In case you have problems with registration contact katja.geiger[at]fu-berlin.de

Exercises/Lab work (bi-weekly!): Guillermo Pérez-Hernández

Language: English or German

SWS: 2+1; LP/Credits: tba

Students: MSc Physics, MSc Chemistry

Requirements:see below

Date | Time | Location | room | Lecturer | |
---|---|---|---|---|---|

Lecture | Wednesdays | 12-14h | Arnimallee 14 (Physics) | 1.1.53 (SR E2) | Wehmeyer, Pérez-Hernández |

Exercise | Wednesdays, bi-weekly! | 14-16h | Arnimallee 6 (Mathematics) | 030 | Wehmeyer, Pérez-Hernández |

First lecture Wednesday 15 October 2014; first exercise Wednesday 22 October 2014

Notions of molecular physical chemistry, thermodynamics and statistical mechanics will be reviewed. Given the short time frame, some concepts will be introduced without extensive explanation. At the end of the seminar, students should be familiar with the process of understanding, setting up, and analyzing MD simulations in a contemporary research environment.

- Introduction and Overview: distributions, phase-space, ensembles, Boltzmann, ergodicity (1-2 lectures)
- Review: Sampling the distribution (Metropolis Monte-Carlo,...) (1 lecture)
- Review: Mechanics. Equations of motion and their discrete integration (2 lectures)
- Review: Modelling intra- and inter-molecular interactions. Forcefields (2 lectures)
- In-depth: Speedup of non-bonded interactions. Neighbor lists, electrostatics, cutoff-schemes (2-3 lectures)
- In-depth: Thermostats and barostats (2 lectures)
- In-depth: Equilibrium, convergence, and sampling problems (1 lecture)
- In-depth: Free energy methods. extended ensembles, umbrella sampling... (2-3 lectures)
- Review: Analysis and interpretation (1 lecture)

- Students should have completed a course in statistical thermodynamics (Chemistry) or statistical physics (Physics) and be familiar with the following concepts: Boltzmann distribution, thermodynamic ensemble, random variables, expectation values.
- Preferably, students should also have attended one or more of the following lectures: Computational Molecular Physics, Methods of Molecular Simulation, Moleküldynamik auf dem Rechner, Computer simulation of biomolecules
- Basic coding skills in at least one of the following languages: Python, C, C++, Java, Matlab

Regular attendance is expected and will be monitored.

There will be an oral exam.

Name | Consultation Hour | |
---|---|---|

Guillermo Pérez-Hernández | appointment by email. Arnimallee 6, R214 | guille.perez[at]fu-berlin.de |

Christoph Wehmeyer | Tue 14-15h. Arnimallee 6, R212a | christoph.wehmeyer[at]fu-berlin.de |

This topic: CompMolBio > Lectures > MolecularModellingSimulation

Topic revision: 22 Jun 2015, KatjaGeiger

Topic revision: 22 Jun 2015, KatjaGeiger