Software Open Access
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
OBC2 models (corresponding to AMBER keywords
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.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
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
5.4*calories/mole/angstroms**2), though users can zero the SA term for
HCTmodels by setting
sa_model="None". No model currently supports setting
solvent_radiusto any value other than
1.4*angstroms. Files containing experimental SMIRNOFF-format implementations of
OBC2GBSA models are included with this release (see below). Additional details of these models, including literature references, are available on the SMIRNOFF specification page.
openforcefield.topology.Topology.to_openmm(), periodic box vectors are now transferred from the Open Force Field Toolkit Topology into the newly-created OpenMM Topology.
openforcefield.typing.engines.smirnoff.parameters.ParameterTypecan now be get/set through normal attribute syntax in addition to the list syntax.
OpenEyeToolkitWrapper.compute_partial_charges_am1bccfall back to using standard AM1-BCC if AM1-BCC ELF10 charge generation raises an error about "trans COOH conformers"
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.