📚 Syllabus & Course Curriculum
Drug Discovery & Pharmaceutical Sciences
Module-by-module breakdown of Advanced Molecular Dynamics Simulations of Protein Structure using GROMACS, from foundations to a certified capstone project.
Setup
• Structure preparation: missing residues, protonation states and disulphides
• Force field selection (AMBER, CHARMM, GROMOS) and the consequences of the choice
• Solvation, ion placement and box geometry to avoid periodic image artefacts
Equilibration
• Minimisation, NVT and NPT equilibration with position restraints
• Thermostats and barostats: correct choices for production versus equilibration
• Verifying equilibration rather than assuming it from wall-clock time
Production
• Integration timestep, constraints and hydrogen mass repartitioning
• GPU acceleration, domain decomposition and realistic performance tuning
• Checkpointing, extending runs and managing trajectory storage
Analysis
• RMSD, RMSF, radius of gyration and hydrogen-bond analysis
• Principal component analysis and free energy landscapes
• Convergence assessment and why a single trajectory rarely suffices
Free Energy
• MM-PBSA and MM-GBSA: usefulness and well-documented limitations
• Alchemical free energy perturbation and thermodynamic integration
• Error estimation and reporting simulation results honestly
Earn government-registered certification in Advanced Molecular Dynamics Simulations of Protein Structure using GROMACS
e-Certificate and e-Marksheet issued on successful completion.
