This is an obvious question to ask, but the value of sitting down and staring at a structure is difficult to overestimate. Structure determination is clearly a critical step toward understanding biological function, but protein function requires motion.
Molecular dynamics is the link between structure and function.
We might, for example, wish to characterize the dependence of a protein's structure and dynamics on environmental conditions. We could perform simulations at different temperatures, different pressures, or different levels of hydration. We could approximate the solution environment by a periodically repeating system in which the repeating unit was a single protein in a box of water. Or the crystalline phase could be simulated as a special case of the periodic system with a particular box size and shape.