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1. Introduction
2. Classical mechanical models of molecules
3. Calculation methods
4. The Morse potential
5. What is a force field?
6. What isn't a force field?
7. Harmonic bond-stretch potential
8. Harmonic angle-bend potential
9. Torsional potentials
10. Van der Waals potentials
11. Lennard-Jones potential curve
12. Potentials - "improper" torsions
13. Electrostatic (Coulomb) interactions
14. "The fallacy of atomic charges"
15. Dipole-dipole interactions
16. Force-field methods (1)
17. Geometry optimization
18. Minima and transition states
19. Energy curve of normal vibrations
20. A physical model to visualize a transition state
21. Geometry optimisation
22. Optimisation techniques
23. Force constant matrix (Hessian)
24. Transition states
25. 2D-reaction profile
26. Force-field methods (2)
27. Hamiltonian and Sampling
28. The danger of using only one conformation
29. Why we need to sample
30. Sampling and statistical mechanics
31. Calculations in statistical mechanics
32. Monte-Carlo simulations
33. Monte-Carlo calculations: an example
34. Thermodynamic equilibrium
35. Importance sampling
36. Metropolis sampling
37. Metropolis Monte-Carlo algorithm
38. Molecular Dynamics (MD)
39. The Ergodic hypothesis
40. Newton's equation of motion
41. Newton's second law of motion (1)
42. Newton's second law of motion (2)
43. MD is driven by numerical integration
44. Typical parameters of a MD simulation
45. Energy
46. Temperature
47. Periodic boundary conditions
48. Simulation time
49. Range of biological motions
50. Time-scale of molecular events
51. Definitions
52. Thermodynamic state definitions
53. Applications of MD
54. Summary and acknowledgments

Topics Covered

• Force fields
• Geometry optimization
• Minima and transition states
• Sampling
• Monte Carlo
• Molecular dynamics

Links

Series:

• Introduction to Cheminformatics

Categories:

• Methods

Talk Citation

Publication History

• Published on May 31, 2011

Financial Disclosures

• Prof. Tim Clark has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.