Molecular Biophysics & Biochemistry 447b3 / 747b3 Bioinformatics
Goal: Model Proteins and Nucleic Acids as Real Physical Molecules
Overview: Methods for the Generation and Analysis of Macromolecular Simulations
Potential Functions
Minimization
Molecular Dynamics
Molecular Dynamics (cont)
Phase Space Walk
Example Phase Space Walk
Monte Carlo
Monte Carlo (cont)
MC vs/+ MD
Periodic Boundary Conditions
Typical Systems: Water v. Argon
Typical Systems: DNA + Water
Typical Systems: Protein + Water
Average over simulation
Timescales
D & RMS
Number Density
Number Density (cont)