The problem of slow movement of such trapped waters persists in relative binding free energy (RBFE) calculations of ligands that bind to a protein with different numbers (and/or positions) of the trapped waters. In an RBFE calculation, the difference in the binding affinities of two ligands to a specific protein is calculated, as opposed to the binding affinities of the two ligands individually in the absolute binding free energy (ABFE) calculations (Figure .) Typical MD simulation workflows treat such calculations by transforming one ligand to the other using alchemical methods. Effectively, this means that one ligand is replaced by the other while keeping the remaining system (i.e., the protein and all water molecules, including the trapped ones) essentially unchanged. If a water molecule is essential for the protein-ligand interactions of one ligand while the other ligand is known to displace it, such methods are likely to yield wrong results if the water molecule does not naturally rearrange itself in the timescale of the simulation. In these cases, the ligand transformation would yield either a binding mode for one ligand that is missing the water molecule essential for its interaction with the protein, or a system in which a water molecule is trapped in a cavity in which it interferes with the binding between the protein and the ligand that is known to displace it. Normally, simulation timescales used for such ligand transformations are not long enough to hope to either displace the trapped water or observe the water moving in to reach its binding site.