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Welcome to the Lecture Wiki Methods of Molecular Simulation, SoSe 2014

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Lecture: Frank Noé, Petra Imhof, Nuria Plattner
Exercise: Christoph Wehmeyer
Language: English
Students: Bioinformatics Master
SWS: 2+1, LP/Credits:


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)  


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


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