Welcome to the lecture wiki Advanced Molecular Simulation WS 2014/15

News

Registration: Prior registration in either Campus Management OR KVV des Fachbereichs is required.
In case you have problems with registration contact katja.geiger[at]fu-berlin.de

General

Lecture (weekly): Guillermo Pérez Hernández, Christoph Wehmeyer
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

Dates

	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

Content

This lecture will provide a perspective on the field of molecular dynamics (MD) simulations as implemented by researchers today, with a focus on methods and algorithmic implementation.

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)

Requirements

• 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

Credit Requirements

The lecture is accompagnied by lab work. Note that you have to sign up for both 20112201 Vorlesung and 20112202 Übung.
Regular attendance is expected and will be monitored.
There will be an oral exam.

Evaluation

Evaluation necessities of the different programs (Physics, Chemistry, Biochemistry) will be accommodated when possible. We will try to address this in the first lecture.

Contact

Name	Consultation Hour	Mail
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