For all protocols, the protein-ligand complex and solvated ligand step short-run simulations, as well as the overall ∆𝐺 𝑏𝑖𝑛𝑑 𝑜 short-run simulations, converged quickly towards their respective long-run averages and were within error after 1-2 ns of simulation time, as seen below in Figure . The restraint addition step short-run simulations, however, remained well outside of error. Analysis of this alchemical step showed that regardless of equilibration protocol employed, over 40 ns of production simulation time per λ-window is required to achieve the average values of approximately 2 kcal/mol (Fig. ), which is significantly more resources than can be dedicated for this purpose. Average protein-ligand complex ΔG, solvated ligand ΔG, restraint addition ΔG and overall ∆𝐺 𝑏𝑖𝑛𝑑 ° of the short-run simulations and long-run simulations with all three equilibration methods were computed and are tabulated in Table . For both the protein-ligand complex and solvated ligand steps, there was not a significant difference between ΔGs obtained from the any of the short-run protocols and any of the long-run equilibration methods. While the restraint addition step did show significant deviation, the overall magnitude is small, and the errors are cancelled on average in the other alchemical steps. However, computational cost did vary across short-run protocols, with Protocol C converging in approximately 50-60% of the simulation time allocated to Protocol A depending on the alchemical step, with Protocol B falling between the two but closer to C.