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Reposted by Open Force Field

Cole Group @colegroupncl.bsky.social · 1d

It's ligand-focussed day at the #CCPBioSim training week, and we've been using @openforcefield.org & @openmm.org to parameterise and run protein-ligand MD, and @mdanalysis.bsky.social & ProLIF for analysis! #compchem

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Open Force Field @openforcefield.org · 6d

Compared to Sage 2.2.1, Sage 2.3.0-rc2 splits torsions so that a single torsional parameter only covers a central bond with a single multiplicity. It also adds some bond and angle types to improve performance of targeted chemistries, such as small rings.

Open Force Field @openforcefield.org · 6d

Sage 2.3.0-rc2 is applicable to drug-like molecules consisting of the elements C, H, O, N, P, S, F, Cl, Br, and I, atomic Xe, and the monoatomic ions Li+, Na+, K+, Rb+, Cs+, F-, Cl-, Br-, and I-.

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Open Force Field @openforcefield.org · 6d

Sage 2.3.0-rc2 is the second force field candidate in Open Force Field using AshGC v1.0. Both vdW and valence parameters have been re-fit, using AshGC charges, to a dataset of physical properties and QM data.

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Open Force Field @openforcefield.org · 6d

AshGC supports most small-molecule chemistries with elements C, O, H, N, S, F, Br, Cl, I, P; a list of excluded SMARTS patterns is included in the documentation. docs.openforcefield.org/projects/nag...

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Open Force Field @openforcefield.org · 6d

AshGC v1.0 is our first neural network charge model. It has been trained to produce charges that are comparable to OpenEye AM1-BCC-ELF10. AshGC 1.0 is identical to the previously released AshGC rc3, except it adds support for single-atom charges.

docs.openforcefield.org/projects/nag...

AM1-BCC GNN v1.0 — OpenFF NAGL Models 2025.9.0.post2+g9309d86.d20250909 documentation

docs.openforcefield.org

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Open Force Field @openforcefield.org · 6d

Then, in a workflow, you can load Sage 2.3.0 rc2 with

`ff = ForceField("openff-2.3.0-rc2.offxml")`

Open Force Field @openforcefield.org · 6d

Or you can update an existing environment:
```
mamba install -c conda-forge "openff-toolkit>=0.17" "openff-interchange>=0.4.6" "openff-nagl>=0.5.3" "openff-nagl-models>=2025.09" "openff-forcefields>=2025.10"
```

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Open Force Field @openforcefield.org · 6d

The easiest way to try Sage 2.3.0 rc2 out is by making a new environment:
```
mamba create -n openff -c conda-forge "openff-toolkit>=0.17"
mamba activate openff
```

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Open Force Field @openforcefield.org · 6d

2. Warnings are sometimes emitted about protons/stereo/charges, those are from a performance heuristic and don’t change the chemistry of the inputs (we’re working on silencing these)

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Open Force Field @openforcefield.org · 6d

Two notes on the example:

1. The first time NAGL is used in a new environment, there may be a few seconds of extra runtime due to pytorch initialization.

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Open Force Field @openforcefield.org · 6d

...
for idx, mol in enumerate(tqdm(mols, desc="Processing molecules")):
interchange = ff.create_interchange(mol.to_topology())
interchange.minimize()
mol.conformers[0] = interchange.positions
mol.to_file(f"minimized_mol_{idx}.sdf", file_format="sdf")
```

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Open Force Field @openforcefield.org · 6d

```
from openff.toolkit import Molecule, ForceField
from tqdm import tqdm # for progress bars
mols = Molecule.from_file("inputs.sdf") # loads 50 different molecules
ff = ForceField("openff_unconstrained-2.3.0-rc2.offxml")
...

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Open Force Field @openforcefield.org · 6d

Because AshGC assigns charges so quickly, use cases like quick conformer minimization are now practical. The following python code will minimize 50 different molecules from an input SDF, saving each minimized structure to an SDF file, in about 1 minute:

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Open Force Field @openforcefield.org · 6d

Please try it out and let us know if you find any substantial improvements, regressions, or other issues in comparison to Sage 2.2.1. If all goes well, we plan to make the full release in a few weeks! See the thread for an example:

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Open Force Field @openforcefield.org · 6d

We’re pleased to announce Sage 2.3.0 Release Candidate 2 (rc2)! Sage 2.3.0 will be the first OpenFF force field to use the AshGC neural network charge model, which was trained to AM1BCC ELF10 charges, and allows for rapid charge assignment for molecules with hundreds or thousands of heavy atoms.

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Open Force Field @openforcefield.org · 23d

OpenFF provides a critical resource for pharmaceutical discovery and design, producing high quality force fields that can be applied at scale without commercial license fees. Learn how your company can partner with us to invest in the future of #openscience app.reclaim.ai/m/james-omsf...

OpenFF / OpenFE informational meeting

Schedule a meeting with leadership of the Open Force Field and Open Free Energy projects to learn more about these projects and how to support them - Powered by Reclaim.ai

app.reclaim.ai

Open Force Field @openforcefield.org · Aug 27

We always love seeing the cool things people do with our force fields!

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Reposted by Open Force Field

Cole Group @colegroupncl.bsky.social · Jul 29

The advanced bio workshop is in full swing now at the #ccp5 summer school, featuring material from ccpbiosim, @openforcefield.org, mdanalysis & @ppxasjsm.bsky.social. Expertly taught by @matteodegiacomi.bsky.social & @jjguven.bsky.social

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Open Force Field @openforcefield.org · Jul 24

Hot take from our Project Director, David Mobley: We should drop bond order and no longer use aromaticity. blog.omsf.io/why-we-shoul...

Do you agree, #chemsky ?

Why We Should Drop (Graph-based) Bond Order and No Longer Use Aromaticity

Written by: David Mobley, PhD OpenFF force fields assign parameters based on queries operating on the chemical graph for molecules, via the SMARTS language. This language is rather flexible, leaving ...

blog.omsf.io

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Open Force Field @openforcefield.org · Jul 1

We're excited to see this work from @micaelamatta.bsky.social and @hannahturney.bsky.social in publication! They have done some really cool work with our toolkit, and pushed us to to make several performance enhancements for loading and parameterizing polymers.

Micaela Matta @micaelamatta.bsky.social · Jun 28

@hannahturney.bsky.social’s #SwiftPol is now a JOSS paper 🥳
Polymer building made 🪄 easy 🪄 thanks to reaction SMARTS and @rdkit.bsky.social

Journal of Open Source Software @joss-openjournals.bsky.social · Jun 27

Just published in JOSS: 'SwiftPol: A Python package for building and parameterizing in silico polymer systems' https://doi.org/10.21105/joss.08053

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Open Force Field @openforcefield.org · Jun 17

Our toolkit is designed to meet the needs of force field scientists -- that's who we are! Here's an example of how easy it is to change parameters in a force field in our format: docs.openforcefield.org/en/latest/ex...

#opensource #compchem

Modifying a SMIRNOFF force field — OpenFF Ecosystem documentation

docs.openforcefield.org

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Open Force Field @openforcefield.org · Jun 12

It's great to see others using NAGL to train GNN charge models. Stay tuned for our own model, coming soon!

Cole Group @colegroupncl.bsky.social · Jun 3

We collect a dataset of quantum mechanical AIM properties computed at a high level of theory (ωB97X-D/def2-tzvpp), in both vacuum and implicit solvent, and use the @openforcefield.org NAGL package to train new GNN charge models to each. github.com/openforcefie...

GitHub - openforcefield/openff-nagl: OpenFF NAGL

OpenFF NAGL. Contribute to openforcefield/openff-nagl development by creating an account on GitHub.

github.com

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Reposted by Open Force Field

Karmen Condic-Jurkic @karmencj.bsky.social · May 9

@jenkescheen.bsky.social showcased his work on @asapdiscovery.bsky.social and more recently with CharmTx, combining ML and more traditional free energy calculations. A lot, if not all, of his work is based on @openfree.energy, #openforcefield, and #alchemsicale. Read his papers for more details!

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Open Force Field @openforcefield.org · Apr 30

This tool has solved some of our CI problems.

#opensource #devops

Ethan Holz @ethanholz.com · Apr 29

Hey everyone! My @omsf.io published my post about why we built a GitHub Actions solution for provisioning self-hosted runners on different clouds! Let us know what you think!

blog.omsf.io/introducing-...

Introducing OMSF Self-Hosted Runners

Written by: Ethan Holz Today marks the official launch of almost a year of work from the OMSF Ecosystem Infrastructure team to deliver a solution for Self-Hosted GitHub Actions runners. This directiv...

blog.omsf.io

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