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.

Citation

@article{Novack2025pylambdaopt,
  title={A simple method for optimizing 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 F.D. and Voelz, Vincent A},
  journal={in preparation},
  year={2025}
}