New features

• Add a WaterCluster testsystem (#322)
• Add exact treatment of PME electrostatics in alchemy.AbsoluteAlchemicalFactory. (#320)
• Add method in ThermodynamicState for the efficient computation of the reduced potential at a list of states. (#320)

Enhancements

• When a SamplerState is applied to many Contexts, the units are stripped only once for optimization. (#320)

Bug fixes

• Copy thermodynamic state on compound state initialization. (#320)

Bug fixes

• Fixed implementation bug where CustomExternalForce restraining atoms to absolute coordinates caused an issue when a Barostat was used (#310)

Enhancements

• MCMC Integrators now attempt to re-initialize the Context object on the last restart attempt when NaN's are encountered. This has internally been shown to correct some instances where normally resetting positions does not work around the NaN's. This is a slow step relative to just resetting positions, but better than simulation crashing.

Critical Fixes

• SamplerState.apply_to_context() applies box vectors before positions are set to prevent a bug on non-Reference OpenMM Platforms which can re-order system atoms and sample the wrong distribution. (#305)

Additional Fixes

• LibYAML is now optional (#304)
• Fix AppVeyor testing against Python 3.4 (now Python 3.5/3.6 and NumPy 1.12) (#307)
• Release History now included in online Docs

In this Release:

Added support for SamplerState slicing (#298)
Added bit operators and and or to math_eval (#301)

In this release:

• Fix pickling of CompoundThermodynamicState (#284).
• Add missing term to OBC2 GB alchemical Force (#288).
• Generalize forcefactories.restrain_atoms() to non-protein receptors (#290).
• Standardize integrator global variables in ContextCache (#291).

This release includes the following features:

• Storage Interface module with automatic disk IO handling
• Option for shifted or switched Reaction Field
• LangevinSplittingDynamic MCMC move with specifiable sub step ordering
• Nose-Hoover Chain Thermostat

Bugs fixed in this release

• Many doc string cleanups
• Tests are based on released versions of OpenMM
• Tests also compare against development OpenMM, but do not fail because of it
• Fixed bug in Harmonic Oscillator tests' error calculation
• Default collision rate in Langevin Integrators now matches docs

In this release:

• Fixed AbsoluteAlchemicalFactory treatment of virtual sites that were previously ignored (#259).
• Add possibility to add ions to the WaterBox test system (#259).

New features:

• Add AbsoluteAlchemicalFactory support for all GB models (#250)
• Added forces and forcefactories modules implementing UnishiftedReactionFieldForce and replace_reaction_field respectively. The latter has been moved from AbsoluteAlchemicalFactory (#253)
• Add restrain_atoms to restrain molecule conformation through an harmonic restrain (#255)

Bugfixes:

• Bugfix for testsystems that use implicit solvent (#250)
• Bugfix for ContextCache: two consecutives calls retrieve the same Context with same thermodynamic state and no integrator (#252)

Hotfix in fringe Python2/3 compatibility issue when using old style serialization systems in Python 2

• Adds Drew-Dickerson DNA dodecamer test system (#223)
• Bugfix and optimization to ContextCache (#235)
• Compress serialized ThermodynamicState strings for speed and size (#232)
  • Backwards compatible with uncompressed serialized ThermodynamicStates