Release History

0.17.0 - Removed Py2 support, faster exact PME treatment

New features

  • Add GlobalParameterFunction that allows to enslave a GlobalParameter to an arbitrary function of controlling

variables (#380). - Allow to ignore velocities when building the dict representation of a SamplerState. This can be useful for example to save bandwidth when sending a SamplerState over the network and velocities are not required (#386).

Enhancements

  • New implementation of the exact PME handling that uses the parameter offset feature in OpenMM 7.3. This comes with a

considerable speed improvement over the previous implementation (#380). - Exact PME is now the default for the alchemical_pme_treatment parameter in the constructor of AbsoluteAchemicalFactory (#386). - It is now possible to have multiple composable states exposing the same attributes/getter/setter in a CompoundThermodynamicState (#380).

Bug fixes

  • Fixed a bug involving the NoseHooverChainVelocityVerletIntegrator with System with constraints. The constraints

were not taken into account when calculating the number of degrees of freedom resulting in the temperature not converging to the target value. (#384) - Fixed a bug affecting reduced_potential_at_states when computing the reduced potential of systems in different ``AlchemicalState``s when the same alchemical parameter appeared in force objects split in different force groups. (#385)

Deprecated and API breaks

  • Python 2 is not supported anymore.
  • The update_alchemical_charges attribute of ``AlchemicalState`, which was deprecated in 0.16.0, has now been removed

since it doesn’t make sense with the new parameter offset implementation. - The methods AlchemicalState.get_alchemical_variable and AlchemicalState.set_alchemical_variable have been deprecated. Use AlchemicalState.get_alchemical_function and AlchemicalState.set_alchemical_function instead.

0.16.0 - Py2 deprecated, GlobalParameterState class, SamplerState reads CVs

New features

  • Add ability for SamplerState to access new OpenMM Custom CV Force Variables (#362).
  • SamplerState.update_from_context now has keywords to support finer grain updating from the Context. This is only recommended for advanced users (#362).
  • Added the new class states.GlobalParameterState designed to simplify the implementation of composable states that control global variables (#363).
  • Allow restraint force classes to be controlled by a parameter other than lambda_restraints. This will enable multi-restraints simulations (#363).

Enhancements

  • Global variables of integrators are now automatically copied over the integrator returned by ContextCache.get_context. It is possible to specify exception through ContextCache.INCOMPATIBLE_INTEGRATOR_ATTRIBUTES (#364).

Others

  • Integrator MCMCMove``s now attempt to recover from NaN automatically by default (with ``n_restart_attempts set to 4) (#364).

Deprecated

  • Python2 is officially deprecated. Support will be dropped in future versions.
  • Deprecated the signature of IComposableState._on_setattr to fix a bug where the objects were temporarily left in an inconsistent state when an exception was raised and caught.
  • Deprecated update_alchemical_charges in AlchemicalState in anticipation of the new implementation of the exact PME that will be based on the NonbondedForce offsets rather than updateParametersInContext().

0.15.0 - Restraint forces

  • Add radially-symmetric restraint custom forces (#336).
  • Copy Python attributes of integrators on deepcopy() (#336).
  • Optimization of states.CompoundThermodynamicState deserialization (#338).
  • Bugfixes (#332, #343).

0.14.0 - Exact treatment of alchemical PME electrostatics, water cluster test system, optimizations

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 ``Context``s, the units are stripped only once for optimization. (#320)

Bug fixes

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

0.13.4 - Barostat/External Force Bugfix, Restart Robustness

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.

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).

0.13.0 - Alternative reaction field models, Langevin splitting MCMCMove

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)

Bug fixes

  • 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)

0.11.2 - Bugfix release

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

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 - Conda forge installation

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

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)

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