# alchemlyb: the simple alchemistry library
[](https://zenodo.org/badge/latestdoi/68669096) [](http://alchemlyb.readthedocs.io/en/latest/) [](https://github.com/alchemistry/alchemlyb/actions/workflows/ci.yaml) [](https://codecov.io/gh/alchemistry/alchemlyb) [](https://anaconda.org/conda-forge/alchemlyb)
**alchemlyb** makes alchemical free energy calculations easier to do by leveraging the full power and flexibility of the PyData stack. It includes:
1. Parsers for extracting raw data from output files of common molecular dynamics engines such as [GROMACS](http://www.gromacs.org/), [AMBER](http://ambermd.org/), [NAMD](http://www.ks.uiuc.edu/Research/namd/) and [other simulation codes](https://alchemlyb.readthedocs.io/en/latest/parsing.html).
2. Subsamplers for obtaining uncorrelated samples from timeseries data (including extracting independent, equilibrated samples [Chodera2016](#chodera2016) as implemented in the [pymbar](http://pymbar.readthedocs.io/) package).
3. Estimators for obtaining free energies directly from this data, using best-practices approaches for multistate Bennett acceptance ratio (MBAR) [Shirts2008](#shirts2008) and BAR (from [pymbar](http://pymbar.readthedocs.io/)) and thermodynamic integration (TI).
## Documentation
The documentation is hosted on [Read the Docs](https://alchemlyb.readthedocs.io/en/latest/).
## Installation
**Install** via `pip` from [PyPi (alchemlyb)](https://pypi.org/project/alchemlyb):
```bash
pip install alchemlyb
```
or as a `conda` package from the [conda-forge (alchemlyb)](https://anaconda.org/conda-forge/alchemlyb) channel:
```bash
conda install -c conda-forge alchemlyb
```
**Update** with `pip`:
```bash
pip install --update alchemlyb
```
or with `conda` run:
```bash
conda update -c conda-forge alchemlyb
```
to get the latest released version.
## Getting involved
Contributions of all kinds are very welcome.
If you have questions or want to discuss alchemlyb please post in the [alchemlyb Discussions](https://github.com/alchemistry/alchemlyb/discussions).
If you have bug reports or feature requests then please get in touch with us through the [Issue Tracker](https://github.com/alchemistry/alchemlyb/issues).
We also welcome code contributions: have a look at our [Developer Guide](https://github.com/alchemistry/alchemlyb/wiki/Developer-Guide). Open an issue with the proposed fix or change in the [Issue Tracker](https://github.com/alchemistry/alchemlyb/issues) and submit a pull request against the [alchemistry/alchemlyb](https://github.com/alchemistry/alchemlyb) GitHub repository.
## References
- <a name="shirts2008"></a> Shirts, M.R., and Chodera, J.D. (2008). Statistically optimal analysis of samples from multiple equilibrium states. The Journal of Chemical Physics 129, 124105.
- <a name="chodera2016"></a> Chodera, J.D. (2016). A Simple Method for Automated Equilibration Detection in Molecular Simulations. Journal of Chemical Theory and Computation 12, 1799–1805.
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"description": "# alchemlyb: the simple alchemistry library\n\n[](https://zenodo.org/badge/latestdoi/68669096) [](http://alchemlyb.readthedocs.io/en/latest/) [](https://github.com/alchemistry/alchemlyb/actions/workflows/ci.yaml) [](https://codecov.io/gh/alchemistry/alchemlyb) [](https://anaconda.org/conda-forge/alchemlyb)\n\n**alchemlyb** makes alchemical free energy calculations easier to do by leveraging the full power and flexibility of the PyData stack. It includes:\n\n1. Parsers for extracting raw data from output files of common molecular dynamics engines such as [GROMACS](http://www.gromacs.org/), [AMBER](http://ambermd.org/), [NAMD](http://www.ks.uiuc.edu/Research/namd/) and [other simulation codes](https://alchemlyb.readthedocs.io/en/latest/parsing.html).\n\n2. Subsamplers for obtaining uncorrelated samples from timeseries data (including extracting independent, equilibrated samples [Chodera2016](#chodera2016) as implemented in the [pymbar](http://pymbar.readthedocs.io/) package).\n\n3. Estimators for obtaining free energies directly from this data, using best-practices approaches for multistate Bennett acceptance ratio (MBAR) [Shirts2008](#shirts2008) and BAR (from [pymbar](http://pymbar.readthedocs.io/)) and thermodynamic integration (TI).\n\n## Documentation\n\nThe documentation is hosted on [Read the Docs](https://alchemlyb.readthedocs.io/en/latest/).\n\n## Installation\n\n**Install** via `pip` from [PyPi (alchemlyb)](https://pypi.org/project/alchemlyb):\n\n```bash\npip install alchemlyb\n```\n\nor as a `conda` package from the [conda-forge (alchemlyb)](https://anaconda.org/conda-forge/alchemlyb) channel:\n\n```bash\nconda install -c conda-forge alchemlyb\n```\n\n**Update** with `pip`:\n\n```bash\npip install --update alchemlyb\n```\n\nor with `conda` run:\n\n```bash\nconda update -c conda-forge alchemlyb\n```\n\nto get the latest released version.\n\n## Getting involved\n\nContributions of all kinds are very welcome.\n\nIf you have questions or want to discuss alchemlyb please post in the [alchemlyb Discussions](https://github.com/alchemistry/alchemlyb/discussions).\n\nIf you have bug reports or feature requests then please get in touch with us through the [Issue Tracker](https://github.com/alchemistry/alchemlyb/issues).\n\nWe also welcome code contributions: have a look at our [Developer Guide](https://github.com/alchemistry/alchemlyb/wiki/Developer-Guide). Open an issue with the proposed fix or change in the [Issue Tracker](https://github.com/alchemistry/alchemlyb/issues) and submit a pull request against the [alchemistry/alchemlyb](https://github.com/alchemistry/alchemlyb) GitHub repository.\n\n## References\n\n- <a name=\"shirts2008\"></a> Shirts, M.R., and Chodera, J.D. (2008). Statistically optimal analysis of samples from multiple equilibrium states. The Journal of Chemical Physics 129, 124105.\n- <a name=\"chodera2016\"></a> Chodera, J.D. (2016). A Simple Method for Automated Equilibration Detection in Molecular Simulations. Journal of Chemical Theory and Computation 12, 1799\u20131805.\n",
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