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Printable Handouts
Navigable Slide Index
- Introduction
- Classical mechanical models of molecules
- Calculation methods
- The Morse potential
- What is a force field?
- What isn't a force field?
- Harmonic bond-stretch potential
- Harmonic angle-bend potential
- Torsional potentials
- Van der Waals potentials
- Lennard-Jones potential curve
- Potentials - "improper" torsions
- Electrostatic (Coulomb) interactions
- "The fallacy of atomic charges"
- Dipole-dipole interactions
- Force-field methods (1)
- Geometry optimization
- Minima and transition states
- Energy curve of normal vibrations
- A physical model to visualize a transition state
- Geometry optimisation
- Optimisation techniques
- Force constant matrix (Hessian)
- Transition states
- 2D-reaction profile
- Force-field methods (2)
- Hamiltonian and Sampling
- The danger of using only one conformation
- Why we need to sample
- Sampling and statistical mechanics
- Calculations in statistical mechanics
- Monte-Carlo simulations
- Monte-Carlo calculations: an example
- Thermodynamic equilibrium
- Importance sampling
- Metropolis sampling
- Metropolis Monte-Carlo algorithm
- Molecular Dynamics (MD)
- The Ergodic hypothesis
- Newton's equation of motion
- Newton's second law of motion (1)
- Newton's second law of motion (2)
- MD is driven by numerical integration
- Typical parameters of a MD simulation
- Energy
- Temperature
- Periodic boundary conditions
- Simulation time
- Range of biological motions
- Time-scale of molecular events
- Definitions
- Thermodynamic state definitions
- Applications of MD
- Summary and acknowledgments
Topics Covered
- Force fields
- Geometry optimization
- Minima and transition states
- Sampling
- Monte Carlo
- Molecular dynamics
Talk Citation
Clark, T. (2011, May 31). Molecular modelling: empirical methods [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved December 3, 2024, from https://doi.org/10.69645/MTME6568.Export Citation (RIS)
Publication History
Financial Disclosures
- Prof. Tim Clark has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.