CM-B-3 Biomolecular Modelling (Lecture + computer lab + project lab)

Course content

Intended learning outcomes:
The students are familiar with modern methods for modelling the structure of biomacromolecules and for simulating their thermodynamic properties. The know empirical force field methods, methods for performing molecular dynamics simulations, as well as modern multicale simulation methods. The students are able to judge the applicability and the limitations of such methods, to choose suitable simulation methods for their own research projects and to perform, analyze, and evaluate molecular dynamics simulations.

Course content:
Lecture: Introduction to the basics of simulations of biomacromolecules - Born-Oppenheimer approximation, potential energy surface, basics of statistical thermodynamics, empirical force fields and their efficient implementation - geometry optimization, molecular dynamics methods, thermodynamic and static description of (bio)chemical processes, analysis of molecular dynamics simulations, calculation of free energies, multiscale simulation methods - implicit solvent models, coarse-grained models, hybrid QM/MM methods, quantum-chemical embedding methods.
Computer Lab: Use of force field programs, visualization of crystal structures, geometry optimization, molecular dynamics and normal mode analysis of polypeptides, simulation of (bio)molecules with different computational methods and their analysis, analysis of dynamical and entropic effects.
Project Lab: Molecular Dynamics Simulations of Biomolecules.