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choderalab / openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
http://openmmtools.readthedocs.io
MIT License
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Adding support for future OpenFF virtual site releases in AbsoluteAlchemicalFactory #745

Open IAlibay opened 2 months ago

IAlibay commented 2 months ago

Follow-up from #509 and #508

We would like to add support for doing AFE calculations using future releases of OpenFF force fields that will contain virtual sites.

This is a partial roadmap item for OpenFE this year, so we would like to help out with this process as much as possible.

To our knowlege, the following actions would be necessary:

  1. Get a technically complete (i.e. no expected changes in vsite types or functional forms) snapshot version of the OpenFF virtual sites FF which we can test against.
  2. Alter AbsoluteAlchemicalFactory to allow for virtual sites, but only when the alchemical region is not directly bonded to any atoms outside the alchemical region.
  3. Add a variety of tests to ensure we retain expected energies, and possibly back to back hydration free energy checks against known results.
IAlibay commented 2 months ago

@ijpulidos this would be a good one to briefly discuss next week.