Overall, the average bootstrapped predictions of the model agree well with predictions from models constructed using the fully-sampled trajectory dataset. For example, our bootstrap analysis of 100-microstate MSMs suggests a large uncertainty (about an order of magnitude) for the slowest implied timescales of some force fields. In all cases, however, the timescales computed using all trajectory data (Figure ) are within the standard deviation computed from the bootstrap analysis. Bootstrap analysis for computed VAMP-2 scores and macrostate populations are further discussed in Results.