As a consequence, properly equilibrating water molecules is essential for attaining accurate results in MD simulations, such as calculating protein-ligand binding free energies with MDbased methods. For example, alchemical methods that decouple the entire ligand from the binding site to compute absolute binding free energies, or which chemically modify the ligand to compute relative binding free energies, may not converge without accounting for resulting changes in the water occupancy of the binding site, especially for deeply buried cavities. This is particularly problematic in drug discovery applications because the system may appear to be converged using standard MD analysis techniques, leading to false positive or false negative predictions.