Fix charge correction validation for membrane (SolvatedPDBComponent) systems#1979
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slochower wants to merge 1 commit into
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Fix charge correction validation for membrane (SolvatedPDBComponent) systems#1979slochower wants to merge 1 commit into
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Replace the monolithic `_get_ion_and_water_parameters` with three focused functions that handle ion parameter lookup in order of preference: 1. Most abundant monovalent ion of the correct charge sign already present in the topology. 2. Divalent or wrong-sign ions are skipped by the monovalent filter. 3. If no suitable ion exists (e.g. zero ionic strength or a SolvatedPDBComponent without ions), a minimal single-ion system is built from the forcefield to obtain NA/CL parameters. This approach is adapted from OpenFE PR OpenFreeEnergy#1978. The key API change is that `handle_alchemical_waters` and `_handle_net_charge` now accept a `forcefield` (from the system generator) instead of a `solvent_component`, since what we actually need is the ability to parameterize an ion — not the component metadata. The mutation only modifies NonbondedForce parameters (charge, sigma, epsilon), leaving bonded terms untouched. This is safe for rigid water models (TIP3P, SPC/E) where geometry is enforced by SETTLE/SHAKE constraints rather than harmonic forces. Added documentation warning that flexible water models would produce unphysical forces on the ghost hydrogens. Also adds SolvatedPDBComponent support to `_validate_charge_difference` so membrane systems can use explicit charge correction.
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@davidslochower thanks for opening this PR - I just wanted to let you know that there is an earlier PR addressing the same thing in #1978 so that will, for now (this may change depending on how things progress), take precedence over this one. That being said, the modifications you made here provide useful insights towards fixing this issue. |
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When a ChemicalSystem contains a ProteinMembraneComponent (which inherits from SolvatedPDBComponent) but no explicit SolventComponent, the charge correction validation raises:
This is because the validation only checks stateA.contains(SolventComponent). However, the system is solvated and the water and ions are part of the ProteinMembraneComponent. The system construction code already handles this correctly (hybridtop_units.py line 203 sets solvent_comp = protein_comp for SolvatedPDBComponents), but the validation doesn't use the same logic.
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newsentry, or the changes are not user-facing.pre-commit.ci autofix.Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).
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