Molecular Dynamics Simulations

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

Applications:

• Simple liquids, mixtures
• Biomolecules: dynamic of proteins and peptides
• Systems with solid interfaces

The successful participation at the course allows the students

• 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 kinetic 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.

Elementary knowledge of statistical mechanics and classical mechanics

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.

Lecturing using the board and providing lecture slides, beamer presentation, exercises at the computer, Internet web-page for the course

• 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.

There will be an oral exam of 30 minutes duration. Therein the achievement of the competencies given in section learning outcome is tested exemplarily at least to the given cognition level using questions of understanding, short calculations and discussions including simple drawings of the student.

For example an assignment in the exam might be:

• What is a symplectic algorithm for molecular dynamics simulations?
• What is meant by coarse-graining of a simulation system?
• What are bonded interactions in a molecular force field?

Participation in the exercise classes is strongly recommended since the exercises prepare for the problems of the exam and rehearse the specific competencies.