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Molecular Simulation

Molecular Simulation. 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. Molecular Simluation. Structures or reliable model structures:

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Molecular Simulation

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  1. Molecular Simulation

  2. 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

  3. Molecular Simluation • Structures or reliable model structures: • X-ray crystallography • NMR spectroscopy • Homology modelling

  4. Molecular Simulation • Where do we get the structures from? • Databases • Brookhaven protein data base • Or homology models

  5. Molecular Simulation • Homology modelling:

  6. 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

  7. Molecular Simulation

  8. 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

  9. Molecular Simulation • Bond stretching • Valence angle bending • Torsions • Van der Waals Interactions • Electrostatic Interactions • Cross terms

  10. Molecular Simulation • Bond Stretching and valence angle bending

  11. Molecular Simulations • Torsions

  12. Molecular Simulation • Interaction of 2 point charges

  13. Molecular Simulation • Van der Waals Interactions

  14. Molecular Simulation • Force Field Energies • Geometry Optimisation • Thermodynamics

  15. 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

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