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 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 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 History_of_Simulation._Concept_4.7 Los_alamos_1943-45 Levinthal_1966 Levinthal_Movies 50_Years_of_Simulation