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Make default SMIRNOFF force field openff-2.2.1 #417

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Merged
peastman merged 3 commits into from
Nov 13, 2025
Merged

Make default SMIRNOFF force field openff-2.2.1 #417

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29ca74c
Make default SMIRNOFF force field openff-2.2.1
epretti Nov 12, 2025
f287834
Update default OpenFF force field for espaloma
epretti Nov 12, 2025
2fa5b68
Merge branch 'main' into smirnoff221
epretti Nov 13, 2025
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12 changes: 6 additions & 6 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -189,7 +189,7 @@ Create a SMIRNOFF template generator for a single molecule (benzene, created fro
from openff.toolkit import Molecule

molecule = Molecule.from_smiles("c1ccccc1")
# Create the SMIRNOFF template generator with the default installed force field (openff-2.1.0)
# Create the SMIRNOFF template generator with the default installed force field (openff-2.2.1)
from openmmforcefields.generators import (
SMIRNOFFTemplateGenerator,
)
Expand All @@ -215,12 +215,12 @@ system = forcefield.createSystem(
)
```

The latest official Open Force Field Initiative release ([`openff-2.1.0`](https://github.com/openforcefield/openff-forcefields) of the ["Sage" small molecule force field](https://openforcefield.org/community/news/general/sage2.1.0-release/)) is used if none is specified.
The latest official Open Force Field Initiative release ([`openff-2.2.1`](https://github.com/openforcefield/openff-forcefields) of the ["Sage" small molecule force field](https://openforcefield.org/force-fields/force-fields/)) is used if none is specified.
You can check which SMIRNOFF force field is in use with

```pycon
>>> smirnoff.smirnoff_filename
'/Users/mattthompson/mambaforge/envs/openmmforcefields/lib/python3.11/site-packages/openforcefields/offxml/openff-2.1.0.offxml'
'/Users/mattthompson/mambaforge/envs/openmmforcefields/lib/python3.11/site-packages/openforcefields/offxml/openff-2.2.1.offxml'
```

Create a template generator for a specific SMIRNOFF force field for multiple molecules read from an SDF file:
Expand All @@ -247,15 +247,15 @@ To check which SMIRNOFF force fields are automatically installed, examine the `I

```pycon
>>> print(SMIRNOFFTemplateGenerator.INSTALLED_FORCEFIELDS)
['ff14sb_off_impropers_0.0.2', 'ff14sb_off_impropers_0.0.1', 'ff14sb_off_impropers_0.0.3', 'tip3p_fb-1.1.0', 'tip3p_fb-1.0.0', 'openff-1.0.1', 'openff-1.1.1', 'openff-1.0.0-RC1', 'opc3', 'opc3-1.0.0', 'openff-2.1.0-rc.1', 'openff-1.2.0', 'openff-1.3.0', 'tip3p-1.0.0', 'opc-1.0.2', 'openff-2.0.0-rc.2', 'opc-1.0.0', 'openff-2.1.0', 'openff-2.0.0', 'tip4p_fb-1.0.1', 'tip3p', 'opc3-1.0.1', 'opc', 'tip3p_fb-1.1.1', 'openff-1.1.0', 'openff-1.0.0', 'openff-1.0.0-RC2', 'tip3p-1.0.1', 'openff-1.3.1', 'openff-1.2.1', 'openff-1.3.1-alpha.1', 'tip4p_fb', 'tip3p_fb', 'tip4p_fb-1.0.0', 'openff-2.0.0-rc.1', 'opc-1.0.1']
['ff14sb_off_impropers_0.0.2', 'ff14sb_off_impropers_0.0.4', 'ff14sb_off_impropers_0.0.1', 'ff14sb_off_impropers_0.0.3', 'tip3p_fb-1.1.0', 'tip3p_fb-1.0.0', 'openff-2.2.1-rc1', 'openff-1.0.1', 'openff-1.1.1', 'spce-1.0.0', 'openff_no_water-3.0.0-alpha0', 'openff-1.0.0-RC1', 'opc3', 'opc3-1.0.0', 'openff-2.1.0-rc.1', 'openff-2.3.0-rc2', 'openff-1.2.0', 'openff-1.3.0', 'tip3p-1.0.0', 'opc-1.0.2', 'openff-2.2.1', 'openff-2.0.0-rc.2', 'opc-1.0.0', 'openff-2.1.0', 'openff-2.0.0', 'tip4p_fb-1.0.1', 'tip3p', 'tip4p_ew', 'opc3-1.0.1', 'opc', 'openff-2.3.0-rc1', 'tip3p_fb-1.1.1', 'openff-1.1.0', 'openff-1.0.0', 'openff-1.0.0-RC2', 'openff-2.2.0-rc1', 'tip3p-1.0.1', 'openff-1.3.1', 'openff-1.2.1', 'tip4p_ew-1.0.0', 'openff-1.3.1-alpha.1', 'tip4p_fb', 'tip3p_fb', 'openff-2.2.0', 'spce', 'tip5p', 'tip4p_fb-1.0.0', 'openff-2.1.1', 'openff-2.0.0-rc.1', 'tip5p-1.0.0', 'opc-1.0.1']
```

You can optionally specify a file that contains a cache of pre-parameterized molecules:

```python
smirnoff = SMIRNOFFTemplateGenerator(
cache="smirnoff-molecules.json",
forcefield="openff-2.1.0",
forcefield="openff-2.2.1",
)
```

Expand Down Expand Up @@ -381,7 +381,7 @@ system_generator = SystemGenerator(
)
```

To use the [OpenFF's Sage `openff-2.1.0`](https://github.com/openforcefield/openff-forcefields) or a newer version, an update of the [Open Force Field ("Parsley") small molecule force field](https://openforcefield.org/news/introducing-openforcefield-1.0/) instead of GAFF 2.2.20, we would have instead specified `small_molecule_forcefield='openff-2.1.0'`.
To use the [OpenFF's Sage `openff-2.2.1`](https://github.com/openforcefield/openff-forcefields) or a newer version, an update of the [Open Force Field ("Parsley") small molecule force field](https://openforcefield.org/news/introducing-openforcefield-1.0/) instead of GAFF 2.2.20, we would have instead specified `small_molecule_forcefield='openff-2.2.1'`.

To use [espaloma](https://github.com/choderalab/espaloma) for assigning small molecule parameters, for example with the [`espaloma-0.3.2` model](https://github.com/choderalab/espaloma/releases/tag/0.3.2) released with the [espaloma preprint](https://arxiv.org/abs/2307.07085), you can specify `small_molecule_forcefield='espaloma-0.3.2'`.

Expand Down
19 changes: 9 additions & 10 deletions openmmforcefields/generators/template_generators.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1326,18 +1326,18 @@ def __init__(self, molecules=None, cache=None, forcefield=None, template_generat
The latest Open Force Field Initiative release is used if none is specified.

>>> smirnoff.forcefield
'openff-2.1.0'
'openff-2.2.1'

You can check which SMIRNOFF force field filename is in use with

>>> smirnoff.smirnoff_filename # doctest:+ELLIPSIS
'/.../openff-2.1.0.offxml'
'/.../openff-2.2.1.offxml'

Create a template generator for a specific SMIRNOFF force field for multiple
molecules read from an SDF file:

>>> molecules = Molecule.from_file('molecules.sdf') # doctest: +SKIP
>>> smirnoff = SMIRNOFFTemplateGenerator(molecules=molecules, forcefield='openff-2.1.0') # doctest: +SKIP
>>> smirnoff = SMIRNOFFTemplateGenerator(molecules=molecules, forcefield='openff-2.2.1') # doctest: +SKIP

You can also add molecules later on after the generator has been registered:

Expand All @@ -1350,7 +1350,7 @@ def __init__(self, molecules=None, cache=None, forcefield=None, template_generat

You can optionally create or use a cache of pre-parameterized molecules:

>>> smirnoff = SMIRNOFFTemplateGenerator(cache='smirnoff.json', forcefield='openff-2.1.0') # doctest: +SKIP
>>> smirnoff = SMIRNOFFTemplateGenerator(cache='smirnoff.json', forcefield='openff-2.2.1') # doctest: +SKIP

Newly parameterized molecules will be written to the cache, saving time next time!
""" # noqa
Expand All @@ -1363,7 +1363,7 @@ def __init__(self, molecules=None, cache=None, forcefield=None, template_generat

if forcefield is None:
# Use latest supported Open Force Field Initiative release if none is specified
forcefield = "openff-2.1.0"
forcefield = "openff-2.2.1"
# TODO: After toolkit provides date-ranked force fields,
# use latest dated version if we can sort by date, such as self.INSTALLED_FORCEFIELDS[-1]
self._forcefield = forcefield
Expand Down Expand Up @@ -1654,7 +1654,7 @@ def __init__(
without .offxml extension}
{"charge_method": str, Charge method supported by espaloma ['nn', 'am1-bcc', 'gasteiger', 'from-molecule']}

Default behavior is to use ``openff_unconstrained-2.0.0`` for ``reference_forcefield`` and
Default behavior is to use ``openff_unconstrained-2.2.1`` for ``reference_forcefield`` and
`nn` for `charge_method`.
User defined charges can be assigned by setting the ``charge_method`` to ``from_molecule``
if charges are assigned to openff.toolkit.Molecule.
Expand Down Expand Up @@ -1699,7 +1699,7 @@ def __init__(

You can also pass a template_generator_kwargs to specify the reference_forcefield and/or charge_method in EspalomaTemplateGenerator:

>>> template_generator_kwargs = {"reference_forcefield": "openff_unconstrained-2.0.0", "charge_method": "nn"}
>>> template_generator_kwargs = {"reference_forcefield": "openff_unconstrained-2.2.1", "charge_method": "nn"}
>>> espaloma_generator = EspalomaTemplateGenerator(cache='smirnoff.json', forcefield='espaloma-0.3.2', template_generator_kwargs=template_generator_kwargs)
""" # noqa

Expand Down Expand Up @@ -1727,12 +1727,11 @@ def __init__(
# Check reference forcefield and charge method
if template_generator_kwargs is not None:
self._reference_forcefield = template_generator_kwargs.get(
"reference_forcefield", "openff_unconstrained-2.0.0"
"reference_forcefield", "openff_unconstrained-2.2.1"
)
self._charge_method = template_generator_kwargs.get("charge_method", "nn")
else:
# Consider upgrading to 2.1.0, the recommended small moleucle force field for general use
self._reference_forcefield = "openff_unconstrained-2.0.0"
self._reference_forcefield = "openff_unconstrained-2.2.1"
self._charge_method = "from-molecule"

# Check to make sure dependencies are installed
Expand Down
6 changes: 3 additions & 3 deletions openmmforcefields/tests/test_template_generators.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1263,7 +1263,7 @@ def test_partial_charges_are_none(self):

def test_keyword_arguments_default(self):
"""
Test the default behavior for the keyword arguments, which is using "openff_unconstrained-2.0.0"
Test the default behavior for the keyword arguments, which is using "openff_unconstrained-2.2.1"
as the reference forcefield and "from-molecule" as the charge method.

Check charges are the same as the input, after passing through the template generator.
Expand All @@ -1280,8 +1280,8 @@ def test_keyword_arguments_default(self):
system = forcefield.createSystem(molecule.to_topology().to_openmm(), nonbondedMethod=NoCutoff)
# Make sure passing through the EspalomaGenerator didn't change the charges
assert self.charges_are_equal(system, molecule), "Expected equal charges."
# Assert the reference forcefield is the default "openff_unconstrained-2.0.0"
default_ref_ff = "openff_unconstrained-2.0.0"
# Assert the reference forcefield is the default "openff_unconstrained-2.2.1"
default_ref_ff = "openff_unconstrained-2.2.1"
generator_ref_ff = generator._reference_forcefield
assert generator_ref_ff == default_ref_ff, f"Expected {default_ref_ff}, received {generator_ref_ff}."

Expand Down
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