Welcome to the Lecture Wiki Methods of Molecular Simulation, SoSe 2014
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General
Lecture: Frank Noé, Petra Imhof, Nuria Plattner
Exercise: Christoph Wehmeyer
Language: English
Students: Bioinformatics Master
SWS: 2+1, LP/Credits:
Dates
| Lecture |
Thursday |
12-14 h |
Arnimallee 14 |
0.1.01 (HS B) |
First lecture:17 April |
| Exercise |
28-30 July |
9-15 h |
Arnimallee 14 |
1.3.21 (SR T1) |
|
Content
This lecture teaches classical (non-quantum-mechanical) modeling and computer simulation of macromolecules.
In more detail, it covers:
- Empirical energy function
- Exploring the energy function: minimization, finding saddle points, vibrational analysis
- Algorithms and data structures: periodic boundary conditions, cutoff, efficient neighbor search
- Long-ranged interactions: coulomb sum, convergence, Poisson equation, Ewald summation, Particle-Mesh methods
- Solvation methods: Explicit and implicit solvation
- Dynamics: Integrators, discretization errors
Literature