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Advanced Molecular Dynamics

Learning outcomes

After completion of this course, you should be able to:

  • Assess all factors that affect the accuracy of molecular dynamics simulations.
  • Understand the algorithms and computational cost of simulations on CPUs and GPUs.
  • Assess the quality of sampling and methods to improve sampling.


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.

Course objectives

When you have finished the course, you will have acquired the following skills:

  • Set up simulations of liquids, polymers and proteins.
  • Analyze structural and dynamical properties.
  • Determine the quality of sampling and choose methods to improve sampling.
  • Set up free energy calculations.
  • Apply systematic coarse-graining.


Basic knowledge of molecular dynamics and statistical mechanics/thermodynamics.


D. Frenkel & B. Smit, Understanding Molecular Simulation, Elsevier, ISBN: 978-0-12-267351-1

Selected articles

Complementary literature

H.J.C. Berendsen, Simulating the Physical World, Cambridge University Press, ISBN: 9780521835275

Course schedule

1 week pre-study exercises 5-8 May 2014
1 week lectures and hands-on 12-16 May 2014 at KTH Royal Institute of Technology
1 week project assignment 19-23 May 2014


  • Berk Hess(hess at kth.se)


Please register here before 28 of April. Indicate also if you apply for a travel grant.