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
