Transferable Double Exponential non-bonded potential for condensed phase simulations of small molecules.
This repository contains general transferable force fields that use the Double Exponential functional form first proposed by Brooks.
These force fields use the SMIRKS Native Open Force Field (SMIRNOFF) format.
By convention these files use the .offxml file extension.
The SMIRNOFF format has a specification and is discussed in a JCTC publication and associated pre-print.
The OpenFF Toolkit (version >0.10.6, <0.11.0) provides a reference implementation of the SMIRNOFF format.
In particular, the ForceField class is used to load SMIRNOFF-format force fields and the create_openmm_system method enables the parametrization of small molecules into OpenMM objects.
Smirnoff-plugins provides a framework to extend the SMIRNOFF specification with custom force field functional forms such as the Double Exponential form used here, using a plugin system.
See smirnoff-plugins for a list of the currently supported potentials.
Detailed 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 (i.e. de-1.0.0.offxml) is suitable for typical molecular dynamics simulations with constrained bonds to hydrogen. The "unconstrained" version of each force field (i.e. de_unconstrained-1.0.0.offxml) should be used when single-point energies are a major concern (e.g. geometry optimizations) and when comparing the force field to QM data.
| Filename | DOI | FF line | Release Date | Major format changes? |
|---|---|---|---|---|
de-force-1.0.1.offxml |
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de-force_unconstrained-1.0.1.offxml |
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de-force-1.0.0.offxml |
https://doi.org/10.26434/chemrxiv-2023-28r9s | DE-Force-1 | Feb 17, 2023 | No |
de-force_unconstrained-1.0.0.offxml |
https://doi.org/10.26434/chemrxiv-2023-28r9s | DE-Force-1 | Feb 17, 2023 | No |
de-forcefields packages are published via conda-forge and are simple to install via the conda package manager.
If you don't have the conda package manager installed already you can follow the guide provided by conda to get started.
Before installing the package we recommend using a virtual environment to avoid dependency conflicts with other packages. You can then create a new environment and install de-forcefields via:
conda create -c conda-forge --name deforce de-forcefieldsThe environment must then be activated before the software can be used:
conda activate deforceTo deactivate the environment use:
conda deactivateFinally, the environment can be removed via:
conda remove -n deforce --allThe package can also be installed into an existing virtual environment via:
conda install -c conda-forge de-forcefieldsInstalling this package exposes an entry point that makes the deforcefields/offxml/ directory easily accessible by other packages in the same Python installation.
If the OpenFF Toolkit is installed, it will automatically detect and use this entry point:
>>> from openff.toolkit.typing.engines.smirnoff import ForceField
>>> ff = ForceField('de-force-1.0.0.offxml', load_plugins=True)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()())Force fields in the DE-Force-1 lines are descended from OpenFF-2.0.0 Sage.
Force fields moving forward will be called name-X.Y.Z
Xdenotes some major change in functional form or fitting strategy.Yis the parameterization epoch / generation, or a minor change that can affect energy.Zis a bugfix version -- e.g. something we've caught and corrected.
DE-Force-1: Proof of concept general transferable Double Exponential force field fit using Sage training data.
Copyright (c) 2023 Josh Horton