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This is an early preview release of the openforcefield toolkit that matches the functionality described in the preprint describing the SMIRNOFF v0.1 force field format: [DOI]
This release features additional documentation, code comments, and support for automated testing.
A significant (though currently unused) problem in handling of improper torsions was corrected.
Previously, non-planar impropers did not behave correctly, as six-fold impropers have two potential chiralities.
To remedy this, SMIRNOFF impropers are now implemented as three-fold impropers with consistent chirality.
However, current force fields in the SMIRNOFF format had no non-planar impropers, so this change is mainly aimed at future work.
Most significantly, this release adds a small but nonzero set of LJ parameters to smirnoff99Frosst, as per (soon forthcoming) SMIRNOFF paper draft/discussion. Additional changes are:
- Minor fixes to cyclobutane parameters in smirnoff99Frosst
- Versioneer support
- Documentation via sphinx
.offxmlto avoid confusion with "normal" OpenMM
.ffxmlfiles, which are a totally different format
- Remove wildcard generics from smirnoff99Frosst; add a separate
.offxmlfile with (improved) generics in case anyone wants to use these.
- Fixes a compatibility issue with updated NetworkX
- Makes extensive updates to documentation
- Adds a considerable number of examples
- Makes OpenMM topologies generated preserve bond order
- Adds monovalent ion parameters
- Changes use of a SMIRKS decorator (
x) in smirnoff99Frosst for better consistency with non-OpenEye SMARTS/SMIRKS parsers
- Removes an extra application of
OEAssignImplicitHydrogenswhich could in some cases result in
openforcefieldchanging the protonation state of a molecule
- Finishes migration of many tools from
- Removes outdated examples and data
- Adds support for
tip3pwater and constraints, tests for the same; adds water monomers
- Extensively updates documentation
- Updates Jupyter notebooks
- Makes some fixes to chemical environments
- Fixes a bug where vdW parameters for mixtures consisting of multiple references molecules could get scrambled (and adds a test for this)
- Fixes a typo in descring the SMIRNOFF format (formerly SMIRFF) and finishes name change from SMIRFF to SMIRNOFF
- Adds an example of generating a mixed force field for a protein-ligand complex (AMBER protein force field, SMIRNOFF ligand)