Strategy (B) can in some cases be much more efficient Multiple free energy calculations can yield a total binding free energy Populations + a single binding free energy calculation can yield the total Figure : Potential free energy efficiency gains using binding mode populations. (A) shows calculations of M different effective binding free energy values ( G i ) for each different metastable binding mode of a ligand in a receptor; these effective binding free energies can be rigorously combined to recover the total binding free energy, with a total computational cost (C) of MNx where N is the number of intermediate alchemical states used and x is the length of the simulation used at each alchemical state. Alternatively, (B) shows how, if relative populations (pi) of different metastable binding modes can be recovered from end state simulations (colored circles, top; each circle represents an amount of simulation time spent in the binding mode, so the populations can be determined from counting time in each mode, with binding modes separated by clustering techniques or any reasonable decomposition of state space 1 ), then the full binding free energy can be recovered from the calculation of a single effective binding free energy (here, G 3 is selected for convenience) and the populations of the different binding modes. This approach has a computational cost (C) of Nx + y, where y is the cost of determining the binding mode populations.