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Update SolventComponent properties to include those that define the composition of the solvent #261

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IAlibay opened this issue Dec 27, 2023 · 2 comments · May be fixed by #262
Open

Update SolventComponent properties to include those that define the composition of the solvent #261

IAlibay opened this issue Dec 27, 2023 · 2 comments · May be fixed by #262

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@IAlibay
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IAlibay commented Dec 27, 2023

Currently we have a mismatch where we have some details about how solvation happens in the SolvationSettings and some in SolventComponent.

My proposal is that anything that defines the molecular composition of the system should be defined in the the SolventComponent.

This includes:

  • The number of waters that will be added
    • Including options such as the padding & mass density used to add the waters
    • Including options such as how the box is defined
      • Box vectors
      • Box shape
  • The type of ions & concentration that will be added (done)
  • The solvent smiles (done)

By comparison, anything that defines the implementation details should be in the SolvationSettings:

  • water model
  • tolerance for any heuristic in water addition (see packmol)
  • solvation backend (OpenMM modeller, packmol, leap, gmx solvate, etc...)
  • centering the solute
@IAlibay IAlibay changed the title Update SolventComponent properties to include those that define how the system is built Update SolventComponent properties to include those that define the composition of the solvent Dec 27, 2023
@IAlibay IAlibay added this to the Release 1.0.0 milestone Dec 27, 2023
@IAlibay IAlibay linked a pull request Dec 27, 2023 that will close this issue
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@richardjgowers
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I've put more detail in the PR, but I don't think I agree that ChemicalSystem is trying to capture all molecular composition. I think it's trying to capture all molecular composition that affects calculated free energies, so solvent padding etc doesn't belong in SolventComponent

@IAlibay
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IAlibay commented Jan 1, 2024

I've responded in the PR - I think there's a fundamental issue where we're trying to be too conservative in where these things will be applied. Defining N is important and really should be a Component thing in my opinion - especially because it's crucial to things like binding enthalpy calculations.

@richardjgowers richardjgowers removed this from the Release 1.0.0 milestone Jan 19, 2024
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Update solventcomponent to encompass all composition properties OpenFreeEnergy/gufe
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@richardjgowers @IAlibay