Simulation Methods in Physics II SS 2012

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Lecture (2 SWS) and Tutorials (2 SWS)
Prof. Dr. Christian Holm, (Lecture); Peter Košovan, Florian Dommert, Georg Rempfer, Tobias Richter (Tutorials)
Course language
Time: Thursdays, 11:30 - 13:00, Room V 57.06
Time: Wednesday, 14:00-15.30, 2 hours, Room U 104

The lecture is accompanied by hands-on-tutorials which will take place in the CIP-Pool of the ICP, Pfaffenwaldring 27, U 104. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis. The tutorials build on each other, therefore continuous attendance is expected.


The course intends to give an overview about modern simulation methods used in physics today. The stress of the lecture will be to introduce different approaches to simulate a problem, hence we will not go too to deep into specific details but rather try to cover a broad range of methods. For an idea about the content look at the lecture schedule.


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++). The knowledge of the previous course Simulation Methods I is expected.

Certificate Requirements

1. Attendance of the exercise classes
2. Obtaining 50% of the possible marks in the hand-in exercises

There will be a final grade for the Module "Simulation Methods" (this module consists of both lectures, Sim I plus Sim II) determined at the end of lecture Simulation Methods II.

The final grade will be determined in the following way: There will be an oral examination performed at (or after) the end of the course Simulation Methods II (SS 2011).

Recommended literature

Useful online resources

  • Linux cheat sheet application_pdf.pnghere (53 KB)Info circle.png.
  • Be careful when using Wikipedia as a resource. It may contain a lot of useful information, but also a lot of nonsense, because anyone can write it.


To access lecture notes from outside the University or VPN, use the password which you obtained last semester. If you do not know it, ask the tutor or your friends in the course.

Date Subject Ressources
12.04.2012 Ab initio methods, Quantum mechanics,Hartree-Fock, Density functional theory Lecture Notes
19.04.2012 Classical force fields, Atomistic simulations, Biomolecules

Lecture Notes Graphic

26.04.2012 Water models, Born model of solvation Lecture Notes
03.05.2012 Coarse-grained models, simulations of macromolecules and soft matter Lecture Notes
10.05.2012 Long range interactions in periodic boundary conditions Lecture Notes
17.05.2012 Holiday (Christi Himmelfahrt)
24.05.2012 Long range interactions in periodic boundary conditions, Further reading
31.05.2012 Holiday (Pfingsten)
07.06.2012 Holiday (Fronleichnam)
14.06.2012 Poisson-Boltzmann theory, charged polymers Lecture Notes Presentation slides
21.06.2012 Hydrodynamic methods: Lattice-Boltzmann, Brownian Dynamics, DPD, SRD Lecture Notes
28.06.2012 Hydrodynamic methods II
05.07.2012 Advanced MC/MD methods Lecture Notes
12.07.2012 Free energy methods I Lecture Notes
19.07.2012 Free energy methods II Lecture Notes


Scheduling of tutorials
New worksheets are handed out every two weeks (see the list below). The following week is dedicated to working on problems related to the last worksheet. Homework in the form of a report should be sent to the tutors before the next worksheet is handed out. The two-week cycle ends with the discussion of results of the previous worksheet and handing out a new one.
Please send the report to the responsible person indicated with the given tutorial.
In general, it should be the same person who handed out the tutorial. The name and e-mail in the worksheet are those of the worksheet author, not the responsible tutor!

Tutorial 1 - Error analysis and correlations

Tutorial 2 - GROMACS

Tutorial 3 - ESPResSo: Simulation of a coarse-grained polymer

Tutorial 4 - ESPResSo: Simulation of a charged rod with counterions

Tutorial 5 - ESPResSo: Lattice-Boltzmann fluid

Tutorial 6 - Advanced MC/MD

  • Handed out on 4.7.2012, continued on 11.7.2012
  • Send reports to Tobias Richter

Tutorial 7 - Closing ceremony

  • 18.7.2011
  • Discussion of the last tutorial
  • Evaluation and discussion of the whole course
  • In case of interest, we may go out together after the end of the tutorial

Tutorials in 2012 are mostly based on the ones from previous year. Updated worksheets will be made available online on the day when they should be handed out. If you want to take a look ahead and see what is coming, have a look at the worksheets from the previous year.

Obtaining extra points
The first person who identifies a bug in the code provided by the tutors gets an extra point and one additional extra point if he/she can fix the bug. The same applies to finding a mistake in the worksheets which significantly changes the meaning. We are also thankful for pointing out misprints, but these are not awarded extra points.
Guidelines for submitting tutorial reports
Same as as in the previous semester.