0.0.6 Solvation Free Energies

This release centers around two key changes -

i) a general refactoring of the protocol classes to be much cleaner and extensible through the removal of the old stub functions and the addition of cleaner descriptors.
ii) the addition of workflows to estimate solvation free energies via the new SolvationYankProtocol and SolvationFreeEnergy classes.

The implemented free energy workflow is still rather basic, and does not yet support calculating parameter gradients or estimation from cached simulation data through reweighting.

A new table has been added to the documentation to make clear which built-in properties support which features.

A richer version of these release notes with live links to API documentation is available
on our ReadTheDocs page

See our installation instructions.

Please report bugs, request features, or ask questions through our
issue tracker.

Please note that this is a pre-alpha release and there will still be major changes to the API
prior to a stable 1.0.0 release.

New Features

• PR #110: Cleanup and refactor of protocol classes.
• PR #125: Support for PBS based HPC clusters.
• PR #127: Adds a basic workflow for estimating solvation free energies with YANK.
• PR #130: Adds a cleaner mechanism for restarting simulations from checkpoints.
• PR #134: Update to a more stable dask version.

Bugfixes

• PR #128: Removed the defunct dask backend processes kwarg.
• PR #133: Fix for tests failing on MacOS due to travis issues.

Breaking Changes

• PR #130: The RunOpenMMSimulation.steps input has now been split into the steps_per_iteration and total_number_of_iterations inputs.

Migration Guide

This release contained several public API breaking changes. For the most part, these can be
remedied by the follow steps:

• Replace all instances of run_openmm_simulation_protocol.steps to run_openmm_simulation_protocol.steps_per_iteration