpack
Useful Collective Variables for OpenMM
https://github.com/redesignscience/cvpack
collective-variables enhanced-sampling metadynamics molecular-dynamics openmm
Last synced: 2 months ago
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Useful Collective Variables for OpenMM
- Host: GitHub
- URL: https://github.com/redesignscience/cvpack
- Owner: RedesignScience
- License: mit
- Created: 2023-01-23T22:08:18.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2024-05-09T16:14:29.000Z (9 months ago)
- Last Synced: 2024-10-30T12:51:30.102Z (3 months ago)
- Topics: collective-variables, enhanced-sampling, metadynamics, molecular-dynamics, openmm
- Language: Python
- Homepage: https://redesignscience.github.io/cvpack/latest
- Size: 6.68 MB
- Stars: 11
- Watchers: 1
- Forks: 1
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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README
Collective Variable Package
===========================
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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](https://anaconda.org/mdtools/cvpack) channel. To install it, run:
```bash
conda install -c conda-forge -c mdtools cvpack
```
Or:
```bash
mamba install -c mdtools cvpack
```
To use CVPack in your own Python script or Jupyter notebook, simply import it as follows:
```python
import cvpack
```
Documentation
-------------
Documentation for the latest CVPack version is available on [Github Pages](https://redesignscience.github.io/cvpack/latest).
Copyright
---------
Copyright (c) 2023-2024 [C. Abreu](https://github.com/craabreu) & [Redesign Science](https://www.redesignscience.com)
Acknowledgments
---------------
Initial project based on the [CMS Cookiecutter] version 1.1.
[BiasVariable]: http://docs.openmm.org/latest/api-python/generated/openmm.app.metadynamics.BiasVariable.html
[CMS Cookiecutter]: https://github.com/molssi/cookiecutter-cms
[CustomCVForce]: http://docs.openmm.org/latest/api-python/generated/openmm.openmm.CustomCVForce.html
[Force]: http://docs.openmm.org/latest/api-python/generated/openmm.openmm.Force.html
[Metadynamics]: http://docs.openmm.org/latest/api-python/generated/openmm.app.metadynamics.Metadynamics.html
[OpenMM]: http://openmm.org
[Angle]: https://redesignscience.github.io/cvpack/latest/api/Angle.html
[Atomic Function]: https://redesignscience.github.io/cvpack/latest/api/AtomicFunction.html
[Attraction Strength]: https://redesignscience.github.io/cvpack/latest/api/AttractionStrength.html
[Centroid Function]: https://redesignscience.github.io/cvpack/latest/api/CentroidFunction.html
[Composite RMSD]: https://redesignscience.github.io/cvpack/latest/api/CompositeRMSD.html
[Distance]: https://redesignscience.github.io/cvpack/latest/api/Distance.html
[Helix angle content]: https://redesignscience.github.io/cvpack/latest/api/HelixAngleContent.html
[Helix H-bond content]: https://redesignscience.github.io/cvpack/latest/api/HelixHBondContent.html
[Helix RMSD content]: https://redesignscience.github.io/cvpack/latest/api/HelixRMSDContent.html
[Helix torsion content]: https://redesignscience.github.io/cvpack/latest/api/HelixTorsionContent.html
[Meta CV]: https://redesignscience.github.io/cvpack/latest/api/MetaCollectiveVariable.html
[Number of contacts]: https://redesignscience.github.io/cvpack/latest/api/NumberOfContacts.html
[OpenMM Force wrapper]: https://redesignscience.github.io/cvpack/latest/api/OpenMMForceWrapper.html
[Path in CV space]: https://redesignscience.github.io/cvpack/latest/api/PathInCVSpace.html
[Path in RMSD space]: https://redesignscience.github.io/cvpack/latest/api/PathInRMSDSpace.html
[Radius of gyration]: https://redesignscience.github.io/cvpack/latest/api/RadiusOfGyration.html
[(Radius of gyration)^2]: https://redesignscience.github.io/cvpack/latest/api/RadiusOfGyrationSq.html
[Residue coordination]: https://redesignscience.github.io/cvpack/latest/api/ResidueCoordination.html
[RMSD]: https://redesignscience.github.io/cvpack/latest/api/RMSD.html
[Sheet RMSD content]: https://redesignscience.github.io/cvpack/latest/api/SheetRMSDContent.html
[Shortest Distance]: https://redesignscience.github.io/cvpack/latest/api/ShortestDistance.html
[Torsion]: https://redesignscience.github.io/cvpack/latest/api/Torsion.html
[Torsion similarity]: https://redesignscience.github.io/cvpack/latest/api/TorsionSimilarity.html