Course overview
Tentitative schedule
May 9, 9:00-11:30: Introduction + integrator exercise
May 9, 13:30-16:00: Force fields
May 10, 9:00-11:30: Tentative: Non-bonded interactions, ensembles
May 10, 13:30-16:00: Tentative: ensembles, water exercise
May 11, 9:00-11:30: Complex models, sampling
May 11, 13:30-16:00: Sampling, free energies
May 12, 9:00-11:30: Hybrid CPU/GPU acceleration & paralllelization (Szilard Pall) + exersize
May 12, 13:30-16:00: Hybrid CPU/GPU acceleration & paralllelization (Szilard Pall) + exersize
May 16, 9:00-11:30: Free-energy exercise
May 16, 13:30-16:00: Systematic coarse graining
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 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.
Eligibility
- Basic knowledge of statistical mechanics / thermodynamics
(the course includes a brief introduction to Molecular Dynamics and force fields)
Literature
- D. Frenkel & B. Smit, Understanding Molecular Simulation
- H.J.C. Berendsen, Simulating the Physical World
- Selected articles
Examination
Based on a project using at least one advanced MD technique. You can choose the project, but your plan needs to be approved by the examiner. There is no deadline for handing in the project report, but I would advise not waiting more than a month, otherwise it might never happen.
Requirements for final grade
- Computer Labs using the Gromacs simulation package
- A report on your final project (of sufficient quality)
Offered by
SCI/Applied Physics
Contact
For information and registration, contact Berk Hess <hess@kth.se>
Examiner
Berk Hess <hess@kth.se>