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
- 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