diff --git a/docs/changelog.rst b/docs/changelog.rst index 2b4382a4f..a88f3b8c8 100644 --- a/docs/changelog.rst +++ b/docs/changelog.rst @@ -11,9 +11,39 @@ The full release history can be viewed `at the GitHub perses releases page `_) +- Bug generated by changes upstream in the ``openmm`` package -- default method for calculating solvent padding changed, which resulted in smaller boxes. Fixed by adding more padding to the simulation box, it is now 1.1 nm. Openmm issue `#3502 `_. Perses issue `#949 `_ (`#953 `_) +- Fixed energy bookkeeping in test of ``HybridTopologyFactory`` when a ring amino acid is involved in transformation. (`#969 `_) +- Avoid changing the global context cache behavior on module imports. Issue `#968 `_ (`#977 `_). +- Benchmark free energy plots now shift data to experimental mean. (`#981 `_) +- Skip introduction of counterion for charge changing mutations in vacuum and fix typo in the phase name in ``test_resume_protein_mutation_no_checkpoint`` (`#991 `_). +- Recovered logging capabilities respecting the ``LOGLEVEL`` environment variable. Issue `#1018 `_ (`#1032 `_). + + Enhancements ------------- -- Introduce ``unsampled_endstates`` boolean option in input YAML file, for enabling/disabling creation of unsampled endstates long-range sterics correction. Issue `#1033 `_ (`#1037 `_). +^^^^^^^^^^^^ +- Improved continuous integration (CI) performance. (`#961 `_) +- ``PointMutationExecutor`` now accepts both solute and solvated PDBs (previously only accepted solute PDBs). (`#967 `_) +- Tests and examples are now using ``openff-2.0.0`` force field instead of ``openff-1.0.0``. (`#971 `_) +- Use names (instead of indices) for fetching the force components of a system, avoiding issues with force reordering upstream in ``openmm``. Issue `#993 `_ (`#976 `_ and `#1007 `_) +- Increase stability of simulations by decreasing the default hydrogen mass to 3 amu in the ``PointMutationExecutor``. Issue `#982 `_ (`#983 `_). +- Improved CI tests on both CPU and GPU. Better handling of temporary directories, closing opened reporter files when tests are finished, and using same environments for CPU and GPU (`#985 `_ `#989 `_ `#1012 `_) +- Performance increase when retrieving the old or new positions from the hybrid positions. Issue `#1005 `_ (`#1020 `_) +- Use of unique names for force components in ``HybridTopologyFactory`` (`#1022 `_). +- New function ``create_endstates_from_real_systems()`` for creating unsampled endstates for currently supported hybrid topology factories (`#1023 `_). +- Improve the readability and usability of ``PointMutationExecutor`` and updates how parameters are specified for solvation (`#1024 `_). + +New features +^^^^^^^^^^^^ +- Introduce ``RESTCapableHybridTopologyFactory``. Hybrid factory that allows for REST scaling, alchemical scaling, and 4th dimension softcore. So far, only working for protein mutations (`#848 `_ `#992 `_). +- New perses command line interface (CLI) ``perses-cli`` using ``click``. Allowing a more friendly interface for users. It tests the running environment, sets the platform for the simulation and allows interactive overriding arbitrary options in the input YAML file. Former ``perses-relative`` CLI entry point is now deprecated (`#972 `_ `#1021 `_ `#1027 `_). +- Support for handling charge changes (by transforming a water into a counterion) for both protein mutations and ligands transformations. `#862 `_ (`#973 `_). +- Hybrid topology factory class name can now be specified using the ``hybrid_topology_factory`` parameter in the input YAML file (`#988 `_). +- Introduce ``unsampled_endstates`` boolean option in input YAML file, which enables/disables creation of unsampled endstates with long-range sterics correction. Issue `#1033 `_ (`#1037 `_). 0.9.5 - Release ---------------