Not only is it important to start the transitions with correctly populated orientations of the Val111 side chain, but the switching also has to be slow enough to allow for rearrangement towards the orientation in the other end state at least in some transitions. Note that it is also possible that, with sufficiently large end state ensembles which populate minor rotamers at exactly the right degree, such transitions during switching might not be necessary, but that was not observed here. Unfortunately, it is not obvious how the NEQ switching rate couples to the rate of side chain reorientation, making it difficult to know the required transition length a priori. As discussed in Sec. 5.2.2, although not all non-equilibrium switches have to sample this reorientation, it has to be sampled in some transitions to obtain overlapping work distributions and a reliable free energy estimate. Here, even with 4 ns/transition, the side chain reoriented only in 8 % of the transitions in the coupling direction (B2A) and 74 % during decoupling of the ligand (A2B), which results in too few transitions sampling the correct rotamer in the coupling direction. Since the conformational change was not sampled sufficiently in 400 ns total simulation time, we decided that it was better to restrain the side chain.