Dive into the world of Molecular Dynamics (MD) with this two-half-day online course on GROMACS for High-Performance Computing (HPC). Learn how to build, run, and analyze simulations from start to finish – from energy minimization and equilibration to trajectory visualization with VMD. With hands-on insights into force fields, GPU optimization, and scalable multi-node workflows, you’ll gain the practical skills needed to launch scientifically sound MD simulations for your own biomolecular research.
| Start date: | 25 March 2026, 09:00 (CET) | Entry level: | Basic | |
| End date: | 26 March 2026, 13:00 (CET) | Subject area: | Molecular Dynamics (MD) | |
| Location: | ONLINE (Zoom) | Topics: | GROMACS | |
| Language: | English | Target audience: | Industry, public admin, academia | |
| Price: | Free (for eligible participants) | Organizers: | ASC & EuroCC Austria |
Molecular Dynamics (MD) simulations with GROMACS must be scientifically sound and efficiently executed on High-Performance Computing systems. This concept is based on three core pillars: accurate physical modeling with force fields, a robust simulation workflow (minimization – equilibration – production), and insightful trajectory analysis.
This two-half-day online course provides an overview of the fundamental workflow of molecular dynamics simulations using GROMACS on multi-node GPU clusters. It introduces the essential steps of energy minimization, equilibration, and production simulation, explains how force fields and parameterization define interactions. Finally the participants will learn how to analyze and visualize simulation results with VMD.
While the course focuses on core concepts and workflows, GROMACS is widely used in areas such as protein structure modeling and folding, biomolecular dynamics, membrane simulations, and computer-aided drug design. Participants interested in these application domains will gain the essential background needed to further explore such use cases in their own research.
At the end of the course, participants will understand how to prepare a molecular system for simulation, how to run it efficiently on high-performance computing resources with GPUs across multiple nodes, and how to carry out basic trajectory analysis and visualization to extract meaningful structural and dynamical insights.
Agenda & Content
For a detailed timetable and additional information, please see Agenda & Content in the left menu.
Target audience, eligibility & prices
Everyone is welcome who wants to learn the fundamentals of molecular dynamics simulations with GROMACS and HPC, including students, researchers, and professionals from academia and industry with an interest in computational chemistry, biophysics, structural biology, or drug discovery.
This course is open and free of charge for all participants from academia, industry, and public administration from EU and/or EuroHPC JU member countries.
Entry level & prerequisites
Beginner – no prior experience with GROMACS or HPC is necessary.
Basic knowledge of molecular structure and classical mechanics is helpful but not required.
Course format
This course will be delivered as a LIVE ONLINE COURSE (using Zoom).
Hands-on labs
All participants will get a temporary user account on one of the ASC systems to do the hands-on labs.
You will use your own laptop or workstation to connect conveniently from your browser to the ASC Jupyterhub and do the hands-on exercises on a suitable CPU or GPU partition of the ASC.
Accepted participants will be contacted a few days before the course and asked to do a short pre-assignment that has to be completed before the course starts.
Lecturer
Thomas Haschka (Campus IT / HPC, TU Wien)
Dr. Thomas Haschka is an Austrian biophysicist and computational scientist specializing in molecular biophysics, high-performance computing, machine learning and Artificial Intelligence. He currently works as an AI Specialist in the dataLAB of the High-Performance Computing Unit at Campus IT, TU Wien, supporting advanced research infrastructure and data-driven innovation. With a PhD from Université de Reims Champagne-Ardenne (highest distinction), he has held research positions at institutions such as the Pasteur Institute, Paris Brain Institute, and the American University of Beirut. His work spans molecular dynamics, epidemiological modeling, genomics, and AI evaluation methods, supported by strong expertise in GPU programming and cloud technologies. He combines academic research excellence with real-world industrial consulting experience.
Language
English
Date, time, and location
25.–26.03.2026, 09:00 – 13:00 (CET), LIVE ONLINE COURSE (Zoom)
Registration
Registration is required, the registration form can be found on top of this page in the menu on the left.
Please register with your official institutional email address to prove your affiliation.
You will get an automatic confirmation by email (subject starting with "[Indico] Registration"), please check your Spam/Junk folders.
Following your successful registration, you will receive further information a few days before the course.
Please do not hesitate to contact us at training@asc.ac.at if you have any questions.
Waitinglist
After the number of registrations has reached its maximum or the registration form has been closed, you may want to send us an email (training@asc.ac.at) stating that you are interested to be put on the waiting list (vacancies may occur due to cancelations, etc.).
To be able to do the hands-on labs on the ASC systems please provide your full international mobile-phone number for the two-factor authentication required to login to the ASC systems.
Modification, withdrawal & no-show policy
Your registration is binding. Please only register for the course if you are really going to attend.
You can update your registration data or withdraw your registration anytime before the registration form has been closed via the link "Manage my registration" which you can find at the bottom of your automatic email confirmation (subject starting with "[Indico] Registration").
Alternatively, or after the registration form has been closed, please inform us about your cancelation or any change in your registration data (especially your mobile-phone number) via email (training@asc.ac.at).
No-show policy: If you do not cancel and do not show up at the course you will be blacklisted and excluded from future training events.
Organizers
This course is jointly organized by Austrian Scientific Computing ASC (aka ASC Research Center, TU Wien) and EuroCC Austria.
Acknowledgements
This course is partially funded by the EuroCC 2 project.
The project has received funding from the European High-Performance Computing Joint Undertaking (JU) under grant agreement No 101101903. The JU receives support from the Digital Europe Programme and Austria, Belgium, Bulgaria, Croatia, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Iceland, Ireland, Italy, Latvia, Lithuania, Luxembourg, Montenegro, Netherlands, North Macedonia, Norway, Poland, Portugal, Romania, Serbia, Slovakia, Slovenia, Spain, Sweden, and Türkiye.
Additional funding for the project comes from the Austrian federal ministries BMBWF and BMK.
