[ WIP ] Support for charge changes in the HybTop protocol for explicitly solvated systems#1978
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[ WIP ] Support for charge changes in the HybTop protocol for explicitly solvated systems#1978hannahbaumann wants to merge 6 commits into
hannahbaumann wants to merge 6 commits into
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…for explicitly solvated systems
hannahbaumann
commented
May 18, 2026
| """ | ||
| Infer positive and negative ion residue names from a topology by | ||
| finding the most common monovalent ion of each charge type. | ||
| Falls back to NA/CL if none are found. |
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I'm doing this mostly because e.g. maestro doesn't always add ions (in the a2a example there were no negative ions in the system).
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hannahbaumann
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May 20, 2026
| system_mapping: dict, | ||
| charge_difference: int, | ||
| solvent_component: SolventComponent, | ||
| positive_ion_resname: str, |
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use element or formal charge instead?
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## main #1978 +/- ##
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- Coverage 94.94% 90.54% -4.40%
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Files 216 216
Lines 20481 20547 +66
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- Misses 1036 1943 +907
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slochower
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May 21, 2026
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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No API break detected ✅ |
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This is just a first idea (and the
_get_ion_resnames_from_topologywas written together with Claude). This is mostly just to show the different things we have to consider, but I don't like the dictionary idea of known ions yet. Maybe it would also be ok to always use Cl and Na ions for explicitly solvated systems, no matter if other ion types were used as counterions?Checklist
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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