Hamiltonian Molecular Dynamics for Computational Mechanicians and Numerical Analysts

Molecular dynamics (MD) is a computer simulation technique where the time evolution of a set of interacting atoms is approximated by integrating their equations of motion. Our goal is to explain the mathematical background of MD for practitioners and researchers in numerical analysis and computational mechanics. The vast majority of these practitioners and researchers work with continuum mechanics. In contrast, an atomistic method such as MD is both culturally and intellectually distinct. The recent interest in multiscale analysis, in particular, Atomisticto-Continuum coupling necessitates a sophisticated understanding of MD, its goals, limitations and computational aspects.