Molecular dynamics is a powerful tool to investigate the structure and dynamics of biologically relevant molecules such as proteins, DNA and lipids in atomistic detail. The insight from MD simulation yields quantitative predictions and a ‘molecular movie’ of important processes that helps experimentalists interpret their results. Such simulations can also be used to predict effects of e.g. point mutations. This course provides an introduction to biomolecular simulation using molecular dynamics, and enhanced sampling methodology to study biomolecular processes.
This course consists of lectures which will cover the following topics: 1) the basics of molecular dynamics, 2) the structural analysis of biomolecules, e.g. through NMR and crystallography, 3) multiscale modeling of biomolecular systems 4) the problem of rare events in conformational changes.
In addition to the lectures there will be tutorial sessions consisting of computer problems. Throughout the course the students will work on a project, during which they will use molecular simulation methods to investigate a realistic biomolecular system.