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Course content
Docking and HADDOCK
- Integrative modeling of biomolecular complexes
- HADDOCK tutorial
Molecular Dynamics Simulations
Simulation workflows with BioBB
- Simulation workflows with BioBB
- Tutorial – Protein-Complex MD Setup with Jupyter Notebooks and BioBB.
Introduction to QM/MM
- Introduction to QM/MM
- Tutorial – Introduction to QMMM simulations using GROMACS-CP2K Interface
Enhanced Sampling Methods
- Modeling molecular recognition through enhanced-sampling methods
- Tutorial – Metadynamics
Free energy calculations
- Introduction to alchemical free energy calculations using PMX
- Applications of alchemical free energy calculations
Trainer biographies
Technical help sheet
Further learning
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Molecular Dynamics Simulations

This section focuses on molecular dynamics simulations, including a practical session which details a step-by-step guide to running simulations in GROMACS, and a short research talk about how to get the best performance in GROMACS.

Basis of molecular dynamics simulations
GROMACS tutorial
Getting good performance in GROMACS

Biomolecular simulations

Molecular Dynamics Simulations