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Free energy diagram for (A) AMBER-TI and (B) AToM-OpenMM. The protein is represented in purple, the membrane bilayer in green, the aqueous solvent in blue, the initial ligand in red, and the final ligand in yellow. For AToM-OpenMM, the λ values for both legs end at 1/2, indicating that 50% of ligands A and B are present in both the binding site and the solvent bulk [R(AB)1/2 + (BA)1/2].
