Module
Molecular dynamics
Simulating the stability of protein-ligand complexes over time: system preparation, solvation, equilibration and trajectory analysis.
Programme indicatif.
Le déroulé ci-dessous décrit le contenu prévu. Les horaires peuvent être ajustés
selon le rythme du groupe. Aucune date de session n'est encore fixée.
Learning objectives
By the end of this module, you will be able to
- Prepare a protein-ligand system for molecular dynamics simulation
- Choose an appropriate force field and parameters
- Run minimisation, equilibration and production phases
- Analyse RMSD, RMSF and hydrogen bond stability
- Estimate the binding free energy (MM/PBSA, MM/GBSA)
Day 1 — Foundations and preparation
| Time | Content | Type |
|---|---|---|
| 09:00 – 09:30 | Welcome, introduction of participants and objectives | Introduction |
| 09:30 – 10:45 | Theory: why dynamics? Limits of static docking | Theory |
| 10:45 – 11:00 | Break | |
| 11:00 – 12:30 | Force fields: AMBER, CHARMM, OPLS. Choosing parameters | Theory |
| 12:30 – 14:00 | Lunch | |
| 14:00 – 15:30 | System preparation: solvation, ions, box size | Practical work |
| 15:30 – 15:45 | Break | |
| 15:45 – 17:15 | Minimisation and equilibration | Practical work |
| 17:15 – 17:45 | Day summary and questions | Wrap-up |
Day 2 — Grid, docking and validation
| Time | Content | Type |
|---|---|---|
| 09:00 – 10:00 | Production phase: duration, time step, trajectory saving | Theory |
| 10:00 – 10:45 | Launching and monitoring the simulation | Practical work |
| 10:45 – 11:00 | Break | |
| 11:00 – 12:30 | RMSD analysis: system stability over time | Practical work |
| 12:30 – 14:00 | Lunch | |
| 14:00 – 15:30 | RMSF analysis: residue flexibility | Practical work |
| 15:30 – 15:45 | Break | |
| 15:45 – 16:45 | Hydrogen bond analysis over the trajectory | Practical work |
| 16:45 – 17:30 | Day summary and questions | Wrap-up |
Day 3 — Consolidation and project
| Time | Content | Type |
|---|---|---|
| 09:00 – 10:30 | Theory: principles of free energy calculation | Theory |
| 10:30 – 10:45 | Break | |
| 10:45 – 12:30 | MM/PBSA and MM/GBSA: practical implementation | Practical work |
| 12:30 – 14:00 | Lunch | |
| 14:00 – 15:30 | Comparing several ligands: per-residue decomposition | Practical work |
| 15:30 – 15:45 | Break | |
| 15:45 – 16:45 | Interpreting results and common pitfalls | Practical work |
| 16:45 – 17:30 | Final assessment and closing | Wrap-up |
Prerequisites
- Module 1, notions of classical mechanics
- Basic notions of classical mechanics
- Comfortable with the command line
Required equipment
- Computer with at least 8 GB RAM
- 8-core processor recommended (dynamics)
- 20 GB free disk space
- Software provided: AutoDock Vina, MGLTools, PyMOL
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