As we found with AMBER14SB, a potential pitfall of using VAMP in this way is that highly time-correlated features can identified as the most important degrees of freedom, when in actuality such features correspond to rare, low-probability and force-field dependent events. For our analysis of AMBER14SB trajectory data, human intervention was required to determine that the slowest motions corresponded to the rare formation of a 2:2 turn, a more typical conformational motion for other force fields. There are several ways to circumvent such pitfalls, such as implementing more robust cross-validation schemes, or label-free modelbuilding (i.e. building MSMs from the joint set of trajectory data regardless of force field).