Molecular Modelling on HPC

Explore the world of molecular modelling and simulation with this two-half-day online course on high-performance computing (HPC). Learn how to predict and refine protein structures, perform molecular docking, and simulate biomolecular systems in realistic environments, including membrane-embedded proteins, using state-of-the-art open-source tools such as AlphaFold 2, ProMod3, AutoDock Vina, and GROMACS. From structure generation and ligand binding to full molecular dynamics simulations and trajectory visualization with VMD, you will gain practical skills to carry out modern computational studies in biomolecular research and drug discovery.

Build end-to-end molecular modelling workflows that are both scientifically rigorous and HPC-efficient. This two-half-day online course covers four core pillars: structure prediction and homology modelling, molecular docking, molecular dynamics simulations, and realistic membrane modelling.

Participants will learn to generate protein structures with AlphaFold 2 and refine comparative models using ProMod3. Using these models, they will prepare ligand datasets and perform docking studies with AutoDock Vina to identify binding modes and rank candidate molecules.

The course then introduces molecular dynamics workflows in GROMACS, including system setup, minimization, equilibration, and production simulations. A dedicated section focuses on membrane proteins, showing how to build and simulate protein-ligand systems in lipid bilayers to study membrane-driven effects on structure and binding.

Participants will also explore scalable HPC workflows, including protein modelling, GPU-accelerated simulations, ligand docking and efficient handling of large biomolecular systems. The course concludes with trajectory analysis and visualization in VMD to evaluate ligand stability, conformational changes, and key molecular interactions.

By the end of the course, participants will be able to build and run a complete molecular modelling pipeline – from structure prediction and docking to membrane-embedded molecular dynamics – and efficiently analyze simulation results on modern CPU/GPU HPC systems.

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 how to do molecular modelling on HPC systems, 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 molecular modelling or HPC is necessary.

Attendants should be comfortable working with the UNIX/LINUX command line. 

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

18.–19.06.2026, 09:00 – 13:00 (CEST), 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.