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Advanced Molecular Dynamics, 5 credits

Intended learning outcomes

After completion of the course, the student should be able to:

  • set up simulations of liquids, polymers and proteins
  • analyze structural and dynamic properties
  • assess the quality of sampling and be aware of methods to improve sampling
  • set up free energy calculations
  • apply systematic coarse-graining

Course main content

This course treats advanced molecular dynamics (MD) methodology for classical simulations of liquids, polymers and proteins. MD simulations provide atomistically detailed information on structural and dynamic quantities, but often at a high computational cost. As vibrations of atoms need to be captured, time steps are in the order of femtoseconds, whereas the time scales of interest are often in the microsecond to second range. This has three main implications. Efficient software and hardware is required, using for instance stream computing (on e.g. GPUs). You always need to carefully check the convergence of properties of interest. And if convergence can not be reached, you might need to use methods to improve sampling, such as free energy calculations and coarse-graining. These topic will be covered in lectures, reading of literature and computer labs.


  • Basic knowledge of statistical mechanics / thermodynamics

(the course includes a brief introduction to Molecular Dynamics and force fields)


  • D. Frenkel & B. Smit, Understanding Molecular Simulation
  • H.J.C. Berendsen, Simulating the Physical World
  • Selected articles


Requirements for final grade

  • Computer Labs using the Gromacs simulation package
  • Presentation of projects which can be adapted to the particular interests of students

Offered by

SCI/Applied Physics


Berk Hess


Berk Hess <hess@kth.se>


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