
Lecture 10: Non Equilibrium MD
05 Jan 2010   Contributor(s):: Ashlie Martini
Topics:Calculating transport coefficientShear flowPerturbation methods

Lecture 9: Dynamic Properties
05 Jan 2010   Contributor(s):: Ashlie Martini
Topics:Time correlation functionsEinstein relationsGreenKubo relations

Lecture 8: Static Properties
05 Jan 2010   Contributor(s):: Ashlie Martini
Topics:Thermodynamic propertiesEntropic propertiesStatic structure

Lecture 7: Initialization and Equilibrium
05 Jan 2010   Contributor(s):: Ashlie Martini
Topics:Initial positionsInitial velocitiesEvaluating equilibrium

Lecture 6: Neighbor Lists
05 Jan 2010   Contributor(s):: Ashlie Martini
Topics:Saving simulation timeVerlet listsCell lists

Lecture 5: Boundary Conditions
05 Jan 2010   Contributor(s):: Ashlie Martini
Topics:Fixed boundariesPeriodic boundary conditionsMinimum image distance

Lecture 4: Temperature Control
05 Jan 2010   Contributor(s):: Ashlie Martini
Topics:Velocity scalingHeat bath/reservoirStochastic methods

Lecture 3: Integration Algorithms
05 Jan 2010   Contributor(s):: Ashlie Martini
Topics:General guidelinesVerlet algorithmPredictorcorrector methods

Lecture 2: Potential Energy Functions
05 Jan 2010   Contributor(s):: Ashlie Martini
Topics:Pair potentialsCoulomb interactionsEmbedded atom modelIntramolecular interactions (bond, angle, torsion)

Lecture 1: Basic Concepts
05 Jan 2010   Contributor(s):: Ashlie Martini
Topics:What is MDNewton’s lawBasic concepts and terminology

Short Course on Molecular Dynamics Simulation
13 Oct 2009   Contributor(s):: Ashlie Martini
This set of ten presentations accompanied a graduate level course on Molecular Dynamics simulation. The specific objective of the course (and the presentations) is to provide:1. Awareness of the opportunities and limitations of Molecular Dynamics as a tool for scientific and engineering...

MIT Tools for Energy Conversion and Storage
13 Sep 2009   Contributor(s):: Jeffrey C Grossman, JooHyoung Lee, Varadharajan Srinivasan, Alexander S McLeod, Lucas Wagner
AtomicScale Simulation Tools to Explore Energy Conversion and Storage Materials

Energy and Nanoscience A More Perfect Union
27 Mar 2009   Contributor(s):: Mark Ratner
Huge problems of energy and sustainability confront the science/engineering community, mankind, and our planet. The energy problem comes in many dimensions, including supply, demand, conservation, transportation, and storage. This overview will stress the nature of these problems, and offer a few...

Illinois Center for Cellular Mechanics: Discovery through the Computational Microscope
09 Feb 2009   Contributor(s):: Klaus Schulten
Computational MicroscopeAllatom molecular dynamics simulations have become increasingly popular as a toolto investigate protein function and dynamics. However, researchers are usuallyconcerned about the short time scales covered by simulations, the apparentimpossibility to model large and...

Illinois PHYS 466, Lecture 4: Molecular Dynamics
05 Feb 2009   Contributor(s):: David M. Ceperley
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 Longterm stability of Verlet...

Nanoparticle and Colloidal Simulations with Molecular Dynamics
05 Dec 2008   Contributor(s):: Steve Plimpton
Modeling nanoparticle or colloidal systems in a molecular dynamics (MD) code requires coarsegraining on several levels to achieve meaningful simulation times for study of rheological and other manufacturing properties. These include treating colloids as single particles, moving from explicit to...

MSE 597G Lecture 4: Interatomic potentials I
14 Nov 2008   Contributor(s):: Alejandro Strachan
Interatomic potentials: pairwise potentials.

MSE 597G Lecture 3: Statistical Mechanics II
14 Nov 2008   Contributor(s):: Alejandro Strachan
Basic physics: statistical mechanics, Algorithms: Integrating the equations of motion.

MSE 597G An Introduction to Molecular Dynamics
13 Nov 2008   Contributor(s):: Alejandro Strachan
The goal of this short course is to provide an introduction to the theory and algorithms behind MD simulations, describe some of the most exciting recent developments in the field and exemplify with a few applications applications. The series also includes a tutorial on the nanoMATERIALS...

Running MD on the nanoHUB: The nanoMATERIALS Simulation Toolkit
13 Nov 2008   Contributor(s):: Alejandro Strachan
A quick demostration of the nanoHUB tool: nanoMaterials Simulation Toolkit.