ALL LECTURES
Introduction Molecular Architecture I Molecular Architecture II Molecular Simulation I Molecular Simulation II Bioinformatics I Bioinformatics II Prediction I Prediction II

CONCEPTS IN THIS LECTURE
Molecular Simulation I
Underlying Principles Simulation Methods Molecular Dynamics Simulating Solutions Simulating alpha-Helix Simulating Folded Protein History of Simulation

4. Molecular Simulation I
4.1. Underlying Principles	4.2. Simulation Methods
SB228 Lecture 4 Lecture4 Lecture 4 Contents Underlying Principles. Concept 4.1 Underlying Principles Boltzmanns Distribution Entropy and Free Energy1 Absolute Probabilities Dynamic Properties Types of Motion Crossing Energy Barriers Rates of Motion	Simulation Methods. Concept 4.2 Simulation Methods Moving Over Energy Surface Reaction Coordinates Protein Folding Landscape Levinthals Paradox Resolve Paradox Simple Energy Minimization Convergent Energy Minimization Monte Carlo Methods Simulated annealing
4.3. Molecular Dynamics	4.4. Simulating Solutions
Molecular Dynamics. Concept 4.3 Molecular Dynamics Molecular Potential Energy Molecular Dynamics theory Molecular Dynamics Procedure Molecular Dynamics Procedure 1 Molecular Dynamics Procedure 2 Molecular Dynamics Procedure 3 Units in Force Fields	Simulating Solutions. Concept 4.4 Simulating Liquids. Water is a Very Simple Molecule Simulating Liquids Liquids argon and Water Pure Water Dynamics Properties of Liquid Water Hydrophobic Effect Simulating Hydrophobic Effect Voronoi Decomposition Voronoi analysis of Contacts Hydrophobic Clusters Cross Box Methane Solution Dynamics Butane Solution Dynamics Benzene Solution Dynamics Hydrophobic Energy and Contact Surface Hydrophobic Solutes Perturb Water Density Large Density Changes
4.5. Simulating alpha-Helix	4.6. Simulating Folded Protein
Simulating alpha-Helix. Concept 4.5 Dynamics of the alpha-Helix Alpha-Helix Dynamics Water allows Hydrogen Bonds to Break	Simulating Folded Protein. Concept 4.6 Dynamics of Folded Protein Protein in Water1 Protein Dynamics RMS Deviation from X-Ray Hydrogen Bond Stability Four Classes of Water Molecules Density of Surface Water Orientation of Surface Water Properties of Water Molecules
4.7. History of Simulation
History of Simulation. Concept 4.7 Los alamos 1943-45 Levinthal 1966 Levinthal Movies 50 Years of Simulation