Determining optimal numbers of MSM microstates to describe chignolin dynamics. To determine the optimal number of MSM microstates used in our force field comparisons, we constructed a series of models (using inverse distance featurization) with various numbers of microstates, and for each calculated the average and standard deviation of the VAMP-2 score over 50 iterations (Figure ). For all force fields, the general trend is that average VAMP-2 scores plateau above 50 microstates. Additionally, the standard deviations are large enough to suggest little difference in models above 50 microstates. Coarse-grained MSM state assignments were also not impacted by the number of microstates (Figure . For consistency in our force field comparison studies, we chose to construct all MSMs using 100 microstates for all force fields.