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OpenBioSim / ghostly Public

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Fix issue #6 and switch to pixi + rattler build system#7

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lohedges wants to merge 15 commits intodevelOpenBioSim/ghostly:develfrom

fix_6OpenBioSim/ghostly:fix_6Copy head branch name to clipboard

Conversation Commits15 (15)Checks Files changed

Open

Fix issue #6 and switch to pixi + rattler build system#7
lohedges wants to merge 15 commits intodevelfrom
fix_6

Commits

Commits on Feb 6, 2026

Physical atoms must be physical at both end states.
lohedges
committed
Treat remaining terms as a dual junction.
lohedges
committed
Remove impropers that bridge the physical and ghost regions.
lohedges
committed
Fix end-state flag at lambda=0.
lohedges
committed
Grammar tweak.
lohedges
committed
Make loop variable name more meaningful.
lohedges
committed
Catch and allow minimisation convergence errors.
lohedges
committed
Remove unused variable.
lohedges
committed
Break loop after first angle optimisation failure.
lohedges
committed
Clarify definition of physical atom.
lohedges
committed
Add ejm49~ejm31 unit test.
lohedges
committed
Switch to pixi and rattler build.
lohedges
committed
Add auto-generated version file to gitignore.
lohedges
committed
Add modifications to handle ring-break and multi-dummy group edge cases.
lohedges
committed
Add placeholders for rotamer anchor modification.
lohedges
committed

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