FSI3450 Advanced Molecular Dynamics 7.5 credits
This course has been discontinued.
Last planned examination: Spring 2021
Decision to discontinue this course:
No information inserted
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 topic 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:
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set up simulations of liquids, polymers and proteins
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analyze structural and dynamic properties
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assess the quality of sampling and be aware of methods to improve sampling
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set up free energy calculations
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apply systematic coarse-graining
Literature and preparations
Specific prerequisites
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Basic knowledge of statistical mechanics / thermodynamics
(the course includes a brief introduction to Molecular Dynamics and force fields)
Recommended prerequisites
Equipment
Literature
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D. Frenkel & B. Smit, Understanding Molecular Simulation
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H.J.C. Berendsen, Simulating the Physical World
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Selected articles
Examination and completion
If the course is discontinued, students may request to be examined during the following two academic years.
Grading scale
Examination
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.
Other requirements for final grade
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Computer Labs using the Gromacs simulation package
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Presentation of projects which can be adapted to the particular interests of students
Opportunity to complete the requirements via supplementary examination
Opportunity to raise an approved grade via renewed examination
Examiner
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.