the simple alchemistry library

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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, AMBER, NAMD and other simulation codes.

  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].

[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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2.4.1

2.4.1rc1 pre-release

2.4.0

2.3.2

2.3.1

2.3.0

2.2.0

2.1.0

2.0.1

2.0.0

1.0.1

1.0.0

0.7.0

0.6.0

0.5.1

0.5.0

0.4.2

This version

0.4.1

0.4.0

0.3.1

0.3.0

0.1.0

0.1.0a0 pre-release

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