We also examined the convergence of the mean potential energies of components of the simulated systems. For each complex simulation, we computed the mean internal energy of ligand i (L i ), selected residues lining the binding site (B), and the combination of the ligand and the binding-site residues (BL i ). For each free ligand simulation, we computed the mean internal energy of just the ligand (L). The uncertainties of these means, estimated by the same methods applied to the whole simulations (Table ), are reported in Table . For the free ligand simulations, the uncertainties in the isolated ligand energies, u Li Li , tend to be larger than those for the total potential energies of the corresponding full systems (Table ), which also include the waters, ions and buffer molecules. Consistent with these results, the curves from reblocking analysis (see Supporting Information) show no plateaus, except for the free cQ ligand, which also has low SEMs in Table . Thus, the ligands' internal energies converge more slowly than do the energies of the full ligand-solvent systems, even though the ligands represent only a tiny part of each full 18,000 atom system. Put differently, the variance of the full system energy is greater than that of the ligand alone. This implies that the ligand internal energy anticorrelates strongly with other energy components of the full system. Such anticorrelation is physically plausible; for example, if the ligand's internal energy falls when the ligand makes an intramolecular H-bond, the ligand-solvent interaction energy will rise, due to the resulting loss of a ligand-solvent H-bond.