53363 Molecular Dynamics Simulations (10 ECTS) autumn 2013

The exam takes place on Wednesday, 11.12. from 10:00 to 14:00 in Physicum D106!

This course is a 10 ECTS credit points course on atomistic simulations. We will concentrate on molecular dynamics simulations (MD) which enable following the evolution of a system of point-like objects over time. During the course, students will write in a supervised manner their own MD code which can be used to model atomic motion in simple metals. Simulations of fluids will be performed with the GROMACS code. The course will also cover some energy minimization methods as well as the nudged elastic band (NEB) method for migration energy barrier calculations. Quantum mechanical and classical atomic interaction models will be covered, main stress being on classical methods. Visualization and analysis methods of atomic data are also discussed. Some knowledge of programming will be immensely helpful during the course, preferably in Unix/Linux environment. In addition, the students should have the basic knowledge of thermodynamics and statistical physics. The course is a part of the MoMoNano Master's programme.

The exam takes place on Wednesday, 11.12. from 10:00 to 14:00 in Physicum D106!

General information



Please give anonymous feedback for the first 6 weeks of the course here . For our improvement it is vital to get your comments. This query was also prepared to be very short to not take much of your time.

Due to feedback already obtained, some sample input files for excercise 6 were added. Thanks to those who already gave feedback!


15 minutes in the beginning of the lecture. Please be there around 10.00 so we have time to set things up.
If you do not still have time or title (and will give a talk instead of an essay), contact Johannes. We can figure out more works.

date name topic
18.09. Junlei MD simulations on Ag induced crystallization in Si Nanoclusters
25.09. Morten TBA (own research)
02.10. - -
09.10. Bartosz MD of biomolecules
16.10. Fabian MD for protein folding
23.10. mid-term break no lecture
30.10. Mehdi MC simulation of binary gas flow
06.11. Ville TBA (own research)
13.11. Ekaterina MD for large systems
20.11. Roope Early MD
27.11. Hakan MD using quaternions

Additional material

The lectures do not follow any particular book. However, there exists several books on molecular dynamics. For example, the following might be interesting: Also, around the internet there exists several lecture notes from other molecular dynamics courses. For example: Fast, flexible and free molecular dynamics simulation code GROMACS can be found and downloaded from here. If you happen to be using Ubuntu, GROMACS can even be installed directly from the Ubuntu Software Centre. Unlike many other simulation software, GROMACS comes with a great manual!