Here, we combine standard MD and well-tempered metadynamics (WT-MetaD) simulations to investigate at the atomistic level the thermodynamic and kinetic behavior of four [2]rotaxanes, used as representative examples and covering different features and architectures in the framework of MIMs. With our in silico approach, we obtain a detailed insight into the thermodynamics of these systems, obtaining results that are consistent with the experimental evidence. We reconstruct the thermodynamics and kinetics of these innately dynamic systems. A decomposition of the free-energy profiles into the enthalpic and entropic components provides detailed insights and an atomistic comprehension of the key mechanisms controlling the intrinsic dynamic behavior of such systems. The computational framework described herein is general and may open the way toward obtaining direct structure-dynamics relationships for a variety of mechanically interlocked molecular systems.