Summary
Transition matrices between metastable states can accurately approximate a protein’s kinetics if the lag time used to build those matrices exceeds the relaxation time within those states (1). This informs the lag time used when running tICA and building Markov state models. A concrete test that can be run is the Chapman-Kolmogorov test.
1.
Zwanzig R. From classical dynamics to continuous time random walks. Journal of Statistical Physics. 1983;30(2):255–62. Available from: https://doi.org/10.1007/bf01012300