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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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Tutorial – Metadynamics

Trainer: Giuliano Malloci, Attilio Vargiu, and Andrea Basciu

Overview: We will exploit enhanced-sampling molecular dynamics, namely metadynamics, to improve the sampling of bound-like (holo) conformations of a generic protein starting from its unbound (apo) one.

Learning outcomes

By the end of this session you will be able to:

Use the EDES workflow to run a simulation using metadynamics with GROMACS
Prepare a structure for simulation with GROMACS
Use PLUMED to create simulation input files for metadynanics
Analyse your results

Materials

Metadynamics tutorial

Biomolecular simulations

Tutorial – Metadynamics