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)