alchemlyb makes alchemical free energy calculations easier to do by leveraging the full power and flexibility of the PyData stack. It includes:
- Parsers for extracting raw data from output files of common molecular dynamics engines such as GROMACS, AMBER, NAMD and other simulation codes.
- Subsamplers for obtaining uncorrelated samples from timeseries data.
- 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. |