Using MD/NCMC, we were able to sample multiple binding modes of different kinase inhibitors and obtain correct occupancy ratio for the binding modes. The observed transition rates were much faster than standard MD and umbrella sampling. We also found that 'flip' moves, where we propose large moves or close to 180 • random rotations of rotatable bonds, was about two times more efficient than random torsional moves where any degree of rotation can be proposed. Thus, MD/NCMC has the potential to be a more general and efficient tool for sampling multiple binding modes of flexible ligands.