Analysis: alchemical free energy¶
On hold
Alchemical transformation is on hold as of 2026-10-13 and is not part of the current release. This page was last run against 0.6.4. See On hold.
One notebook over a prepared leg from the hydration free energy page.
| notebook | what it shows |
|---|---|
free-energy.ipynb |
MBAR, BAR, TI and both EXP directions over one set of samples |
micromamba activate analysis-env # see Installing, step 5
export MD_ALCHEMY_LEG=/path/to/AHFE-leg1-run1
jupyter lab docs/tutorial/ethanol/analysis/
Four estimators are not four measurements¶
They are four probes of ONE dataset. Their spread says how well the ladder overlaps, not how uncertain the free energy is — the uncertainty comes from repeats. If the estimators agree, the sampling supports all of them; if they disagree, read the overlap before the physics, because EXP in one direction is the first to break when its exponential average is carried by its tail. MBAR far from BAR would mean something is wrong with the samples themselves.
The run in the notebook gives MBAR −3.787 ± 0.103 kcal/mol with a smallest neighbour overlap of 0.178 — a ladder is in trouble below about 0.03. That quoted uncertainty is MBAR's asymptotic covariance for one ladder, and it is not the error bar to publish.