v0.2.2

Updated version of fes-ml 0.2, which includes the following changes:

• Added support for associating modifications with alchemical groups, enabling more complex transformations. Users can now define multiple alchemical groups that can be transformed independently. This is particularly useful when applying different transformations to distinct regions of a system, or when using multiple instances of the same modification type for the same group of atoms (e.g., transforming one set of LJ parameters into another). (#15)
• LJSoftCore now applies Tang–Toennies damping when only the long-range term is used. (#15)
• Various other miscellaneous code updates and improvements. (#15)

v0.2.1

What's Changed

Updated version of fes-ml 0.2, which includes the following changes:

• Support for EMLE Torch models.
• Fixes a bug that caused the intramolecular electrostatics of the ML region to vanish when using EMLE (see related OpenBioSim/sire#227).
• Enables the application of hydrogen mass repartitioning (HMR) to water models with virtual sites (see related https://github.com/openforcefield/openff-interchange/blob/426e3ebc630604b2f15fab014410fac0e48aa514/openff/interchange/interop/openmm/__init__.py#L173-L226).
• Improved handling of restarts.
• Instructions for installing fes-ml on aarch64 and ppc64le systems.
• More examples, utility scripts, etc.
• Other miscellaneous updates to the code.

Full Changelog: v0.2.0...v0.2.1

v0.2.0

Improved version of fes-ml, which includes:

• Support for the OpenFF strategy.
• A new architecture to enable flexible alchemical perturbations using a graph-based approach.
• Several new multi-time step integration features.
• Updated examples and documentation.
• Enhanced logging, output handling, and reporter support for more robust and informative output.

What's Changed

• Add OpenFF Strategy, Graph-Based Perturbations, and MTS Features by @JMorado in #13

Full Changelog: v0.1.0...v0.2.0

v0.1.0

Basic but well-tested version of fes-ml that supports the following modifications to OpenMM systems:

• Lennard-Jones 12-6 softcore potentials
• Charge scaling
• ML<->MM interpolation (ML/MM mechanical embedding)
• ML Δ correction
• EMLE<->MM interpolation (ML/MM electrostatic embedding)

Additionally, this version offers basic features for working with multitimestep integrators. Please note that the only strategy available to create OpenMM systems is the Sire strategy.

What's Changed

• Code Refactoring and Feature Enhancements by @JMorado in #1
• Miscellaneous fixes and features enhancements by @JMorado in #2
• Add integration tests by @JMorado in #3
• Fixes, improvements, and examples by @JMorado in #4
• Fixes and MTS features by @JMorado in #5
• Enhancements: Improved Restart, DCD Writing, Logging, Examples, and MTS Support by @JMorado in #6
• Continuos integration and README update by @JMorado in #7
• Updates and ML correction support by @JMorado in #8
• Integrate OpenMM reporters and auto-generate topology by @JMorado in #9

Full Changelog: https://github.com/michellab/fes-ml/commits/v0.1.0