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Molecular dynamics is a form of computer simulation in which atoms and molecules are allowed to interact for a period of time by approximations of known physics, giving a view of the motion of the particles. This kind of simulation is frequently used in the study of proteins and biomolecules, as well as in materials science. More information on Molecular dynamics can be found here.
Lecture 10: Non Equilibrium MD
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05 Jan 2010 | Notes | Contributor(s): Ashlie Martini
Topics: Calculating transport coefficient Shear flow Perturbation methods
Lecture 1: Basic Concepts
Topics: What is MD Newton’s law Basic concepts and terminology
Lecture 2: Potential Energy Functions
Topics: Pair potentials Coulomb interactions Embedded atom model Intra-molecular interactions (bond, angle, torsion)
Lecture 3: Integration Algorithms
Topics: General guidelines Verlet algorithm Predictor-corrector methods
Lecture 4: Temperature Control
Topics: Velocity scaling Heat bath/reservoir Stochastic methods
Lecture 5: Boundary Conditions
Topics: Fixed boundaries Periodic boundary conditions Minimum image distance
Lecture 6: Neighbor Lists
Topics: Saving simulation time Verlet lists Cell lists
Lecture 7: Initialization and Equilibrium
Topics: Initial positions Initial velocities Evaluating equilibrium
Lecture 8: Static Properties
Topics: Thermodynamic properties Entropic properties Static structure
Lecture 9: Dynamic Properties
Topics: Time correlation functions Einstein relations Green-Kubo relations
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