Non-resident students please contact katja.geiger[at]fu-berlin.de to register.

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) | 017 | Wehmeyer, Pérez-Hernández |

First lecture 14.10.2015; first exercise 21.10.2015

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 (1, GPH)
- Review: Sampling the distribution/ensemble:
- Metropolis Monte-Carlo [integrate over configuration space] (1, CW)
- Discrete integration [integrate equations of motion] (2, CW)

- Review: Modelling intra- and inter-molecular interactions. Forcefields (2, GPH)
- In-depth: Speedup of non-bonded interactions. Neighbor lists, electrostatics, cutoff-schemes (2, GPH)
- In-depth: Thermostats and barostats (2, GPH)
- In-depth: Rare events and sampling problems:
- Equilibrium and convergence (1, CW)
- Free energy methods and extended ensembles (2, CW)

- Review: Analysis and interpretation (1, GPH)

- 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 | appointment by email. Arnimallee 6, R212a | christoph.wehmeyer[at]fu-berlin.de |

This topic: CompMolBio > Lectures > MolecularModellingSimulation15_16

Topic revision: 20 Oct 2015, GuillermoPerezHernandez

Topic revision: 20 Oct 2015, GuillermoPerezHernandez