Molecular Dynamics Simulation: Trp-cage Miniprotein

This lecture introduces the MD simulation of the Trp-cage miniprotein, a small protein ideal for computational folding simulations. The instructor explains the use of an implicit solvent model to reduce computational cost and replicate the folding dynamics of the protein. The lecture covers the creation of the system, energy minimization, heating, and dynamics using OpenMM. Students will analyze the simulation results by comparing properties like RMSD, RMSF, hydrogen bonds, and dihedral angles to experimental structures. The session also includes practical guidance on setting up Google Colab for GPU access and uploading simulation files for analysis.