Examples of recent macromolecular simulations will be presented which explore the relationship between modeled systems and real systems probed by experiment. In particular, data from neutron scattering, NMR, and crystallography can be compared and contrasted with corresponding results from molecular dynamics simulation. Also presented will be examples where simulation can provide insights that are difficult to obtain with experiment. There will be some discussion of recently developed methods that enhance our ability to accurately model interfacial systems and interactions between macromolecules. Also, protein conformational change and enzyme catalysis can be examined with a variety of methods. We present several methods, such as the Replica/Path method and extensions of the Nudged Elastic Band method, for examining such events and their application to interesting biological systems.