Simulations of Biological Systems with GROMACS

Course programme

Session times: 14:30 - 17:30

 

Session 1 (17.06.2025) | Lecturer: Alfredo Carvalho

1. Introduction to Molecular Dynamics
2. Gromacs Overview
3. Force Fields in MD Simulations

Session 2 (18.06.2025) | Lecturer: Paulo Martel

1. Proteins: Introduction to Protein Disulphide Isomerase (PDI)
2. Proteins: Preparation of WT and mutant PDIs  and Simulation Setup
3. Proteins: Analysis of simulation results and discussion

Session 3 (20.06.2025) | Lecturer: António Canto

1. Biomembranes: System setup and equilibration
2. Biomembranes: Running MD Simulations with Gromacs
3. Biomembranes: Analysis of MD Trajectories