Short Course on Molecular Dynamics Simulation
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Abstract
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
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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) |