Smoother transformations with EDS

DOI: https://pubs.acs.org/doi/10.1021/acs.jctc.6c00581

What this is

Run alchemical free energy molecular dynamics (MD) simulations using either equilibrium (EQ) or nonequilibrium (NEQ) protocols with either the energy interpolation (EI) or Enveloping Distribution Sampling (EDS) coupling schemes.

What this contains

• /data: code to reproduce the published data.
  • /data/freesolv: notebooks and scripts to download the required files from the freesolv database (get_freesolv_data.ipynb) and run EQ/NEQ calculations using sdf files as input (run_xxx.py), the simulation settings (settings.json), and an analysis notebook which reproduces the paper figures (analysis.ipynb)
  • /data/toy-systems: c++ source code, python scripts/notebooks and bash wrappers to run the toy systems and demonstrate the analytical solutions of the EDS coupling scheme on harmonic potentials. A simplified conda environment can be installed using mamba env create -f environment-toy-only.yml, but the scripts also run with the main environment.
• /examples: notebooks that showcase individual alchemical transformations
• /src: python source code containing the necessary functions used by the scripts in /data and /examples

Installation

git clone <repo-url>

cd SmoothTransformationWithEDS

mamba env create -f environment.yml

pip install -e .