The central question of biophysics is how we get from physics – the interactions between molecules – to biological function. We will use rhodopsin, the mammalian dim-light receptor, as an example to explore this question via computer simulations. While we have a significant amount of structural information about rhodopsin, including crystal structures of both the inactive and active forms, the atomic-level fluctuations that control function are not well-understood. We have used molecular dynamics simulations to characterize the interplay between rhodopsin and the lipid membrane surrounding it as a means to understand the physics controlling the prevalence of the active and inactive states. More recently, we have collaborated with groups performing time-resolved X-ray scattering experiments using X-ray free electron lasers to characterize the early events following photon absorption. The key take-home is that structural diversity in the dark (inactive) state of the protein leads to a complex reaction to photon absorption in the nanoseconds immediately following. The same complexities are seen in the longer-timescale models of the inactive and active states.