GROMACS tutorial

Trainer: Alessandra Villa

Overview: The tutorial will take you through a complete protocol for setting up, simulating, and analysing the results from a molecular dynamics simulation of a small protein using GROMACS. For this tutorial, Factor Xa, a protein playing a critical role in the formation of blood clots, is used as an example.

Learning outcomes

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

• Prepare a structure for an MD simulation
• Describe the components of a topology file
• Explain each step of a simulation
• Post-process a simulation run
• Analyse and plot your results with GROMACS tools and python

Materials

• GROMACS tutorial