Molecular dynamics simulation is a widely used tool for exploring properties of biomolecules. However, there are many challenges to overcome before its full potential can be realized. One prominent example is the notorious time scale gap: biologically relevant molecular processes take place in milliseconds to seconds while molecular dynamics simulations are currently limited to nanoseconds to microseconds. Recently, researchers have started using Markov models to extract long time dynamics from short trajectories and thereby bridge the time scale gap. I will lay out the basic theory of Markov models, and present my work in which I applied Markov models to folding and misfolding of the collagen triple helix in an effort to understand the molecular mechanism of genetic diseases such as osteogenesis imperfecta (brittle bone disease).