Release History

0.13.3 - Critical Bugfix to SamplerState Context Manipulation

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. (#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

0.13.2 - SamplerState Slicing and BitWise And/Or Ops

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

0.13.1 - Bugfix 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).

OpenMMTools 0.13.0

New 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

Bug Fixes

  • 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

0.12.1 - Add virtual sites support in alchemy

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

0.12.0 - GB support in alchemy and new forces module

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 consecutive calls retrieve the same Context with same thermodynamic state and no integrator (#252)

Hotfix 0.11.2

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

Release 0.11.1: Optimizations

  • 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

0.11.0

New Features:

  • LangevinIntegrator now sets measure_heat=False by default for increased performance (#211)
  • AbsoluteAlchemicalFactory now supports disable_alchemical_dispersion_correction to prevent 600x slowdowns with nonequilibrium integration (#218)
  • We now require conda-forge as a dependency for testing and deployment (#216)
  • Conda-forge added as channel to conda packages

Release 0.10.0 - Optimizations of ThermodynamicState, renamed AlchemicalFactory

  • BREAKS API: Renamed AlchemicalFactory to AbsoluteAlchemicalFactory (#206)

  • Major optimizations of ThermodynamicState (#200, #205)

    • Keep in memory only a single System object per compatible state
    • Fast copy/deepcopy
    • Enable custom optimized serialization for multiple states
  • Added readthedocs documentation (#191)

  • Bugfix for serialization of context when NaN encountered (#199)

  • Added tests for Python 3.6 (#184)

  • Added tests for integrators (#186, #187)

Release 0.9.4 - Nonequilibrium integrators overhaul

Major changes

  • Overhaul of LangevinIntegrator and subclasses to better support nonequilibrium integrators
  • Add true reaction-field support to AlchemicalFactory
  • Add some alchemical test systems

Updates to openmmtools.integrators.LangevinIntegrator and friends

API-breaking changes

  • The nonequilibrium integrators are now called AlchemicalNonequilibriumLangevinIntegrator and ExternalPerturbationLangevinIntegrator, and both are subclasses of a common NonequilibriumLangevinIntegrator that provides a consistent interface to setting and getting protocol_work
  • AlchemicalNonequilibriumLangevinIntegrator now has a default alchemical_functions to eliminate need for every test to treat it as a special case (#180)
  • The get_protocol_work() method allows you to retrieve the protocol work from any NonequilibriumLangevinIntegrator subclass and returns a unit-bearing work. The optional dimensionless=True argument returns a dimensionless float in units of kT.
  • Integrator global variables now store all energies in natural OpenMM units (kJ/mol) but the new accessor methods (see below) should b used instead of getting integrator global variables for work and heat. (#181)
  • Any private methods for adding steps to the integrator have been prepended with _ to hide them from the public API.

New features

  • Order of arguments for all LangevinIntegrator derivatives matches openmm.LangevinIntegrator so it can act as a drop-in replacement. (#176)
  • The get_shadow_work() and get_heat() methods are now available for any LangevinIntegrator subclass, as well as the corresponding properties shadow_work and heat. The functions also support dimensionless=True. (#163)
  • The shadow_work and heat properties were added to all LangevinIntegrator subclasses, returning the values of these properties (if the integrator was constructed with the appropriate measure_shadow_work=True or measure_heat=True flags) as unit-bearing quantities
  • The get_protocol_work() and get_total_work() methods are now available for any NonequilibriumLangevinIntegrator, returning unit-bearing quantities unless dimensionless=True is provided in which case they return the work in implicit units of kT. get_total_work() requires the integrator to have been constructed with measure_shadow_work=True.
  • The protocol_work and total_work properties were added to all NonequilibriumLangevinIntegrator subclasses, and return the unit-bearing work quantities. total_work requires the integrator to have been constructed with measure_shadow_work=True.
  • The subclasses have been reworked to support any kwargs that the base classes support, and defaults have all been made consistent.
  • Various reset() methods have been added to reset statistics for all LangevinIntegrator subclasses.
  • All custom integrators support .pretty_format() and .pretty_print() with optional highlighting of specific step types.

Bugfixes

  • Zero-step perturbations now work correctly (#177)
  • AlchemicalNonequilibriumLangevinIntegrator now correctly supports multiple H steps.

Internal changes

  • Adding new LangevinIntegrator step methods now uses a self._register_step_method(step_string, callback_function, supports_force_groups=False) call to simplify this process.
  • Code duplication has been reduced through the use of calling base class methods whenever possible.
  • run_nonequilibrium_switching() test now uses BAR to test dragging a harmonic oscillator and tests a variety of integrator splittings (["O { V R H R V } O", "O V R H R V O", "R V O H O V R", "H R V O V R H"]).
  • Integrator tests use deterministic PME and mixed precision when able.

Updates to openmmtools.alchemy.AlchemicalFactory

  • Reaction field electrostatics now removes the shift, setting c_rf = 0.
  • A convenience method AlchemicalFactory.replace_reaction_field() has been added to allow fully-interacting systems to be modified to force c_rf = 0 by recoding reaction-field electrostatics as a CustomNonbondedForce

New openmmtools.testsystems classes

  • AlchemicalWaterBox was added, which has the first water molecule in the system alchemically modified