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Fix issue #124#126

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lohedges merged 10 commits intodevelfrom
fix_124
Mar 6, 2026
Merged

Fix issue #124#126
lohedges merged 10 commits intodevelfrom
fix_124

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@lohedges lohedges commented Mar 5, 2026

This PR closes #124 by using the new sire.mol.dynamics.current_energies() method, rather than extracting the current energies from the last row of the energy trajectory, which grows linearly in time. This requires OpenBioSim/sire#403 to be merged first.

(The diff is larger than necessary since I also bumped the pre-commit version and autoformatted.)

@akalpokas

@lohedges lohedges added the bug Something isn't working label Mar 5, 2026
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Thanks for this! I have checked that for the merged_molecule.s3 (ethane --> methanol) solvated leg dG is unchanged a result of this PR (-3.05 vs. -2.99 kcal/mol without and with PR respectively, based on a 10ns, 12 lambda repex protocol with default settings).

@lohedges lohedges merged commit b617e42 into devel Mar 6, 2026
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@lohedges lohedges deleted the fix_124 branch March 6, 2026 17:25
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[BUG] Progressive slowdown of SOMD2 calculations

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