0000000205 20S 2SWS VO Molecular Dynamics Simulations: from Principles to Application   Hilfe Logo

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Molecular Dynamics Simulations: from Principles to Application 
Summer semester 2020
Chair of Theoretical Biophysics (T38) - Biomolecular Dynamics (Prof. Zacharias)
(Contact information)
Allocations: 1 
Angaben zur Abhaltung
Simulation methods
Molecular dynamics simulation methods
Monte Carlo methods
Brownian Dynamics simulations
Force field description of a molecule
Boundary conditions in simulations
Temperature and pressure control
Thermodynamic and kinetic quantities from simulations
Non-equilibrium simulations
Mixed quantum-mechanical and classical simulations
Simple liquids, mixtures
Biomolecules: dynamic of proteins and peptides
Systems with solid interfaces
Elementary knowledge of statistical mechanics and classical mechanics
The successful participation at the course allows the student

• to understand the preparation, setup and analysis of molecular simulations and to evaluate the results
• to independently perform molecular dynamics, Monte Carlo or Brownian dynamics simulations on molecules
• to be able to extract thermodynamic and kikinetic quantities from simulations
• to develop an understanding of many body systems
• to develop objectives and tasks that can be tackled by simulations.
• to select appropriate simulation techniques for a desired task
  • German
  • English
In the course the theoretical concepts and their applications will be explained by the lecture and the understanding will be assisted by explaining examples. A particular focus is on involving the students to participate in discussions and to promote conversation between students and lecturer on the contents of the course. The lecture notes contain links on original literature that should promote the independent search for related work and references. In the exercise sessions the students will learn in a stepwise manner how to work with molecular simulation programs and how to evaluate the results. The content of the lecture will be supplemented by several examples that deepen the understanding and allow for the independent application of state-of-the are analysis tools. The students will be able to evaluate the examples from the lecture and learn how to use simulation approaches to tackle relevant research tasks by simulations.
Für die Anmeldung zur Teilnahme müssen Sie sich in TUMonline als Studierende/r identifizieren.
Note: Elementary knowledge of statistical mechanics and classical mechanics
D. Frenkel, B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, Academic Press. 2014
M.P. Allen, D.J. Tildesley, Computer simulation of liquids, Oxford University Press, 1999.
Mark E. Tuckerman, Statistical Mechanics: Theory and Molecular Simulation, Oxford Graduate Press, 2016
Tamar Schlick, Molecular Modeling and Simulation: an Interdisciplinary Guide, Springer Science, 2006.
A. Leach, Introduction to Molecular Modelling, Oxford Academic Press. 2016
Griebel, Knapek, Zumbusch, Caglar, Numerische Simulation in der Moleküldynamik, Springer Press. 2014
Online information
e-learning course (moodle)