Figure : Estimated ∆G against sampling time for the bound vanish stages of the initial test systems. Data were split into 20 equal blocks and MBAR was run on each block. "adaptive" refers to the "optimised" adaptive protocol, and the non-adaptive results were obtained by averaging the non-adaptive 6 ns and 30 ns runs to more clearly show the differences in equilibration behaviour. The data for the non-adaptive runs was truncated before analysis so that the per-stage computational costs were equal to the adaptive calculation. For this reason the 95 % t-based confidence intervals (shaded areas) are expected to be a factor of √ 2 smaller for the adaptive protocol. The final non-adaptive ∆G is taken from the 30 ns non-adaptive result (black dotted line with 95 % CIs shown by sparser dotted lines). The y-axis spacings are the same for all plots. Plots for all stages are shown in Section S20.