Changelog

All notable changes to molecular-simulations will be documented here.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

v0.3.28 (2025)

Current release.

Added

  • MM-PBSA binding free energy calculations with frame-level parallelization

  • ipSAE interface scoring for AlphaFold-predicted structures

  • Relative SASA calculations

  • Support for constant-pH simulations

  • Parsl settings for ALCF Polaris

Changed

  • Improved test coverage to ~50%

  • Updated minimum OpenMM version to 8.0

Fixed

  • OpenBLAS threading conflicts in HPC environments

  • PDB format handling for non-standard residues

v0.3.0

Added

  • Protein-protein interaction analysis (PPInteractions)

  • Automatic clustering with KMeans++

  • Interaction energy fingerprinting

  • HPC deployment via Parsl

v0.2.0

Added

  • OpenMM simulation runner with automatic equilibration

  • Explicit and implicit solvent builders

  • Small molecule parameterization with GAFF2

v0.1.0

Initial release.

  • Basic system building with tleap

  • Simple simulation runner