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Molecular Simulation
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Molecular Simluation
• Introduction:• Prerequisition: • A powerful computer, fast graphics
card,• An efficient way to solve
Schroedingers wave equation for many atoms,
• A reliable structure or structural model
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Molecular Simluation
• Structures or reliable model structures:
• X-ray crystallography• NMR spectroscopy• Homology modelling
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Molecular Simulation
• Where do we get the structures from?
• Databases• Brookhaven protein data base• Or homology models
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Molecular Simulation
• Homology modelling:
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Molecular Simulation
• Molecular Mechanics:• The Potential energy surface (PES):• Born-Oppenheimer approx. allows us to
separate electronic and nuclear motion • when nuclei move, the electrons re-adjust
quickly • energy of molecule is a function of the
positions of the nuclei • potential energy surface describes energy
of a molecule in terms of its structure
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Molecular Simulation
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Molecular Simulation
• Structure • determined from the potential energy surface • minimum corresponds to an equilibrium structure • first order saddle point corresponds to a transition state for a
reaction • a reaction path is the steepest descent path connecting a
transition state to minima
• Dynamics • molecules move on the potential energy surface • dynamics can be treated classically or quantum mechanically • small amplitude motions - normal modes of vibration • large amplitude motions - trajectories, wave packets, reactions • statistical mechanics to connect microscopic to macroscopic
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Molecular Simulation
• Bond stretching• Valence angle bending• Torsions• Van der Waals Interactions• Electrostatic Interactions• Cross terms
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Molecular Simulation
• Bond Stretching and valence angle bending
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Molecular Simulations
• Torsions
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Molecular Simulation
• Interaction of 2 point charges
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Molecular Simulation
• Van der Waals Interactions
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Molecular Simulation
• Force Field Energies• Geometry Optimisation• Thermodynamics
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Molecular Simulation
• Modern Force Fields
• CHARMM Biomolecules• CHARMm Bio and org. molecules• CFF/CVFF org. and bio molecules• GROMOS Biomolecules• MM2 organics• MM3 org. and bio molecules• OPLS all-atom and united atom version• SYBYL/TRIPOS org. and bio molecules