Short Course on Molecular Dynamics Simulation

By Ashlie Martini

University of California, Merced



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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,"

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Lecture Number/Topic Online Lecture Video Lecture Notes Supplemental Material Suggested Exercises
Lecture 1: Basic Concepts Notes (pdf)
Lecture 2: Potential Energy Functions Notes (pdf)
Lecture 3: Integration Algorithms Notes (pdf)
Lecture 4: Temperature Control Notes (pdf)
Lecture 5: Boundary Conditions Notes (pdf)
Lecture 6: Neighbor Lists Notes (pdf)
Lecture 7: Initialization and Equilibrium Notes (pdf)
Lecture 8: Static Properties Notes (pdf)
Lecture 9: Dynamic Properties Notes (pdf)
Lecture 10: Non Equilibrium MD Notes (pdf)