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the simple alchemistry library

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Warning: This library is young. It is not API stable. It is a nucleation point. By all means use and help improve it, but note that it will change with time.

alchemlyb is an attempt to make 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 [Abraham2015].
  2. Subsamplers for obtaining uncorrelated samples from timeseries data.
  3. Estimators for obtaining free energies directly from this data, using best-practices approaches for multistate Bennett acceptance ratio (MBAR) [Shirts2008] and thermodynamic integration (TI).

In particular, it uses internally the excellent pymbar library for performing MBAR and extracting independent, equilibrated samples [Chodera2016].

[Abraham2015]Abraham, M.J., Murtola, T., Schulz, R., Páll, S., Smith, J.C., Hess, B., and Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25.
[Shirts2008]Shirts, M.R., and Chodera, J.D. (2008). Statistically optimal analysis of samples from multiple equilibrium states. The Journal of Chemical Physics 129, 124105.
[Chodera2016]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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