As with the CDK2 mutations, the amount of simulation time applied to each λ-window varied by λ-window, simulation protocol, alchemical step, and mutation, as seen below in Figure . We note that λ-windows of the protein-ligand complex step with elevated simulation times in Protocol A also tended to have elevated simulation times in Protocols B-D, and the same pattern holds with respect to Protocols B and C. This demonstrates that different λ-windows converge at different rates and that this pattern is consistent. This pattern is not clear in the solvated ligand step as these λ-windows converged much faster than the protein-ligand complex step. additional simulation lengths. Significant deviation in the protein-ligand complex step for this difficult mutation is observed between all short-run protocols and the long-run protocols.