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

Researchers should cite this work as follows:

• Ashlie Martini (2009), "Short Course on Molecular Dynamics Simulation," https://nanohub.org/resources/7570.

1. algorithms
2. material science
3. molecular dynamics
4. short course