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