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SepTop analysis notebook #225

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Merged
IAlibay merged 13 commits into from
Sep 1, 2025
Merged

SepTop analysis notebook #225

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a20960f
First pass at SepTop analysis notebook
hannahbaumann Aug 27, 2025
b830a2b
Add example result
hannahbaumann Aug 27, 2025
d686e69
Big rework to match more the CLI behaviour
hannahbaumann Aug 27, 2025
59eb387
Add dg analysis
hannahbaumann Aug 28, 2025
3915f27
Use MBAR error for one repeat, remove doublicate functions
hannahbaumann Aug 28, 2025
1fb8566
Some cleanup
hannahbaumann Aug 28, 2025
71a0471
Add some more explanations
hannahbaumann Aug 28, 2025
02480a3
Add more data so people can test out the notebook
hannahbaumann Aug 28, 2025
6fb8bd6
Use Femap object instead of gather dg way
hannahbaumann Aug 28, 2025
88bce0a
fix error estimation, clean imports
jthorton Aug 29, 2025
ea4676b
Apply black to notebook
IAlibay Sep 1, 2025
2a36ce9
Clean up and moving things to zenodo
IAlibay Sep 1, 2025
6515f80
black the notebook
IAlibay Sep 1, 2025
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1 change: 1 addition & 0 deletions openmm_septop/results_0/rbfe_1_25.json
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1 change: 1 addition & 0 deletions openmm_septop/results_0/rbfe_1_7a.json
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1 change: 1 addition & 0 deletions openmm_septop/results_0/rbfe_1_7b.json
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1 change: 1 addition & 0 deletions openmm_septop/results_0/rbfe_7a_7b.json
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1 change: 1 addition & 0 deletions openmm_septop/results_1/rbfe_1_7a.json
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1 change: 1 addition & 0 deletions openmm_septop/results_2/rbfe_1_7a.json
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1,024 changes: 1,024 additions & 0 deletions openmm_septop/septop_analysis.ipynb
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