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Lecture 10: Non Equilibrium MD
05 Jan 2010 | | Contributor(s):: Ashlie Martini
Topics:Calculating transport coefficientShear flowPerturbation methods
Lecture 9: Dynamic Properties
Topics:Time correlation functionsEinstein relationsGreen-Kubo relations
Lecture 8: Static Properties
Topics:Thermodynamic propertiesEntropic propertiesStatic structure
Lecture 7: Initialization and Equilibrium
Topics:Initial positionsInitial velocitiesEvaluating equilibrium
Lecture 6: Neighbor Lists
Topics:Saving simulation timeVerlet listsCell lists
Lecture 5: Boundary Conditions
Topics:Fixed boundariesPeriodic boundary conditionsMinimum image distance
Lecture 4: Temperature Control
Topics:Velocity scalingHeat bath/reservoirStochastic methods
Lecture 3: Integration Algorithms
Topics:General guidelinesVerlet algorithmPredictor-corrector methods
Lecture 2: Potential Energy Functions
Topics:Pair potentialsCoulomb interactionsEmbedded atom modelIntra-molecular interactions (bond, angle, torsion)
Lecture 1: Basic Concepts
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, Joo-Hyoung Lee, Varadharajan Srinivasan, Alexander S McLeod, Lucas Wagner
Atomic-Scale 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 MicroscopeAll-atom 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 Long-term stability of Verlet...
Nanoparticle and Colloidal Simulations with Molecular Dynamics
out of 5 stars
05 Dec 2008 | | Contributor(s):: Steve Plimpton
Modeling nanoparticle or colloidal systems in a molecular dynamics (MD) code requires coarse-graining 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
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 nano-MATERIALS Simulation Toolkit
A quick demostration of the nanoHUB tool: nano-Materials Simulation Toolkit.