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feature_gromacs_energy #39

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chryswoods opened this issue Apr 3, 2023 · 1 comment
Closed

feature_gromacs_energy #39

chryswoods opened this issue Apr 3, 2023 · 1 comment

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@chryswoods
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This feature branch contains the code developed to support calculating internal energies of molecules parameterised to include Gromacs-style dihedrals (e.g. specifically the harmonic improper term). This will also include adding support to the OpenMM converter for writing Urey-Bradley angle terms and harmonic improper terms.

API Proposal

This should be fully automatic and require no changes to the API. Essentially molecules that contain such internal terms will now not trigger exceptions saying that only amber-style dihedrals are supported.

>>> mols = sr.load("files_containing_gromacs_dihedrals")
>>> mols.energy()
Result!
>>> mols = mols.dynamics().run(5*sr.units.picosecond).commit()
Result!
@chryswoods chryswoods self-assigned this Apr 3, 2023
@chryswoods chryswoods added 2023.3.0 roadmap Issue relating to the roadmap and development labels Apr 3, 2023
@chryswoods chryswoods added this to the 2023.3.0 milestone Apr 3, 2023
@chryswoods chryswoods modified the milestones: 2023.3.0, 2023.4.0 Jun 2, 2023
@chryswoods chryswoods removed their assignment Sep 11, 2023
@chryswoods chryswoods modified the milestones: 2023.4.0, 2023.5.0 Sep 11, 2023
@chryswoods chryswoods removed roadmap Issue relating to the roadmap and development 2023.5.0 labels Oct 25, 2023
@chryswoods chryswoods removed this from the 2023.5.0 milestone Oct 25, 2023
@chryswoods
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I'm archiving this as I haven't had a chance to look at it. It can be revived later if there is interest.

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