Molecular Dynamics Methods for Modeling Complex Interactions in Biomaterials

The molecular dynamics method is a powerful computer simulation technique which provides access to the detailed time evolution (trajectory) of a system in specified conditions, such as a particular temperature or pressure. The full trajectory of the system can be analyzed using statistical mechanics tools to obtain thermodynamical quantities and dynamical properties; the mechanism of chemical reactions and other time-dependent processes, such as diffusion, can also be revealed in high detail. When applied to model extended and complex system such as biomaterials, MD simulations represent an invaluable tool to discover structure–activity relationships and rationalize biomedical applications.