Recipes, utilities, and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy (OpenFE) toolkits.

Currently it hosts utilities and code for Nonequilibrium cycling protocol, with support for protein mutations, that use and integrate with the OpenFE ecosystem.

feflow is available through conda-forge packages. We recommend creating an environment with it as follows

mamba create --name feflow-env feflow

Copyright (c) 2023, ChoderaLab Copyright (c) 2024, The Open Free Energy development team

Choderalab -- Perses

Open Free Energy Consortium

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.

[1] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30.

[2] Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex Ivy Zhang, Dominic A. Rufa, Iván Pulido, Michael M. Henry, Laura E. Rosen, Kevin Hauser, Sukrit Singh, and John D. Chodera Journal of Chemical Theory and Computation 2023 19 (15), 4863-4882 DOI: 10.1021/acs.jctc.3c00333

[3] Chodera, J. et al., 2023. choderalab/openmmtools: 0.23.1.

[4] Eastman, P. et al., 2017. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics R. Gentleman, ed.. PLOS Computational Biology, 13(7), p.1005659.