The dynamics of biomolecules on the ps-μs timescales can be directly probed by neutron scattering experiments. However, in complex systems many of the underlying dynamical processes may exist on similar timescales, which makes it difficult to assign processes seen experimentally to specific structural rearrangements. In this talk I show how Markov models and can be used to connect structural changes observed in the molecular dynamics simulation directly to the relaxation processes probed by neutron scattering experiments. The talk covers the required mathematical framework and illustrates the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. The result is a 9-state MSM in the space of the backbone dihedral angles and the side- chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.