A hands-on workshop in preparing biomolecular systems for molecular dynamics simulations

Building Molecular Systems for MD is a two day workshop designed for researchers who want to learn practical approaches to preparing and building molecular systems for MD simulations.

What will we cover?

Day 1 – 26/11/2026

🫧 Molecular assemblies with Shapespyer (morning session)
Build larger molecular assemblies from individual components, including placing proteins into lipid bilayers to create membrane systems suitable for simulation.
⚙️ Protein structure preparation with prepmd (afternoon session)
Clean up and prepare protein structures, including alignment, scoring, and identifying structures that best fit experimental EM maps. We will also look at adding missing loops and hydrogen atoms, and relaxing unwanted structural clashes.

Day 2 – 27/11/2026

🧩 Peptide assemblies with FibrilGen (morning session)
Generate cross-beta peptide assemblies and explore how these structures can be constructed for studying fibrils and other supramolecular systems.
🧬 DNA systems with MDNA (afternoon session)
Build, modify and analyse DNA strands, providing practical experience of preparing nucleic-acid systems for molecular simulation.

Who is it for?

The workshop is open to undergraduate and postgraduate students, researchers and anyone interested in learning how molecular systems are prepared for MD simulations.

No previous experience of any of the tools is expected. Whether you are new to molecular simulation or looking to broaden your existing skills, the workshop will provide practical experience and guidance in a friendly, collaborative environment.