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Molecular Dynamics Simulations

Module PH2019

This module handbook serves to describe contents, learning outcome, methods and examination type as well as linking to current dates for courses and module examination in the respective sections.

Module version of SS 2019 (current)

There are historic module descriptions of this module. A module description is valid until replaced by a newer one.

available module versions
SS 2019SS 2018SS 2017SS 2011

Basic Information

PH2019 is a semester module in English or German language at Master’s level which is offered in summer semester.

This Module is included in the following catalogues within the study programs in physics.

  • Specific catalogue of special courses for Biophysics
  • Specific catalogue of special courses for Applied and Engineering Physics
  • Elective Modules Natural Sciences in the Master Program Matter to Life
  • Complementary catalogue of special courses for condensed matter physics
  • Complementary catalogue of special courses for nuclear, particle, and astrophysics

If not stated otherwise for export to a non-physics program the student workload is given in the following table.

Total workloadContact hoursCredits (ECTS)
150 h 60 h 5 CP

Responsible coordinator of the module PH2019 is Martin Zacharias.

Content, Learning Outcome and Preconditions


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

Learning Outcome

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.


No preconditions in addition to the requirements for the Master’s program in Physics.

Courses, Learning and Teaching Methods and Literature

Courses and Schedule

Learning and Teaching Methods

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.

Module Exam

Description of exams and course work

There will be an oral exam of about 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 tutorials is strongly recommended since the exercises prepare for the problems of the exam and rehearse the specific competencies.

Exam Repetition

The exam may be repeated at the end of the semester. There is a possibility to take the exam in the following semester.

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