Binding ∆G calculations where sampling of the decoupled ligand state is initialized with the final structures from 1 µs simulations show this shift and have the same accuracy as those started with the crystallographic apo state 1wfc (Fig 4 and). This confirms our previous observation that the rotameric state of T106 plays a crucial role in the ligand binding to p38α. All in all, the observations from the long simulations suggest that, at least in some cases, we can rely on longer (or enhanced) sampling to recover a protein's apo state for the subsequent ∆G calculations.