pylambdaopt

Python code and scripts to optimize lambda values in FEP calculations

• A16F_relative/ - Simulation files for the A16F alchemical transformation of the A8 miniprotin. Also contains results of unoptimized and optimized EE simulations that were analyzed in the manuscript.
• biceps_xi_optimization
• examples - working examples of how to use the pylambdaopt scripts
• figures - an incomplete collection of figures generated for the manuscript
• scripts - code and command-line tools to optimize alchemical intermediates
• toy_model - code and scripts to performing EE sampling and analysis of the toy 1D harmonic potential system discussed in the manuscript.

The paper can be read here ---> https://doi.org/10.1021/acs.jcim.5c00704

Citation

@article{novack2025simple,
  title={Simple Method to Optimize the Spacing and Number of Alchemical Intermediates in Expanded Ensemble Free Energy Calculations},
  author={Novack, Dylan and Raddi, Robert M and Zhang, Si and Hurley, Matthew FD and Voelz, Vincent A},
  journal={Journal of Chemical Information and Modeling},
  year={2025},
  publisher={ACS Publications}
}