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Fix README link checks #2165

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Merged
j-wags merged 3 commits into from
Mar 16, 2026
Merged

Fix README link checks #2165

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d70d73d
fix FAQ links and modernize adjacent text
j-wags Mar 13, 2026
4181daa
delete now-unused FAQ
j-wags Mar 13, 2026
9a8f0f9
other small README modernizations
j-wags Mar 13, 2026
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18 changes: 11 additions & 7 deletions README.md
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Expand Up @@ -31,10 +31,12 @@ Detailed installation instructions can be found [here](https://open-forcefield-t

Two major force field development efforts have been undertaken by the Open Force Field Initiative, with results hosted in separate repositories.

* The [Open Force Fields repository](https://github.com/openforcefield/openff-forcefields/), which features the [Parsley](https://openforcefield.org/community/news/general/introducing-openforcefield-1.0/) and [Sage](https://openforcefield.org/community/news/general/sage2.0.0-release/) force field lines. These are the Open Force Field Initiative's efforts toward building _new_ force fields. The initial parameters are taken from smirnoff99Frosst, but software and data produced by the Initiative's efforts have been used to refit parameter values and add new SMIRKS-based parameters.
* The [smirnoff99Frosst repository](https://github.com/openforcefield/smirnoff99Frosst/), which is descended from AMBER's parm99 force field as well as Merck-Frosst's parm@frosst. This line of force fields does not aim to alter parameter values, but is instead a test of accurately converting an atom type-based force field to the SMIRNOFF format.
* The [OpenFF Force Fields repository](https://github.com/openforcefield/openff-forcefields/), which features the [Parsley](https://openforcefield.org/community/news/general/introducing-openforcefield-1.0/) and [Sage](https://openforcefield.org/community/news/general/sage2.0.0-release/) force field lines. These are the Open Force Field Initiative's efforts toward building _new_ force fields. The initial parameters are taken from smirnoff99Frosst, but software and data produced by the Initiative's efforts have been used to refit parameter values and add new SMIRKS-based parameters.
* The [smirnoff99Frosst repository](https://github.com/openforcefield/smirnoff99Frosst/), which is descended from AMBER's parm99 force field as well as Merck-Frosst's parm@frosst. This line of force fields did not aim to alter parameter values, but is instead a test of accurately converting an atom type-based force field to the SMIRNOFF format. This repository is now archived, meaning that while the data files will remain available, the python tooling is no longer maintained.

Force fields from both of these packages are available in their respective GitHub repositories and also as conda packages. Tables detailing the individual file names/versions within these force field lines are in the README of each repository. By default, installing the Open Force Field toolkit using `conda` or the single-file toolkit installers will also install these conda packages. A [plugin architecture](https://github.com/openforcefield/openff-toolkit/blob/main/FAQ.md#how-can-i-distribute-my-own-force-fields-in-smirnoff-format) is provided for other force field developers to produce python/conda packages that can be imported by the Open Force Field Toolkit as well.
Tables detailing the individual file names/versions within these force field lines are in the README of each repository. By default, installing the `openff-toolkit` conda package will also install the `openff-forcefields` conda packages.

A plugin architecture is provided for other force field developers to produce python/conda packages that can be imported by the Open Force Field Toolkit as well. See "How can I distribute my own force fields in SMIRNOFF format?" in [our FAQ](https://docs.openforcefield.org/en/latest/faq.html) for details.

# Toolkit features

Expand Down Expand Up @@ -63,20 +65,22 @@ topology = Topology.from_molecules(molecule)

# Load the latest OpenFF force field release: version 2.1.0, codename "Sage"
from openff.toolkit import ForceField
forcefield = ForceField('openff-2.1.0.offxml')
forcefield = ForceField('openff-2.3.0.offxml')

# Create an OpenMM system representing the molecule with SMIRNOFF-applied parameters
openmm_system = forcefield.create_openmm_system(topology)

# Create an Interchange object for representations in other formats
interchange = forcefield.create_interchange(topology)

# Create an OpenMM system representing the molecule with SMIRNOFF-applied parameters
openmm_system = interchange.to_openmm(topology)

```

Detailed examples of using SMIRNOFF with the toolkit can be found [in the documentation](https://open-forcefield-toolkit.readthedocs.io/en/stable/examples.html).

# Frequently asked questions (FAQ)

See [`FAQ.md`](FAQ.md) for answers to a variety of common problems, such as:
See [our software ecosystem FAQ](https://docs.openforcefield.org/en/latest/faq.html) for answers to a variety of common problems, such as:
* Why do I need to provide molecules corresponding to the components of my system, or a `Topology` with bond orders?
* Can I use an Amber, CHARMM, or GROMACS topology/coordinate file as a starting point for applying a SMIRNOFF force field?
* What if I am starting from a PDB file?
Expand Down
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