Day 1 (17 June 2026; 14:30-17:30) | Lecturer: Alfredo Carvalho
14:30 Welcome
1. Introduction to Molecular Dynamics
- Overview of molecular dynamics simulations
- Theoretical foundations: Newton's equations and integration algorithms
- Simulation components: force fields, coordinates, and time steps
2. Gromacs Overview
- Introduction to Gromacs software
- Installation and basic setup
- File formats and file preparation
3. Force Fields in MD Simulations
- Overview of force fields used in biomolecular simulations
- Parameterization and limitations
- Choice of force field for biomembrane simulations
17:30 End of Day 1
Day 2 (18 June 2026; 14:30-17:30) | Lecturer: Paulo Martel
14:30 Welcome
1. Introduction to Protein Disulfide Isomerase (PDI)
- Physiological role of PDI
- Structure of PDI
- Mutation studies
2. Structure preparation
- Selection of PDB structures
- Structure cleaning
- Preparation of wild-type and mutant PDI forms
3. MD setup, running, and analysis
- Preparation of simulation box
- Simulation parameters
- Equilibration runs
- Running production and how to manage long simulations
- Comparing WT vs. mutant simulation data
17:30 End of Day 2
Day 3 (19 June 2026; 14:30-17:30) | Lecturer: António Canto
14:30 Welcome
7. Biomembranes: System setup and equilibration
- Building the system
- Preparing the environment
- Equilibration steps
8. Biomembranes: Running MD Simulations with Gromacs
- Configuring the production run
- Running the simulation
- Stability checks
9. Biomembranes: Analysis of MD Trajectories
- Membrane physical properties
- Dynamical properties
- Molecular interactions
17:30 Farewell and end of the course
