Molecular Dynamics

Prof. Martin Zacharias

Research Field

The function of proteins and nucleic acids in living systems is strongly coupled to the molecular motion and dynamics of these biomolecules. Our group uses computer simulation methods to study the structure, function and dynamics of biomolecules. Our goal is to better understand structure formation processes and to elucidate the mechanism of ligand-receptor association in atomic detail. As the main computational technique we employ Molecular Dynamics simulations based on a classical force field to follow molecular motions including the surrounding solvent and ions. This allows us to extract thermodynamic and kinetic properties of the biomolecular system using methods of statistical mechanics. We also develop computational docking approaches to predict how proteins interact with other proteins or RNA and DNA molecules or how small drug-like compounds bind to biomolecular targets.


James-Franck-Str. 1
85748 Garching b. München
+49 89 289 12393
Fax: +49 89 289 12444

Members of the Research Group




Course with Participations of Group Members

Current and Finished Theses in the Group

Erforschung der DNA Hybridisierung
Abschlussarbeit im Bachelorstudiengang Physik
Themensteller(in): Martin Zacharias
Coarse-graining of non-equilibrum Systems
Abschlussarbeit im Masterstudiengang Physics (Applied and Engineering Physics)
Themensteller(in): Martin Zacharias
Studying biomolecular association using advanced sampling techniques
Abschlussarbeit im Masterstudiengang Physik (Biophysik)
Themensteller(in): Martin Zacharias
Study of the Role of Side Chain Mutations on the Receptor Proteins FKBP51/52 by Free Energy Molecular Dynamics Simulations.
Abschlussarbeit im Bachelorstudiengang Physik
Themensteller(in): Martin Zacharias


Biological systems, from proteins to living cells and organisms, obey physical principles. Our research groups in biophysics shape one of Germany's largest scientific clusters in this area.