We currently alleviate this sampling problem by doing two independent ABFE calculations for the same docked pose and keeping the more favorable of the two resulting BFEs, since the tightestbinding post-equilibration pose is the more stable one and hence presumably more realistic. Additional independent runs would further increase the possibility of including the best post-equilibration ligand conformation, but this would come at a cost of lower computation throughput. One might expect that initiating ABFE calculations directly from docked poses -i.e., skipping the MD equilibration step -would solve this problem, but in practice it led to worse AUC statistics when we tried it. This may result from incompatibility between the simplifications made in docking and the more detailed description used in explicit-solvent MD simulations, or from differences between the OPLS2005 ligand force field used in Glide docking and the GAFF ligand force field used in the MD simulations.A more effective approach might be to devise a fast method of estimating the relative stabilities of multiple poses discovered during the MD equilibration stage.