Jun 11 – 13, 2024 ONLINE
Évora
Europe/Lisbon timezone

Course programme

Day 1 (11 June 2024; 14:30-17:30)

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 (12 June 2024; 14:30-17:30)

14:30 Welcome

4: Biomembrane Structure and Composition

  • Introduction to biomembrane structure
  • Lipid bilayers, membrane proteins, and solvent models 
  • Membrane composition and its influence on simulations 

5: System Setup and Equilibration

  • System preparation: solvation, ion addition, and membrane insertion 
  • Energy minimization and equilibration protocols 
  • Temperature and pressure coupling in MD simulations

6: Running MD Simulations with Gromacs

  • Configuration files in Gromacs
  • Simulation protocols: NVT and NPT ensembles 
  • Controlling and monitoring simulations

17:30 End of Day 2

 

Day 3 (13 June 2024; 14:30-17:30)

14:30 Welcome

7: Analysis of MD Trajectories

  • Trajectory file formats and visualization tools 
  • Calculation of structural properties (e.g., area per lipid) 
  • Analysis of membrane fluctuations and order parameters

8: Advanced Topics in MD Simulations

  • Enhanced sampling techniques (e.g., umbrella sampling, metadynamics) 
  • Free energy calculations Combining experimental data with simulations 
  • Challenges and considerations for membrane protein simulations Protein-lipid interactions and lipid-protein interfaces 
  • Membrane protein stability and conformational changes

9: Case Studies and Research Applications

  • Overview of research studies involving Gromacs and biomembrane simulations 
  • Success stories and recent advancements 
  • Discussion on potential research projects and directions

17:30 Farewell and end of the course