Course Info
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The aim of this course is to provide the student with an understanding of the methods, capabilities, and limitations of molecular simulation.  This should enable the student to: (1) make sound judgements regarding the quality of molecular simulation studies reported in the literature; (2) decide whether molecular simulation is suited for application to their research, and if so, to know how to begin developing a simulation program applicable to their problems; (3) understand the workings and limitations of commercial molecular simulation software.  Further, it is expected that completion of this course will leave the student with a much deeper understanding of the molecular basis of physical behavior.

Outline of course content

  • Molecular dynamics of hard spheres, demonstrating elementary concepts of temperature, ensemble averaging, error estimation, periodic boundaries.  Structure of a simulation program and introduction to programming methods used in the course.
  • Elementary classical statistical mechanics.  Ensembles and fluctuations.
  • Monte Carlo integration, importance sampling, Markov chains.  Monte Carlo simulation, and extension to other ensembles.
  • Equilibrium molecular dynamics simulations of continuous potentials.  Integration algorithms.  Extended Lagrangians and simulations in other ensembles.  Evaluation of transport coefficients.  Hybrid molecular dynamics/Monte Carlo methods.
  • Modeling of molecules, including hard potentials, soft potentials, multiatomic models.  Torsion, stretch and bend potentials.  Electrostatics and polarizability.  Ewald sum and reaction field methods for treating long-range electrostatic interactions.
  • Free energy calculations.  Examination of several methods:  thermodynamic integration, free-energy perturbation (including umbrella sampling), and histogram methods.
  • Phase equilibria calculations.  Gibbs ensemble and Gibbs-Duhem integration methods. Interfacial properties.
  • Advanced molecular dynamics methods, including constraints and non-equilibrium molecular dynamics.
  • Rare events and evaluation of kinetic properties.
  • Complex fluids and biased-sampling techniques.  Hydrogen-bonding molecules.  Chain molecules.  Rosenbluth sampling and configurational bias methods.


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