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Short Course on Molecular Dynamics Simulation

By Ashlie Martini

University of California, Merced



Published on


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

Cite this work

Researchers should cite this work as follows:

  • Ashlie Martini (2009), "Short Course on Molecular Dynamics Simulation,"

    BibTex | EndNote


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Lecture Number/Topic Online Lecture Video Lecture Notes Supplemental Material Suggested Exercises
Lecture 1: Basic Concepts Notes
Lecture 2: Potential Energy Functions Notes
Lecture 3: Integration Algorithms Notes
Lecture 4: Temperature Control Notes
Lecture 5: Boundary Conditions Notes
Lecture 6: Neighbor Lists Notes
Lecture 7: Initialization and Equilibrium Notes
Lecture 8: Static Properties Notes
Lecture 9: Dynamic Properties Notes
Lecture 10: Non Equilibrium MD Notes, a resource for nanoscience and nanotechnology, is supported by the National Science Foundation and other funding agencies. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.