For MD, we ran 20000 integration steps of MD during one iteration to mimic the number of NCMC energy evaluations per iteration. For MD with MC we ran 20000 integration steps followed by 10 MC random rigid body ligand rotations using the Metropolis criteria for each iteration. We ran each of these methods for 5000 iterations and then compared the trajectories and binding mode populations found in our NCMC simulation. The code used to perform these calculations can be found in the SI.