The course will explore physical models and computational approaches used for the simulations of macromolecular systems. A mixture of lectures and hands-on tutorials will serve to provide a roadmap for setting investigations of macro-molecular structure and dynamics at the atomic level of detail. The course is based on practical exercises with the biophysical programs NAMD and VMD. In particular, the case studies of various biological systems will be discussed. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling and molecular dynamics on parallel computers