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It might be nice to consider an the Foyer `Forcefield` as a generic lookup table. With #382 on the way, the actual parameters can be queried based on AtomTypes/Classes. Which means if you have a gener…
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Seems like there's an issue saving the JSON state of a topology, where the parameters aren't stored at all. Maybe this is a good place to discuss if that's a feature we would want to have.
```pytho…
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I am working on a forcefield that combines MM4 and MM3 parameters, and one of the many cross-references I look at is your repository. Allinger made a typo in the MM3 silicon paper (1997) specifying ef…
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I'm starting a thread to discuss how we should best deal with small molecules.
I'd love for YANK to make use of the nice OpenMM app tools `Modeller` and `ForceField` to set up protein systems, but th…
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**I want to create a topology for a drug like molecule which is not in the 20 canonical amino acids**
**Expand the from_pdb method to accept drug like molecule**
**Create a new method to rea…
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@marjanAlbouye and I were experiencing some very slow performance with `gmso.parameterization.apply` and have been doing some digging into what the problem could be.
It doesn't seem to be an issue …
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**Describe the bug**
Trying to create an openmm system with no nonbonded force results in an error due to the post-processing done [here](https://github.com/openforcefield/openff-toolkit/blob/893575a…
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We'd love to benchmark `espaloma` with this benchmark framework. To do this, we'd need to recognize espaloma force field names as input, and generate an `Interchange` object (or an OpenMM `System`) as…
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**Description**
I am trying to use openFF forcefields (Sage) to parameterize a molecular dynamics calculation of free energy of solvation of hydrofluorocarbons in ethanol through Gromacs. For di-,tri…
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No disagreement on the current priorities described in #1 , but of the many options available to include in version 2, I would be interested to see additions to dataset towards larger solvated peptide…