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FSK3523 Advanced Molecular Dynamics 5.0 credits

Course offerings are missing for current or upcoming semesters.
Headings with content from the Course syllabus FSK3523 (Autumn 2018–) are denoted with an asterisk ( )

Content and learning outcomes

Course contents

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 topics will be covered in lectures, reading of literature and computer labs.

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

Literature and preparations

Specific prerequisites

Admitted as a PhD student

Recommended prerequisites

Basic knowledge of molecules and statistical mechanics / thermodynamics

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


Access to a laptop or computer


D. Frenkel & B. Smit, Understanding Molecular Simulation

H.J.C. Berendsen, Simulating the Physical World

Selected articles

Examination and completion

If the course is discontinued, students may request to be examined during the following two academic years.

Grading scale

P, F


  • PRO1 - Project Work, 5.0 credits, grading scale: P, F

Based on recommendation from KTH’s coordinator for disabilities, the examiner will decide how to adapt an examination for students with documented disability.

The examiner may apply another examination format when re-examining individual students.

Opportunity to complete the requirements via supplementary examination

No information inserted

Opportunity to raise an approved grade via renewed examination

No information inserted


Ethical approach

  • All members of a group are responsible for the group's work.
  • In any assessment, every student shall honestly disclose any help received and sources used.
  • In an oral assessment, every student shall be able to present and answer questions about the entire assignment and solution.

Further information

Course room in Canvas

Registered students find further information about the implementation of the course in the course room in Canvas. A link to the course room can be found under the tab Studies in the Personal menu at the start of the course.

Offered by

Main field of study

This course does not belong to any Main field of study.

Education cycle

Third cycle

Add-on studies

No information inserted


Berk Hess (

Postgraduate course

Postgraduate courses at SCI/Applied Physics