FSK3523 Advanced Molecular Dynamics 5.0 credits

Avancerad molekyldynamik

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Course information

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

Course Disposition

Pre-study on basic of molecular dynamics, if required.

Full week of lectures and computer exercises.

Individual project, ideally based on your own research topic.

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)

Equipment

Access to a laptop or computer

Literature

D. Frenkel & B. Smit, Understanding Molecular Simulation

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

Selected articles

Examination and completion

Grading scale *

P, F

Examination *

  • 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

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Opportunity to raise an approved grade via renewed examination

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Examiner

Berk Hess

Further information

Course web

Further information about the course can be found on the Course web at the link below. Information on the Course web will later be moved to this site.

Course web FSK3523

Offered by

SCI/Applied Physics

Main field of study *

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Education cycle *

Third cycle

Add-on studies

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Contact

Berk Hess (hess@kth.se)

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.

Postgraduate course

Postgraduate courses at SCI/Applied Physics