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Filter bridge-extension dihedrals#10

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lohedges merged 4 commits into
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fix_bridge_extension_dihedrals
Jun 29, 2026
Merged

Filter bridge-extension dihedrals#10
lohedges merged 4 commits into
develfrom
fix_bridge_extension_dihedrals

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The _remove_residual_ghost_dihedrals function previously handled two patterns of spurious ghost/physical dihedral coupling (cross-bridge and ghost-middle), but missed a third: dihedrals of the form real–ghost–ghost–ghost, where a real bridge atom sits at one terminal and the remaining three atoms lie inside a ghost group. This pattern arises when the ghost group contains a ring, most critically cyclopropyl, where the ring topology creates multiple dihedral paths from the bridge into the ring interior (bridge–CP1–CP2–X) with large force constants (~4.6 kcal/mol). Left in place, these terms constrain the ghost ring's orientation relative to the real scaffold even at λ=0, introducing spurious torsional coupling.. A new bridge_extension case removes all such dihedrals; the intended anchor dihedrals (real–real–ghost–ghost) are unaffected. The fix also removes analogous depth-extension terms in linear ghost chains, which were previously left in by omission but are equally unphysical and have no role in the Boresch factorisation.

@lohedges lohedges added the bug Something isn't working label Jun 29, 2026
@lohedges lohedges merged commit c8a4816 into devel Jun 29, 2026
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@lohedges lohedges deleted the fix_bridge_extension_dihedrals branch June 29, 2026 10:01
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