The goal of this short course is to provide an introduction to the theory and algorithms behind MD simulations, describe some of the most exciting recent developments in the field and exemplify with a few applications applications. The series also includes a tutorial on the nanoMATERIALS simulation tool, an online MD simulation tool available at the nanoHUB. This provides users with a hands-on experience with MD simulations and enables further exploration of some of the concepts described in the lectures.

This set of ten presentations accompanied a graduate level course on Molecular Dynamics simulation. The specific objective of the course (and the presentations) is to provide: 1. Awareness of the opportunities and limitations of Molecular Dynamics as a tool for scientific and engineering research 2. Understanding of the compromise between model complexity/realism and computational expense 3. Background that enables interpretation of Molecular Dynamics-based studies reported in the literature