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https://github.com/choderalab/openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
https://github.com/choderalab/openmmtools

alchemical-free-energy-calculations free-energy-calculations integrators markov-chain-monte-carlo mcmc molecular-dynamics molecular-simulations openmm python replica-exchange

Last synced: about 1 month ago
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A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

Host: GitHub
URL: https://github.com/choderalab/openmmtools
Owner: choderalab
License: mit
Created: 2014-10-19T02:52:35.000Z (over 9 years ago)
Default Branch: main
Last Pushed: 2024-02-26T16:35:03.000Z (4 months ago)
Last Synced: 2024-04-14T12:14:27.057Z (2 months ago)
Topics: alchemical-free-energy-calculations, free-energy-calculations, integrators, markov-chain-monte-carlo, mcmc, molecular-dynamics, molecular-simulations, openmm, python, replica-exchange
Language: Python
Homepage: http://openmmtools.readthedocs.io
Size: 32.8 MB
Stars: 233
Watchers: 38
Forks: 75
Open Issues: 224
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md

Lists

awesome-python-chemistry - openmmtools - A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine. (Simulations)
awesome-python-chemistry - openmmtools - A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine. (Simulations)

README

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## OpenMMTools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

`openmmtools` is a Python library layer that sits on top of [OpenMM](http://openmm.org) to provide access to a variety of useful tools for building full-featured molecular simulation packages.

Features include:

 - high-quality [Langevin integrators](https://openmmtools.readthedocs.io/en/stable/integrators.html#langevin-integrators), including [g-BAOAB](http://rspa.royalsocietypublishing.org/content/472/2189/20160138), [VVVR](http://pubs.acs.org/doi/abs/10.1021/jp411770f), and other splittings

 - [nonequilibrium integrators](https://openmmtools.readthedocs.io/en/stable/integrators.html#nonequilibrium-integrators) for free energy calculations or [nonequilibrium candidate Monte Carlo (NCMC)](http://dx.doi.org/10.1073/pnas.1106094108)

 - an extensible [Markov chain Monte Carlo (MCMC) framework](https://openmmtools.readthedocs.io/en/stable/mcmc.html) for molecular simulations

 - enhanced sampling methods, including replica-exchange (REMD) and self-adjusted mixture sampling (SAMS)

 - [alchemical factories](https://openmmtools.readthedocs.io/en/stable/alchemy.html) for generating [alchemically-modified](http://alchemistry.org) systems for absolute and relative free energy calculations

 - a suite of [test systems](https://openmmtools.readthedocs.io/en/stable/testsystems.html) for benchmarking, validation, and debugging

 - user-friendly storage interface layer

See the [full documentation](http://openmmtools.readthedocs.io) at [ReadTheDocs](http://openmmtools.readthedocs.io).

#### License

OpenMMTools is distributed under the [MIT License](https://opensource.org/licenses/MIT).

#### Contributors

A complete list of contributors can be found [here](https://github.com/choderalab/openmmtools/graphs/contributors).

Major contributors include:

* [Andrea Rizzi](https://github.com/andrrizzi) 

* [John D. Chodera](https://github.com/jchodera)

* [Levi N. Naden](https://github.com/Lnaden)

* [Patrick Grinaway](https://github.com/pgrinaway)

* [Kyle A. Beauchamp](https://github.com/kyleabeauchamp)

* [Josh Fass](https://github.com/maxentile)

* [Bas Rustenburg](https://github.com/bas-rustenburg)

* [Gregory Ross](https://github.com/gregoryross)

* [David W.H. Swenson](https://github.com/dwhswenson)

* [Hannah Bruce Macdonald](https://github.com/hannahbrucemacdonald)

* [Iván Pulido](https://github.com/ijpulidos)

* [Ivy Zhang](https://github.com/zhang-ivy)

* [Dominic Rufa](https://github.com/dominicrufa)

* [Mike Henry](https://github.com/mikemhenry)