alchemlyb 2.5.0

the simple alchemistry library

alchemlyb: the simple alchemistry library

alchemlyb makes alchemical free energy calculations easier to do by leveraging the full power and flexibility of the PyData stack Wu2024. It includes:

1. Parsers for extracting raw data from output files of common molecular dynamics engines such as GROMACS, AMBER, NAMD and other simulation codes.

2. Subsamplers for obtaining uncorrelated samples from timeseries data (including extracting independent, equilibrated samples Chodera2016 as implemented in the pymbar package).

3. Estimators for obtaining free energies directly from this data, using best-practices approaches for multistate Bennett acceptance ratio (MBAR) Shirts2008 and BAR (from pymbar) and thermodynamic integration (TI).

How to Cite

If you use this software in your research, please cite it as follows:

Wu, Z., Dotson, D. L., Alibay, I., Allen, B. K., Barhaghi, M. S., Hénin, J., Joseph, T. T., Kenney, I. M., Lee, H., Li, H., Lim, V., Liu, S., Marson, D., Merz, P. T., Schlaich, A., Mobley, D., Shirts, M. R., Beckstein, O. (2024). alchemlyb: the simple alchemistry library. Journal of Open Source Software, 9 (101), 6934. https://doi.org/10.21105/joss.06934

Documentation

The documentation is hosted on Read the Docs.

Installation

Install via pip from PyPi (alchemlyb):

pip install alchemlyb

or as a conda package from the conda-forge (alchemlyb) channel:

conda install -c conda-forge alchemlyb

Update with pip:

pip install --update alchemlyb

or with conda run:

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.

If you have bug reports or feature requests then please get in touch with us through the Issue Tracker.

We also welcome code contributions: have a look at our Developer Guide. Open an issue with the proposed fix or change in the Issue Tracker and submit a pull request against the alchemistry/alchemlyb GitHub repository.

References

• Shirts, M.R., and Chodera, J.D. (2008). Statistically optimal analysis of samples from multiple equilibrium states. The Journal of Chemical Physics 129, 124105.
• Chodera, J.D. (2016). A Simple Method for Automated Equilibration Detection in Molecular Simulations. Journal of Chemical Theory and Computation 12, 1799–1805.
• Wu, Z., Dotson, D. L., Alibay, I., Allen, B. K., Barhaghi, M. S., Hénin, J., Joseph, T. T., Kenney, I. M., Lee, H., Li, H., Lim, V., Liu, S., Marson, D., Merz, P. T., Schlaich, A., Mobley, D., Shirts, M. R., Beckstein, O. (2024). alchemlyb: the simple alchemistry library. Journal of Open Source Software, 9 (101), 6934. https://doi.org/10.21105/joss.06934