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OpenFreeEnergy / openfe

The Open Free Energy toolkit
https://docs.openfree.energy
MIT License
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Solvate with non-cubic boxes #585

Closed IAlibay closed 1 week ago

IAlibay commented 10 months ago

OpenMM now supports non-cubic boxes, we should see if we could pass this as a user input (through SolventComponent?).

IAlibay commented 10 months ago

pinging @hannahbaumann

richardjgowers commented 10 months ago

As a sanity check, could we first quickly check for a sample set of protein structures (PLB?) how much solvent we can avoid adding and as a post-step quickly check that the benchmarking figures are agreeing with this being quicker.

I'm also curious if aligning the protein's gyration tensor along box primary vectors would help here

jameseastwood commented 2 months ago

Can we get a review on this (really the associated PR) sometime soon? @IAlibay @hannahbaumann Low priority though. [] Work out if it makes sense [] Try it out on a few systems