We note that the ability of the adaptive algorithm to detect sampling issues is highly dependent on using diverse starting conformations. We performed two adaptive runs of the T4L system with 5 replicate runs, a runtime constant of 0.0005 kcal 2 mol -2 ns -1 , and λ-windows spaced with a speed of 1 kcal mol -1 . The first protocol used the default of independently equilibrated (in the fully interacting state) structures for each repeat, while the second protocol used the input structure generated for the first repeat for all repeats.