This EMBnet-funded course focused on molecular dynamics (MD) simulation methods in studying large biomolecules. Lectures covered both overall methods and more detailed theoretical background of MD simulations of biomolecules. The lectures were given by Prof. H.J.C. Berendsen (University of Groningen, Netherlands) and Dr André Juffer (University of Oulu). Exercises focused on advanced MD simulations using the program package Gromacs 3.2. The instructor for the exercises was Dr David van der Spoel (Uppsala University, Sweden), one of the main developers of Gromacs.
Protein-membrane association. Theoretical model, Lekner summation
Beyond MD: Stochastic methods. Mesoscopic approaches
pKa calculations - methods and applications
Electrostatic interactions; continuum methods
Free energy calculations. Analysis of simulation results
Molecular Dynamics simulations. Methods and applications
Introduction to Modelling. From quantum to classical mechanics