2025-11-18 Introduction to Molecular Modelling and Computational Chemistry on HPC Systems at LRZ (hbio1w25)

Contents

This online course introduces the fundamental principles and key concepts of molecular modeling on LRZ high-performance computing systems. Participants will be introduced to several molecular dynamics software packages and learn how to use them effectively. The training will also provide insights into scientific workflows commonly used in molecular simulation applications.

Topics covered include:

• an overview of molecular simulation software applications,
• an introduction to visualisation of molecules using VMD, pymol and VESTA,
• hands-on experience running GROMACS, CP2K, DFBT+ and LAMMPS on LRZ hardware.

The program combines lectures with hands-on exercises, giving participants the opportunity to apply methods directly to real-world cases and to gain deeper insights into scientific workflows in molecular simulations. 

The course offers targeted training for users working in life science, biophysics, computational chemistry, material science, and related disciplines. While tailored to LRZ users, the course is also open to other interested European researchers from academia and industry.

Preliminary Agenda

Day 1:

• Introduction to the computing facilities at LRZ and login to the JupyterLab and SLURM cluster
• Introduction to molecular modelling
• Protein Database (PDB), BioSym Sim and force fields
• Visualisation using Pymol
• Molecular simulation using Gromacs

Day 2:

• Visualisation using VMD
• Molecular simulation using CP2K, ASE and QMMM
• Post processing and analysis
• Visualisation using VESTA
• Molecular simulation using DFBT+

Day 3:

• Molecular simulation with LAMMPS
• Visualisation using Ovito

Prerequisites

• Basic understanding of molecular simulations,
• basic knowledge of chemistry, biology and physics,
• basic knowledge of Linux, shell commands and ssh,
• basic knowledge of Jupyter (Lab/Notebook).

Hands-On

Hands-on sessions will be provided through the Gauss Centre for Supercomputing (GCS) portal: https://portal.gauss-centre.eu/

Content Level

The content level of the course is broken down as:

Language

English

Lecturers

Dr. Ferdinand Jamitzky, Dr. Plamen Dobrev, Dr. Prasanth Ganta, Dr. Birkan Emrem , Dr. Elmira Birang, Matteo Foglieni (all LRZ)

Prices and Eligibility

The course is open and free of charge for people from academia and industry from the Member States of the European Union (EU) and Associated Countries to the Horizon 2020 programme.

Registration

Please register with your official e-mail address to prove your affiliation.

Withdrawal Policy

See Withdrawal

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