For WESTPA to facilitate the key conformational transitions, progress coordinates must be defined that clearly distinguish the slowly interconverting states. We chose two-dimensional progress coordinates -a rotor-stator rotation angle (17-18-2-1) and the stator pucker -that clearly distinguish among the slowly interconverting metastable substates MS1, MS2, and MS3/MS4, as well as the stable form, as shown in Fig 10 . WESTPA calculations were run for both Motor S and Motor N, using the same starting points as their respective plain classical MD simulations (Section 3. In experimental studies, increasing the solvent viscosity significantly decreased the THI rate constant . Our simulations reproduced this trend (Fig ) by comparing THI rate constants from simulations using different Langevin collision frequencies, as the largest collision frequency, 10/ps, which simulates the largest effective viscosity, resulted in a smaller THI rate constant than 1/ps and 0.1/ps. The smallest collision frequency, 0.01/ps, also appears to decrease the THI rate, in agreement with a prior study about how collision frequency influences conformational sampling of a peptide . Overall, however, the computed THI rate constant is not very sensitive to the somewhat arbitrary choice of collision frequency.