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openforcefield/openforcefield: 0.5.0 GBSA support and quality-of-life improvements

Jeff Wagner; David L. Mobley; John Chodera; Caitlin Bannan; Andrea Rizzi; Camila; Christopher Bayly; SimonBoothroyd; Nathan M. Lim; Victoria Lim; Yutong Zhao; Lee-Ping


This release adds support for the GBSA tag in the SMIRNOFF specification. Currently, the HCT, OBC1, and OBC2 models (corresponding to AMBER keywords igb=1, 2, and 5, respectively) are supported, with the OBC2 implementation being the most flexible. Unfortunately, systems produced using these keywords are not yet transferable to other simulation packages via ParmEd, so users are restricted to using OpenMM to simulate systems with GBSA.

OFFXML files containing GBSA parameter definitions are available, and can be loaded in addition to existing parameter sets (for example, with the command ForceField('test_forcefields/smirnoff99Frosst.offxml', 'test_forcefields/GBSA_OBC1-1.0.offxml')). A manifest of new SMIRNOFF-format GBSA files is below.

Several other user-facing improvements have been added, including easier access to indexed attributes, which are now accessible as torsion.k1, torsion.k2, etc. (the previous access method torsion.k still works as well). More details of the new features and several bugfixes are listed below.

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 there may still be some changes to the API prior to a stable 1.0.0 release.

New features
  • PR #363: Implements openforcefield.typing.engines.smirnoff.parameters.GBSAHandler, which supports the GBSA tag in the SMIRNOFF specification. Currently, only GBSAHandlers with gb_model="OBC2" support setting non-default values for the surface_area_penalty term (default 5.4*calories/mole/angstroms**2), though users can zero the SA term for OBC1 and HCT models by setting sa_model="None". No model currently supports setting solvent_radius to any value other than 1.4*angstroms. Files containing experimental SMIRNOFF-format implementations of HCT, OBC1, and OBC2 GBSA models are included with this release (see below). Additional details of these models, including literature references, are available on the SMIRNOFF specification page.
  • PR #363: When using openforcefield.topology.Topology.to_openmm(), periodic box vectors are now transferred from the Open Force Field Toolkit Topology into the newly-created OpenMM Topology.
  • PR #377: Single indexed parameters in openforcefield.typing.engines.smirnoff.parameters.ParameterHandler and openforcefield.typing.engines.smirnoff.parameters.ParameterType can now be get/set through normal attribute syntax in addition to the list syntax.
  • PR #394: Include element and atom name in error output when there are missing valence parameters during molecule parameterization.
  • PR #385: Fixes Issue #346 by having OpenEyeToolkitWrapper.compute_partial_charges_am1bcc fall back to using standard AM1-BCC if AM1-BCC ELF10 charge generation raises an error about "trans COOH conformers"
  • PR #399: Fixes issue where openforcefield.typing.engines.smirnoff.forcefield.ForceField constructor would ignore parameter_handler_classes kwarg.
  • PR #400: Makes link-checking tests retry three times before failing.
Files added
  • PR #363: Adds test_forcefields/GBSA_HCT-1.0.offxml, test_forcefields/GBSA_OBC1-1.0.offxml, and test_forcefields/GBSA_OBC2-1.0.offxml, which are experimental implementations of GBSA models. These are primarily used in validation tests against OpenMM's models, and their version numbers will increment if bugfixes are necessary.

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