Typically a variable λ is used to control the alchemical transformation from a ligand L 1 to a ligand L 2 in these relative alchemical free energy methods. More details on RBFE calculations and best practices can be found in Mey et al. and Hahn et al. 2.1 Modeling metals can be a challenge for alchemical free energy calculations Modeling metals is difficult not only with RBFE calculations but also with other MD methods. This is especially true for transition metals, where molecular mechanics (MM) force fields do not correctly describe the interactions between the metal and coordinating residues.