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
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
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
Examination and completion
If the course is discontinued, students may request to be examined during the following two academic years.
Grading scale *
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