Molecular Dynamics Simulations in Biophysics

Bad Honnef Physics School

26 Apr - 01 May 2020


Physikzentrum Bad Honnef

Scientific organizers:

Prof. Dr. Dominik Horinek, University of Regensburg • Prof. Dr. Martin Zacharias, TU Munich


Molecular Dynamics (MD) simulations have become a powerful tool in modern biomolecular science. During MD simulations one can follow the motion of a molecule or an ensemble of molecules comprising up to millions of atoms at atomic resolution and at femtosecond time resolution. While the trajectory itself gives already valuable insight into atom-scale structure and motion, the full potential of MD lies in the link between this information and experimental properties: with the help of statistical mechanics it is possible to extract a variety of thermodynamic and kinetic properties of a molecular system. A major focus will be on efficient methods to extract thermodynamic quantities such as solvation properties and free energies from simulations. Advanced techniques such as multi-scale methods and combinations of classical molecular mechanics combined with quantum mechanical approaches will also be covered. The computational methods will be reviewed and illustrated on several examples of different complexity and further evaluated in Discussion sessions. Basic knowledge of theoretical and statistical mechanics is expected. Participants are invited to present posters or to give short talks in extra sessions.