A free energy calculation approximates the unknown but true changes in free energy, 𝚫𝐆 𝐓𝐫𝐮𝐞 (with boldface indicating an array), of 𝑛 ligands that occur upon some physical process such as binding or solvation. In our particular case, we simulate 𝑘 transformations to measure relative changes in binding free energy, 𝚫𝚫𝐆 𝐨𝐛𝐬 , and collect known reference free energy values for one or more of these ligands, 𝚫𝐆 𝐫𝐞𝐟 , from experimental work. Our goal is to use the simulation results, reference values, and subsequent analysis to approximate 𝚫𝐆 𝐓𝐫𝐮𝐞 as accurately as possible.