For this MUP system, we checked the effects of varying threshold of energy, E cut , to send an MC try from a fast, coarse energy calculation to a slower, full pmemd calculation. The higher the value, more MC tries are sent to full pmemd calculation rather than being immediately rejected, and therefore the runtime is slower. Note that using a higher value can lead to an increase in the acceptance rate, but not a lower acceptance rate. This is because configurations that would otherwise have been rejected get a second chance to be accepted following a full energy calculation, as detailed in Section 4.2. We also investigated the effect of NMC on the results and timings for this system. Thus, the number of MD steps per cycle was held at 10 3 , while NMC was set to the following values: 10 3 , 10 4 , 2.5×10 4 , 5×10 , and 10 5 .