
Lecture 10: Non Equilibrium MD
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Calculating transport coefficient
Shear flow
Perturbation methods
http://nanohub.org/resources/8125

Lecture 1: Basic Concepts
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
What is MD
Newton’s law
Basic concepts and terminology
http://nanohub.org/resources/7795

Lecture 2: Potential Energy Functions
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Pair potentials
Coulomb interactions
Embedded atom model
Intramolecular interactions (bond, angle, torsion)
http://nanohub.org/resources/8117

Lecture 3: Integration Algorithms
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
General guidelines
Verlet algorithm
Predictorcorrector methods
http://nanohub.org/resources/8118

Lecture 4: Temperature Control
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Velocity scaling
Heat bath/reservoir
Stochastic methods
http://nanohub.org/resources/8119

Lecture 5: Boundary Conditions
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Fixed boundaries
Periodic boundary conditions
Minimum image distance
http://nanohub.org/resources/8120

Lecture 6: Neighbor Lists
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Saving simulation time
Verlet lists
Cell lists
http://nanohub.org/resources/8121

Lecture 7: Initialization and Equilibrium
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Initial positions
Initial velocities
Evaluating equilibrium
http://nanohub.org/resources/8122

Lecture 8: Static Properties
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Thermodynamic properties
Entropic properties
Static structure
http://nanohub.org/resources/8123

Lecture 9: Dynamic Properties
05 Jan 2010  Presentation Materials  Contributor(s): Ashlie Martini
Topics:
Time correlation functions
Einstein relations
GreenKubo relations
http://nanohub.org/resources/8124