
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 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

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 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 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 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 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 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 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 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