Single Topology, Hybrid Topology, and Dual Topology. Dual topology variants, such as linked dual topology and separated dual topology, represent the changing molecules in the end-states by independent sets of coordinates, allowing a straightforward representation of large ligand transformations with the respective restraint placement algorithm. The opposite extreme to dual topology is the single topology approach, where a minimal set of coordinates represents both end-states. The single topology approach reduces the separation of the phase space between the two end-states significantly and is proposed to give an efficiency win compared to dual topology approaches, but allows for less diverse molecule changes. The hybrid topology approach offers improved calculation efficiency compared to dual topology approaches as coordinates of shared parts of the molecules are merged to the so-called core region, and differing parts of the molecule are represented by dual-topology-like regions. This approach is an intermediate between dual-and single-topology approaches. Its primary challenge is to find the mapping of atoms Figure : The Binding Free Energies Thermodynamic Cycle can be employed to calculate relative binding free energies (∆∆G RBF E BA ) by comparing two molecules A and B. The absolute free energy differences ∆G abs bind A and ∆G abs bind B represent the change of molecules A and B's environment from water to the protein complex, and can be combined to calculate ∆∆G RBF E BA . Alternatively, calculating the RBFE between A and B in a specific environment (∆∆G rel y BA ) can be often used to more efficiently calculate ∆∆G RBF E BA . The environments, such as water and complex can be exchanged with e.g. the combination of vacuum and water in order to retrieve RHFEs.