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Table of contents
- Parameterization of force fields
- Classical molecular dynamics: Algorithms, starting conditions, boundary conditions, correlation functions, ...
- Description of the molecular surrounding: QM/MM
- On-the-fly dynamics
- Combined Marcus-Smoluchowski model for the microscopic description of electron transfer
Hands-on Sessions:
- MM calculations with standard program packages
- Introduction to MatLab
- Practical implementation of the classical dynamics of a Lennard-Jones-Fluid
Recommended Textbooks:
- D. Frenkel, B. Smit, Understanding Molecular Simulation - From Algorithms to Applications,
Academic Press (2002), ISBN 0-12-267351-4.
- A. R. Leach, Molecular Modelling - Principles and Applications,
Prentice Hall (2001), ISBN 0-582-38210-6.
- M. Griebel, S. Knapek, G. Zumbusch, A. Caglar, Numerische Simulationen in der Moleküldynamik,
Springer (2004), ISBN 3-540-41856-3.
- T. Schlick, Molecular Modeling and Simulation - An Interdisciplinary Guide,
Academic Press (2002), ISBN 0-387-95404-X.
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