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Solvate with non-cubic boxes #585

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IAlibay opened this issue Oct 25, 2023 · 2 comments · May be fixed by #673
Open

Solvate with non-cubic boxes #585

IAlibay opened this issue Oct 25, 2023 · 2 comments · May be fixed by #673

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@IAlibay
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IAlibay commented Oct 25, 2023

OpenMM now supports non-cubic boxes, we should see if we could pass this as a user input (through SolventComponent?).
@IAlibay
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IAlibay commented Oct 25, 2023

pinging @hannahbaumann

@richardjgowers
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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

@IAlibay IAlibay mentioned this issue Dec 13, 2023
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@IAlibay IAlibay linked a pull request Dec 29, 2023 that will close this issue
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OpenMMSolvation: Support for non-cubic boxes and defined box properties OpenFreeEnergy/openfe
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@richardjgowers @IAlibay