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.

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.

  • General catalogue of special courses
  • Specific catalogue of special courses for Applied and Engineering Physics
  • Specific catalogue of special courses for Biophysics

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 75 h 5 CP

Responsible coordinator of the module PH2019 is Martin Zacharias.

Content, Learning Outcome and Preconditions


I Simulation methods

Molecular Dynamics simulations

Monte Carlo Simulations

Brownian Dynamics
- MD basics (equations of motion, integrators etc.), Temperature, pressure control
- MD in various ensembles, extraction of thermodynamic and kinetic data

- Long-range interactions
- Free energy simulations
- Car-Parinello MD
- Non-equilibrium simulations
- Force fields
II Applications
- Water and aqeuous solutions
- Biomolecules
- Interfacial systems

Learning Outcome

Understanding molecular simulations

abbility to perform simulaitons


Basic knowledge of statistical mechanics, thermodynamics

Courses, Learning and Teaching Methods and Literature

Courses and Schedule

VU 4 Molekulardynamik-Simulationen: von den Grundlagen zu Anwendungen Zacharias, M.
Mitwirkende: Reif, M.
Montag, 10:00–12:00
sowie Termine in Gruppen

Learning and Teaching Methods

Lecture using Beamer and board,

Practical sessions at the Computer


Beamer. lecture nodes, Internet side for the course


D. Frenkel, B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, Academic Press.

Module Exam

Description of exams and course work

In an oral exam the learning outcome is tested using comprehension questions and sample problems.

In accordance with §12 (8) APSO the exam can be done as a written test. In this case the time duration is 60 minutes.

Exam Repetition

There is a possibility to take the exam at the end of the semester. There is a possibility to take the exam in the following semester.

Condensed Matter

When atoms interact things can get interesting. Fundamental research on the underlying properties of materials and nanostructures and exploration of the potential they provide for applications.

Nuclei, Particles, Astrophysics

A journey of discovery to understanding our world at the subatomic scale, from the nuclei inside atoms down to the most elementary building blocks of matter. Are you ready for the adventure?


Biological systems, from proteins to living cells and organisms, obey physical principles. Our research groups in biophysics shape one of Germany's largest scientific clusters in this area.