Discover the world of Molecular Modeling

Are you intrigued by the fascinating possibilities of molecular modeling techniques, such as molecular docking or molecular dynamics (MD) simulations? We, as a computational biochemistry research group, are happy to share our knowledge, either in our on-site BioSim course at the Heinrich-Heine University, through our comprehensive online MD Tutorial or by joining our group for an internship

Class room of the BioSim Module at the Heinrich-Heine University

Simulation of Biomolecules (BioSim) course

Our BioSim course aims to provide hands-on training in simulating biomolecules. You will learn how to set up and conduct MD simulations using the powerful and freely available MD software package, GROMACS.

Where: Heinrich-Heine University, Selbstlernzentrum
When: Two and a half weeks in March, from 9 am to 5 pm with lectures in the morning and practical sessions in the afternoon 
Who: Open to students at all levels (Bachelor, Master, PhD and Postdocs), no previous knowledge necessary
How: You can apply to this course through the HIS-LSF system at the Heinrich-Heine University or by contacting us directly
What to bring: None, computers are provided on-site
 
For more information and registration, follow these links:

Online Tutorial for molecular dynamics (MD) simulations with GROMACS

For those eager to dive into MD simulations but seeking guidance, we’ve developed an extensive online MD tutorial using GROMACS. Our tutorial provides a structured introduction to the subject, walking you through every step of preparing and conducting an MD simulation. 
In our MD tutorial, we present a practical example involving on the peptide [KIGAKI]3, which consists of 18 amino acids and serves as a model for studying protein aggregation.

Our online MD tutorial will guide you through the following topics:

⊕ Simulation setup

⊕ Energy minimization

⊕ Equilibration

⊕ MD Production run

⊕ A comprehensive selection of analysis methods

⊕ Enhanced sampling methods, such as replica exchange MD simulation

Molecular interactions modelled by the force field of a molecular dynamics simulation

To get started, you’ll need a computer or laptop with a Linux (Ubuntu, openSUSE, etc.) or MacOS operating system, as GROMACS operates through a terminal interface. If you’re on Windows, you can use a virtual box with a Linux system.

Reading recommendations for MD simulations

Recommended Reading

If you want to learn more about the theory and practical applications of MD simulations, we recommend the following books:

  1. “Understanding Molecular Simulation” by Daan Frenkel and Berend Smit (1996)
  2. “Molecular Modelling: Principles and Applications” by Andrew R. Leach (2001)
  3. “Molecular Modeling and Simulation” by Tamar Schlick (2002)

Become part of our group​

For those who cannot get enough of computational biochemistry, we also offer the opportunity to engage in an internship within our group, lasting from one to three months. During this immersive experience, you won’t just be learning about MD simulations—you’ll be actively involved in cutting-edge research projects, applying your knowledge to practical scenarios, and gaining hands-on experience in this dynamic field. 

This internship, or the successful completion of our BioSim course, can pave the way for those interested in writing their bachelor’s or master’s theses within our group. To learn more about our ongoing research, please visit our research site for an in-depth look into our projects and achievements.

Strodel Group of 2023