Open Force Fields

This repository contains force fields released by the Open Force Field Initiative. These files are in SMIRKS Native Open Force Field (SMIRNOFF) format. Details about this new format are documented in our recent publication (doi:10.1021/acs.jctc.8b00640 or bioRxiv), and the most recent specification can be found in the Open Force Field Toolkit documentation. You can parameterize small molecules with SMIRNOFF using the ForceField class in the Open Force Field toolkit for simulations with OpenMM. The resulting system can also be converted to several other simulation formats using ParmEd.

Usage examples can be found in the openff-toolkit repository.

Each force field is currently available in two forms -- Both with and without bond constraints to hydrogen. The default version of each force field is suitable for typical molecular dynamics simulations with constrained bonds to hydrogen. The unconstrained version of each force field should be used when single-point energies are a major concern (e.g. geometry optimizations) and when comparing the force field to QM data.

To cite the Parsley line of force fields (openff-1.X.Y) please use this citation. Optionally, consider also citing the version-specific Zenodo DOI for the particular force field from the table below.

Details for each force field in this repository can be found in the following table:

Filename	DOI	FF line	Release Date	Major format changes?
openff-2.0.0.offxml		Sage	Aug 16, 2021	No
openff_unconstrained-2.0.0.offxml		Sage	Aug 16, 2021	No
openff-2.0.0-rc.2.offxml		Sage	Aug 3, 2021	No
openff_unconstrained-2.0.0-rc.2.offxml		Sage	Aug 3, 2021	No
openff-2.0.0-rc.1.offxml		Sage	June 21, 2021	No
openff_unconstrained-2.0.0-rc.1.offxml		Sage	June 21, 2021	No
openff-1.3.1.offxml		Parsley	June 21, 2021	No
openff_unconstrained-1.3.1.offxml		Parsley	June 21, 2021	No
openff-1.3.1-alpha.1.offxml		Parsley	Apr 15, 2021	No
openff_unconstrained-1.3.1-alpha.1.offxml		Parsley	Apr 15, 2021	No
openff-1.3.0.offxml		Parsley	Oct 21, 2020	No
openff_unconstrained-1.3.0.offxml		Parsley	Oct 21, 2020	No
openff-1.2.1.offxml		Parsley	Sep 9, 2020	No
openff_unconstrained-1.2.1.offxml		Parsley	Sep 9, 2020	No
openff-1.2.0.offxml		Parsley	May 29, 2020	No
openff_unconstrained-1.2.0.offxml		Parsley	May 29, 2020	No
openff-1.1.1.offxml		Parsley	Apr 14, 2020	No
openff_unconstrained-1.1.1.offxml		Parsley	Apr 14, 2020	No
openff-1.1.0.offxml		Parsley	Mar 3, 2020	No
openff_unconstrained-1.1.0.offxml		Parsley	Mar 3, 2020	No
openff-1.0.1.offxml		Parsley	Apr 14, 2020	No
openff_unconstrained-1.0.1.offxml		Parsley	Apr 14, 2020	No
openff-1.0.0.offxml		Parsley	Oct 12, 2019	No
openff_unconstrained-1.0.0.offxml		Parsley	Oct 12, 2019	No
openff-1.0.0-RC2.offxml		None	Oct 4, 2019	No
openff_unconstrained-1.0.0-RC2.offxml		None	Oct 4, 2019	No
openff-1.0.0-RC1.offxml	None	None	Oct 4, 2019	N/A
openff_unconstrained-1.0.0-RC1.offxml	None	None	Oct 4, 2019	N/A

Installation

conda install -c conda-forge openff-forcefields

Use

Installing this package exposes an entry point that makes the openforcefield-forcefields/offxml directory easily accessible by other packages in the same python installation. If the Open Force Field toolkit is installed, it will automatically detect and use this entry point:

>>> from openff.toolkit.typing.engines.smirnoff import ForceField
>>> ff = ForceField('openff-1.0.0-RC1.offxml') 

Otherwise, the entry point can be accessed by querying the openforcefield.smirnoff_forcefield_directory entry point group.

>>> from pkg_resources import iter_entry_points
>>> for entry_point in iter_entry_points(group='openforcefield.smirnoff_forcefield_directory'):
...     print(entry_point.load()())

What it is

The provided OFFXML (force field) files are successive versions of a general-purpose small molecule force field, written in the SMIRNOFF format; this force field should cover all or almost all of drug-like chemical space, and illustrate some of the major functionality of the SMIRNOFF format as well as how it simplifies the specification of force field parameters in a compact and chemically sensible way.

History

Force fields in the openff-X.Y.Z line are descended from the SMIRNOFF99Frosst line of force fields. The first official release was made in September 2019 as a result of the Open Force Field Initiative's refitting efforts.

General versioning guidelines

Applicable in general to SMIRNOFF-format FFs produced by the Open Force Field Consortium

Force fields moving forward will be called name-X.Y.Z

• X denotes some major change in functional form or fitting strategy.
• Y is the parameterization epoch / generation, or a minor change that can affect energy.
• Z is a bugfix version -- e.g. something we've caught and corrected.

Versions

• v1.0.0 Parsley : First major forcefield release.

  • v1.0.1 Parsley : This bugfix release contains following changes: (1) Addition of monatomic ion LibraryCharges.

• v1.1.0 Parsley : This minor release contains following changes: (1) Addition of new proper torsions and improper torsions for tetrazole; (2) Corrections to N-N bond rotation periodicity; (3) Removal of redundant periodicity component in t19; (4) Addition of three new bond and angle terms, a22a, b14a and b36a.

  • v1.1.1 Parsley : This bugfix release contains following changes: (1) Addition of monatomic ion LibraryCharges.

• v1.2.0 Parsley : This minor release contains following changes: (1) New, carefully designed quantum chemical dataset was utilized in training valence parameters in the force field and (2) Removal of redundancy in t108 SMIRKS pattern

• v1.2.1 Parsley : This bugfix release manually changes two bond force constants to resolve an issue seen in propyne substituents when using hydrogen mass repartitioning with a 4fs timestep. Full details are available at #19 .

• v1.3.0 Parsley : This minor release contains a fix of amide-related issues; (1) a poor performance of v1.2 in reproducing amide torsional energy profiles and (2) absence of appropriate torsion parameters for dialkyl amides.

• v1.3.1-alpha.1 Parsley: The new force field files in this release are adapted from the openff-1.3.0 release, except that two angle parameters have been reverted to their original values from smirnoff99Frosst 1.1.0, in an attempt to fix sulphonamide geometries.

• v1.3.1 Parsley: This release is identical to v1.3.1-alpha.1 Parsley.

• v2.0.0-rc.1 Sage: This major release candidate contains both refit valence and vdW terms. Full details are available at https://github.com/openforcefield/openff-sage/releases/tag/2.0.0-rc.1

• v2.0.0-rc.2 Sage: This major release candidate is identical to v2.0.0-rc.1 Sage except that the angle value for a16 has been changed to 180.0 * degree, as the previous value of 183... * degree causes geometry optimizers to fail to converge.

• v2.0.0 Sage: This major release contains the same physical parameters as v2.0.0-rc.2 Sage, but has the parameter ids changed. For more information see the openff-sage repository.

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.0.