Each iteration consisted of 1000 MD steps and 3400 NCMC switching steps, except in section 4.3 where we varied the number of NCMC switching steps. During the NCMC protocol, the ligand interactions are varied by scaling the λ parameter which control the strength of the non-bonded interactions. The NCMC steps were not evenly distributed across the λ schedule. For λ values between 0.2 to 0.8, we performed additional four perturbation steps for each alchemical step as shown in Figure . For example, for 3400 switching steps, 200 steps were used for λ values 0.0 to 0.2, 3000 steps for λ values 0.2 to 0.8, and 200 steps for λ values 0.8 to 1.0. Only the MD steps contributed to the final trajectory, thus each iteration corresponded to 1000*0.002 fs/step = 2 ps worth of production run.