Highlights:

• Support for new pymbar 4 branch.
• Gentle equilibration utility function.
• Support for newer netcdf versions (1.6 branch)

Detailed information as follows:

Enhancements

• Openmmtools now supports both Pymbar 3 and 4 versions. (PR #659)
• Gentle equilibration protocol utility function available in openmmtools.utils.gentle_equilibration (PR #669).
• Timing information for multiple state sampler is now reported by default (PRs #679 and #671).

Bugfixes

• Users were not able to distinguish the exceptions caught during dynamics. Warnings are now raised when an exception is being caught (Issue #643 PR #658).
• Deserializing MCMC moves objects from versions <=0.21.4 resulted in error finding the key. Fixed by catching the exception and raising a warning when key is not found (Issue #618 PR #675).
• Different improvements in documentation strings and readthedocs documentation generation (Issues #620 #641 #548. PR #676)
• Support for newer NetCDF versions (1.6 branch) by not using zlib compression for varying length variables. (PR #654).

Full Changelog: 0.21.5...0.22.0

What's changed

Changed behaviors

• LangevinDynamicsMove now uses openmm.LangevinMiddleIntegrator (a BAOAB integrator) instead of openmm.LangevinIntegrator (an OBABO integrator). Issue #599 (PR #600).

Bugfixes

• Velocities were being incorrectly updated as zeros when resuming simulations or broadcasting from different mpi processes. Fixed by specifying ignore_velocities=False in _propagate_replica. Issue #531 (PR #602).
• Bug in equilibration detection 1: The user was allowed to specify statistical_inefficiency without specifying n_equilibration_iterations, which doesn't make sense, as n_equilibration_iterations and n_effective_max cannot be computed from statistical_inefficiency alone. Fixed by preventing user from specifying statistical_inefficiency without n_equilibration_iterations. Issue #609 (PR #610).
• Bug in equilibration detection 2: If the user specified n_equilibration_iterations but not statistical_inefficiency, the returned n_equilibration_iterations did not include number of equilibration iterations as computed from _get_equilibration_data_per_sample(). Fixed by always including the _get_equilibration_data_per_sample() result in in the returned n_equilibration_iterations. Issue #609 (PR #610).
• Bug in equilibration detection 3: get_equilibration_data_per_sample returns 0 for n_equilibration_iterations. Fixed by always discarding the first time origin returned by get_equilibration_data_per_sample. To control the amount of data discarded by the first time origin, the user can now specify max_subset when initializing MultiStateSamplerAnalyzer. Issue #609 (PR #610).
• Deserializing simulations from openmmtools<0.21.3 versions resulted in error. Fixed by catching the missing key, KeyError exception, when deserializing. Issue #612, PR #613.
• Not specifying a subdirectory for the reporter file resulted in PermissionError when writing the real time analysis file. Fixed by using os.path.join for creating the output paths. Issue #615, PR #616.

Enhancements

• LangevinDynamicsMove now allows constraint_tolerance parameter and public attribute, for specifying the fraction of the constrained distance within which constraints are maintained for the integrator (Refer to Openmm's documentation for more information). Issue #608, PR #611.
• Platform is now reported in the logs in DEBUG mode. Issue #583, PR #605.

Full Changelog: 0.21.4...0.21.5

Bugfixes

• Bug in statistical inefficiency computation where self.max_n_iterations wasn't being used was fixed (#577).
• Bug in estimated performance in realtime yaml file fixed by iterating through all MCMC moves (#578)
• Potential bug fixed by explicitly updating and broadcasting thermodynamic states in replicas, when used in an MPI (distributed) context.
  Issue #579 (#587).
• Bug in handling unsampled states in realtime/offline analysis fixed by using MultiStateSampler._unsampled_states to build the mbar estimate array.
  Issue #592 (#593)

Enhancements

• DHFR test system does not require parmed as dependency, since OpenMM can now handle prmtop/inpcrd files.
  Issue #539 (#588).
• MultiStateSamplerAnalyzer now allows to manually specify n_equilibrium_iterations and statistical_inefficiency parameters. (#586).

What's Changed

Bugfixes

• Bug in replica mixing in MPI multi-GPU runs--where some replicas were simulated in incorrect states--was fixed (#449) & (#562).
• Velocities are now stored in the checkpoint file to eliminate issue with "cold restart". Fixes issue #531 (#555).
• Documentation now correctly builds via CI. Fixes issue #548 (#554).
• Failing windows CI (issue #567) is fixed. (#573)

Enhancements

• Real time MBAR analysis and timing information is now produced in yaml format at user-specified intervals (#565), (#561) & (#572).
• Information of what CUDA devices are available is now provided in log output (#570).
• Replica exchanges are now attempted during equilibration phase to enhance mixing (#556).
• An example of resuming a MultiStateSampler simulation using API is now provided (#569)

New Contributors

• @jfennick made their first contribution in #556

Full Changelog: 0.21.2...0.21.3

What's Changed

• Add test to check platform precision using a string + fix error by @mikemhenry in #551

Full Changelog: 0.21.1...0.21.2

What's Changed

• More streamlined context caches usage by @ijpulidos in #547

Full Changelog: 0.21.0...0.21.1

What's Changed

• Catch LennardJonesGenerator made NB functions. by @Lnaden in #511
• Remove logic for missing file when retrying to open a dataset by @mikemhenry in #515
• Constants codata 2018 update by @ijpulidos in #525
• deal with openmm 7.6 package unwrapping by @sroet in #528
• Overriding deepcopying behavior to avoid creating new ContextCaches. by @ijpulidos in #524
• Try closing reporter in test for windows fix by @Lnaden in #535
• Add Git Attributes File Required by Versioneer by @SimonBoothroyd in #496
• Fix for issue #435 by @mjw99 in #534
• Update changelog for #511 by @Lnaden in #512
• Testing updated python versions by @ijpulidos in #542
• ContextCache usage cleanup by @ijpulidos in #538
• Release 0.21.0 by @mikemhenry in #545

New Contributors

• @ijpulidos made their first contribution in #525
• @SimonBoothroyd made their first contribution in #496
• @mjw99 made their first contribution in #534

Full Changelog: 0.20.3...0.21.0

Fix critical bug in which GPU contexts would fail to recognize mixed precision was available PR #506 (Resolves issue #505 )

Remove leftover six imports and xrange See PR #504

This release fixes several bugs and eliminates cython compiled acceleration of replica-exchange all-swap (replacing it with numba) to enable working release on conda-forge.

Bug Fixes

• #485: Replace cython-accelerated all-swap replica mixing with numba implementation
• #488: Fix ParallelTemperingSampler temperature spacing
• #501: Do unit conversion first to improve precision (fixes issue #500)