One more avenue we would like to pursue is to use the nonequilibrium work generated from the BLUES protocol to enhance our binding mode population comparisons. During our protocol in BLUES we are essentially performing two nonequilibrium simulations-a ligand deletion followed by an insertion. By separating the work done during these two phases we should then be able to use those work values to alternatively estimate the relative free energies of the different binding modes using the Jazinski equality. The resulting free energies could provide a check of the binding mode populations during our BLUES simulations, potentially providing a way to recover correct populations from partial sampling.