SI3450 Advanced Molecular Dynamics 7.5 credits
Educational levelThird cycle
Academic level (A-D)D
At present this course is not scheduled to be offered.
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 main content
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.
Basic knowledge of statistical mechanics / thermodynamics
(the course includes a brief introduction to Molecular Dynamics and force fields)
D. Frenkel & B. Smit, Understanding Molecular Simulation
H.J.C. Berendsen, Simulating the Physical World
Requirements for final grade
Computer Labs using the Gromacs simulation package
Presentation of projects which can be adapted to the particular interests of students
Berk Hess <firstname.lastname@example.org>
Course plan valid from: Autumn 11.