Illinois PHYS 466, Lecture 4: Molecular Dynamics
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Recommendations
- Illinois PHYS 466, Lecture 3: Basics of Statistical Mechanics
- Illinois PHYS 466, Lecture 1: Introduction
- Illinois PHYS 466, Lecture 5: Interatomic Potentials
- Illinois PHYS 466, Lecture 19: The Ising Model
- Illinois PHYS 466, Lecture 10: Sampling
- Illinois PHYS 466, Lecture 17: Simulation of Polymers
- Illinois PHYS 466, Lecture 16: Free Energies from Simulations
- Illinois PHYS 466, Lecture 8: Temperature and Pressure Controls
- Illinois PHYS 466, Lecture 11: Importance Sampling
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Abstract
Molecular Dynamics
- What to choose in an integrator
- The
Verlet algorithm - Boundary Conditions in Space and time
- Reading assignment: Frenkel and Smit Chapter 4
Content:
- 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
Credits
Submitted and Breezed by Omar Sobh
Cite this work
Researchers should cite this work as follows:
-
David M. Ceperley (2009), "Illinois PHYS 466, Lecture 4: Molecular Dynamics," https://nanohub.org/resources/6239.