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Molecular Simulation

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This is a book on computer simulation of matter. In particular, it focuses on condensed matter (e.g., liquids). The book is built on the framework of statistical thermodynamics. It is intended to serve as the textbook for an advanced undergraduate / graduate physical chemistry course in molecular simulation.

Table of Contents[edit | edit source]

  1. Molecular forces
    1. Charge-Charge Interactions
    2. Charge-Dipole Interactions
    3. Dipole-Dipole Interactions
    4. Quadrupole-Quadrupole Interactions
    5. Induced Polarization
    6. Repulsive Interactions
    7. Hydrogen Bonds
    8. Rotational Averaging
    9. The Lennard-Jones Potential
    10. Intramolecular Forces
    11. Molecular Mechanical Force Fields
    12. Calculation of molecular forces using quantum chemistry
  2. Classical Statistical Thermodynamics
    1. Statistical properties
    2. Thermodynamic ensembles
    3. Phase space
    4. Dilute gases
    5. Potential of mean force
    6. Langevin dynamics
  3. Simulation Methods
    1. Periodic Boundary Conditions
    2. Treatment of Long Range Forces
    3. Monte Carlo Methods
    4. Molecular Dynamics
    5. Molecular Dynamics of the Canonical and Isothermal-Isobaric Ensembles
    6. Umbrella Sampling
    7. Free Energy Methods
    8. Replica Exchange Molecular Dynamics
    9. Coarse grain models
    10. Polarizable force fields
  4. Liquid Properties
    1. Radial Distribution Functions
    2. Dielectric constants
    3. Diffusion Coefficients
    4. Interfacial properties
    5. Transport properties
  5. Solid Properties
    1. Solids
  6. Understanding Chemistry Through Molecular Simulation
    1. Hydrophobic Solvation
    2. Membrane permeability
    3. Protein folding
  7. Appendices
    1. Definition of variables
    2. Molecular Dynamics Simulations Using NAMD