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Data supplement: Nonadiabatic force matching for alchemical free-energy estimation

This repository contains all of the numerical results presented in the journal article titled Nonadiabatic force matching for alchemical free-energy estimation, authored by Jorge L. Rosa-Raíces and David T. Limmer at UC Berkeley. The article is available on arXiv and has been published in the Journal of Chemical Theory and Computation (DOI: 10.1021/acs.jctc.5c01478).

This repository is organized as follows:

  • Folder simulation_scripts encloses all of the Python 3 scripts that were used to generate the raw simulation data for the WCA monomer solvation and the LJ solid formation problems. The scripts crucially depend on CUDA-enabled installations of the HOOMD-blue and PyTorch packages. Alongside the Python 3 scripts, each folder contains bash scripts with command-line instructions to generate the trajectory data for each system with the appropriate simulation parameters.
  • Folder post-processing_scripts encloses Python 3 scripts to postprocess the raw trajectory data generated by the code in simulation_scripts, and bash scripts with command-line instructions to run the corresponding Python 3 scripts.
  • Folder plotting_scripts encloses Python 3 scripts to generate the figures in the article from the post-processed trajectory data generated by the scripts in post-processing_scripts for each system.
  • Folder numerical_results encloses the simulation data plotted in the article as generated by the scripts in post-processing_scripts from our own numerical data.

While the code provided herein should be sufficient to fully reproduce the numerical results presented in the article, the authors will gladly provide the raw and post-processed numerical data upon reasonable request.