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Illinois PHYS 466, Lecture 4: Molecular Dynamics

By David M. Ceperley

University of Illinois at Urbana-Champaign

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Molecular Dynamics

  • What to choose in an integrator
  • The Verlet algorithm
  • Boundary Conditions in Space and time
  • Reading assignment: Frenkel and Smit Chapter 4


  • Characteristics of simulations
  • The Verlet Algorithm
  • Higher Order Methods?
  • Quote from Berendsen
  • Long-term stability of Verlet
  • Spatial Boundary Conditions
  • Why use Periodic Boundary Conditions?
  • Periodic Boundary Conditions
  • Periodic distances
  • LJ Force Computation
  • Complexity of Force Calculations
  • Neighbor Lists: O(N2) to O(N)
  • A Neighbor Table
  • Constructing Neighbor Lists: use skin depth
  • Improvements: the Cell Method
  • Next time


Submitted and Breezed by Omar Sobh

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Researchers should cite this work as follows:

  • David M. Ceperley (2009), "Illinois PHYS 466, Lecture 4: Molecular Dynamics,"

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