Molecular Dynamics Simulations in Biophysics

Bad Honnef Physics School

So, 26.04.2020 18:30  –   Fr, 01.05.2020 14:00
Physikzentrum Bad Honnef
Hauptstr. 5, Hauptstr. 5, 53604 Bad Honnef, Germany

Dr. Victor Gomer (Physikzentrum Bad Honnef),


Scientific organizers:
Prof. Dominik Horinek (University of Regensburg), Prof. Martin Zacharias (TU Munich)

April 26 - May 1, 2020, Physikzentrum Bad Honnef, Germany
supported by




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.

Confirmed Speakers/ Topics:

  • Frauke Gräter (HITS Heidelberg, Germany): Multi-Scale Simulations and force distribution analysis
  • Helmut Grubmüller (MPI Göttingen, Germany): Simulations studies on molecular machines
  • Dominik Horinek (University of Regensburg, Germany): Free energy simulations
  • Petra Imhof (University of Stavanger, Norway): Simulation studies on systems containing RNA and DNA
  • Pavel Jungwirth (Charles University, Prague, Czech Republic): Charge scaling methods and applications
  • Bettina Keller (FU-Berlin, Germany): Extracting kinetics form enhanced sampling and Markov models
  • Roland Netz (FU-Berlin, Germany): Non-Markovian simulation of equilibrium and non-equilibrium systems
  • Chris Oostenbrink (BOKU, Vienna, Austra): Alchemical Transformations
  • Lars Schäfer (University of Bochum, Germany): Membrane and membrane protein systems
  • Gerhard Stock (University of Freiburg, Germany): Collective motions and Markov Modeling of simulation data
  • Nico van der Vegt (TU Darmstadt, Germany): Macromolecular solvation
  • Martin Zacharias (TU Munich, Germany): Molecular Dynamics /Advanced Sampling. Protein/peptide Simulations.

FEES: 200 € full board and lodging (for DPG* members 100 € )
* The German Physical Society (DPG)

⇒ Schedule
⇒ Poster
⇒ List of confirmed participants