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If I understand the rationale for the current design, we currently keep distinct `topology.TopologyMolecule/Bond/Atom` and `molecule.Molecule/Bond/Atom` because we don't want to include all the inform…
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Hi Folks,
**Is your feature request related to a problem? Please describe.**
Feature/documentation request
We are running simulations of various SARS-CoV-2 proteins. There are certain simulat…
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I have a system consisting of a peptide and a polymeric linker (a 3 amino acid - 16 C fatty acid conjugate), which I parameterize using a combination of amber14 protein ff and gaff-2.1 through openmmf…
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A while ago a discussion about API change leads to the adding of physical units explicitly for each parameter. #291
This leads to a new feature where parameters belongs to the same force field type…
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Something that would be *really* nice for interactive applications of OpenMM would be the ability to store extra information about a residue (e.g. long-format name(s), SMILES string, etc.) directly in…
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A function taking multiple sets of molecule labels from **Parameterization of molecules** #10 to generate coverage reports should go into `openff.benchmark.parameterization`. This will the produce a r…
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This is part of my crusade against API consumption of `Topology` :stuck_out_tongue:
Would it be crazy to refactor the parts of `from_smirnoff` that apply the force field out into an `parametrize_s…
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Hi, I'm trying to parameterize two molecules "NBD" & "Methoxy Coumarin" in their ground state but I keep landing on this error:
`"""
Traceback (most recent call last):
File "/home/akhanna2/anacon…
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**Describe the bug**
Not really sure if this falls under the bug category, but still an issue I was running into. When assigning parameters using the parameter assignment example (examples/using_smir…
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We should start considering what features we want to include in the next release after 7.6 (whatever we end up calling it). Here's my first pass at reviewing open feature requests. To start with, he…