Chapter 2:Molecular Dynamics Computer Simulations of Biological Systems

In this chapter, we discuss the application of molecular dynamics computer simulation to investigate biological molecules. Starting with the basics of molecular dynamics we discuss state-of-the-art force fields for biomolecular simulations, advanced simulation techniques for enhanced sampling, computation of free energies, investigation of rare events, and quantification of elastic properties of biological membranes. A critical discussion of current opportunities in the development of integrated experimental and simulation approaches in the area of NMR and scattering techniques is provided. We close the chapter with an overview of future directions for biomolecular simulations, and how these directions can build on our current ability to perform very large simulations of, for example, organelles and viruses.