Difference between revisions of "Simulation Techniques for Soft Matter Sciences (SS 2008)"

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! 5.6.
| /ESPResSo|Introduction to MD simulations with ESPResSo
| /ESPResSo|Introduction to MD simulations with ESPResSo
{{Download|espresso_tutorial_summer_2008.tar‎|Handout and sources|tar.bz2}}
{{Download|espresso_tutorial_summer_2008.tar‎|Handout and sources|tar}}
| [[Mehmet Süzen]]
| [[Mehmet Süzen]]

Revision as of 10:42, 16 June 2008


Lecture (2 SWS) and Tutorials (2 SWS)
PD Dr. Christian Holm (Lecture) and working group (Tutorials)
Course language
Time and Room
Lecture: Thu special appointment, FIAS Room 200
Tutorials: Thu 16:00-18:00, Phys 1.120

Soft matter science is the science of "soft" materials, like polymers, liquid crystals, colloidal suspensions, ionic solutions, hydrogels and most biological matter. The phenomena that define the properties of these materials occur on mesoscopic length and time scales, where thermal fluctuations play a major role. These scales are hard to tackle both experimentally and theoretically. Instead, computer simulations and other computational techniques play a major role.

The course will give an introduction to the computational tools that are used in soft matter science, like Monte-Carlo (MC) and Molecular dynamics (MD) simulations (on- and off-lattice) and Poisson-Boltzmann theory (and extensions).


The course is intended for participants in the Master Program "Computational Science", but should also be useful for FIGSS students and for other interested science students.

We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, electrodynamics, and partial differential equations, as well as knowledge of a programming language (preferably C or C++).

Lecture and tutorials

The lecture is accompanied by hands-on-tutorials which will be held in the computer room (Physics, 1.120). They consist of practical excercises at the computer, like small programming tasks, simulations, visualisation and data analysis.

The tutorials build on each other, therefore continous attendance is expected.

The dates of the tutorials will be scheduled in the first lecture.


Date Subject
10.4. Monte-Carlo integration/simulation (Simple vs. Importance sampling)

Look at Zuse's Z3 computer from 1941: Z3 and read something about the first big US computer at Los Alamos Evolving from Calculators to Computers

17.4. 2D Random walks (RW) and Self-avoiding random walks (SAW)--Ising model I (Phase transitions, Critical phenomena, Finite size scaling)
24.4. 2D Ising model II (Reweighting, Cluster Algorithm)
1.5. Holiday
08.5. Error Analysis (Binning, Jackknife, ...)

15.5. Molecular Dynamics I (Velocity Verlet algorithm, Reduced units, Langevin thermostat, Potentials, Forces, Atomistic force fields)
22.5. Holiday
29.5. Molecular Dynamics II

5.6. Long range interactions (Direct sum, Ewald summation, P3M, Fast Multipole method)

This pdf file application_pdf.pnglong_range_lecture.pdf (216 KB)Info circle.png contains surely too many details, but I will walk you through in class. In case you like to have some more background material, here is a review article by A. Arnold and me about this topic (arnold05a.pdf (file does not exist!))

12.6. Continuation of long range lecture, beginning of How to simulate Polymers and Polyelectrolytes.
19.6. Continuation on How to simulate Polymers and Polyelectrolytes and background of Poisson-Boltzmann Theory.
26.6. Introduction to the Project work: charged infinite rods in ionic solution-comparison to PB theory. application_pdf.pngCompMethods.pdf (1.65 MB)Info circle.png

A good background reading is the thesis of M. Deserno application_pdf.pngthesis_deserno.pdf (3.57 MB)Info circle.png

03.7. Extended tutorial: project work
July. Oral examination in my office FIAS 02.301, date to be fixed .


Materials on the tutorials will be sent to students by tutors via mail!

Date Subject Tutors
17.4. Introductory tutorial, random walks Nadezhda Gribova
24.4. Monte Carlo: The Ising model I Marcello Sega
1.5. Holiday
8.5. Monte Carlo: The Ising model II Marcello Sega
15.5. Error analysis Joan Josep Cerdà
22.5. Holiday
29.5. Molecular Dynamics: tar.pngLennard-Jones liquid (687 KB)Info circle.png Florian Dommert
5.6. Introduction to MD simulations with ESPResSo

tar.pngHandout and sources (360 KB)Info circle.png

Mehmet Süzen
12.6. Long range interactions: Direct sum and Ewald summation: tar.pngLong range interactions (40 KB)Info circle.png Kai Grass

19.6. Simulation of polymers and polyeletrolytes; Project work Mehmet Süzen
26.6. Visualisation of MD simulations with VMD Olaf Lenz

Recommended literature