A Properties of the Transfer operator

In this section, we outline the'relaxation' or'decay' of the spectral components of Each trajectory is simulated for 100000 steps. A separate testing set was generated in an identical manner but with a different random seed. The original data was obtained upon request from DE Shaw Research, and details about the simulations are available in the original publication [19]. Figures 8, 9 and 10, show conditional distributions generated by CG-SE3-ITO models and comparisons of MD with ITO simulations on the fast folders Trp-Cage, BBA, and Villin, respectively. Reference value and observables We compute observables using Markov state models.