Protein Folding Simulations

This lecture covers the theory and practical applications of molecular dynamics simulations in protein folding. It discusses solvent models, such as explicit and implicit solvents, and their impact on simulation accuracy. The exercises include analyzing hydrogen bonds, calculating RMSD, and understanding the folding dynamics of the Trp-cage miniprotein using OpenMM. Students will explore the influence of solvent environments on protein properties and learn to interpret simulation results.