We further tested the adaptive protocol on the bound vanish stage of the T4L complex, again with 20 runs per protocol and with a shared λ schedule selected with a speed of 1.0 kcal mol -1 (Section S13). Here, the sampling issue resulted from the occasional water molecule moving into the empty binding site around λ = 1.0. This issue was also noted by Lagardère et al. The adaptive algorithm allocated substantially more sampling time to the affected windows, but in contrast to the PIP2 example, this did not produce any observable benefit. This is because the timescale of water entry to the binding site is far greater than what was allocated by our algorithm. Hence, we expect that the adaptive algorithm will rarely offer dramatic within-stage improvements, because the timescales of most sampling issues are expected to be much longer than the simulation times that can reasonably be allocated. This is in agreement with the recent work of Yu et al., who investigated the performance of a similar algorithm for computing the hydration free energies of trivalent rare earth elements in ionic liquids. They found that the algorithm offered substantial reductions in uncertainty at equivalent computational cost for the Coulombic contribution at 600 K. However, at 300 K the timescale of the sampling issue was dramatically increased and the adaptive protocol offered little improvement over equal-time allocation.