A two-day online course on molecular dynamics will be jointly organized by Austrian Scientific Computing (ASC) and EuroCC Austria on 18 and 19 June 2026.
This course explores the world of molecular modeling and simulation on high-performance computing (HPC). Participants will 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, they will gain practical skills to carry out modern computational studies in biomolecular research and drug discovery.
Participants will learn how to build end-to-end molecular modeling workflows that are both scientifically rigorous and HPC-efficient. This two-half-day online course covers four core pillars: structure prediction and homology modeling, molecular docking, molecular dynamics simulations, and realistic membrane modeling.
Participants will also 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 also 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 modeling, 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 modeling pipeline – from structure prediction and docking to membrane-embedded molecular dynamics – and efficiently analyze simulation results on modern CPU/GPU HPC systems.
