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Lecture 6: Neighbor Lists
Presentation Materials | 05 Jan 2010 | Contributor(s):: Ashlie Martini
Topics:Saving simulation timeVerlet listsCell lists
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Lecture 5: Boundary Conditions
Presentation Materials | 05 Jan 2010 | Contributor(s):: Ashlie Martini
Topics:Fixed boundariesPeriodic boundary conditionsMinimum image distance
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Lecture 4: Temperature Control
Presentation Materials | 05 Jan 2010 | Contributor(s):: Ashlie Martini
Topics:Velocity scalingHeat bath/reservoirStochastic methods
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Lecture 3: Integration Algorithms
Presentation Materials | 05 Jan 2010 | Contributor(s):: Ashlie Martini
Topics:General guidelinesVerlet algorithmPredictor-corrector methods
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Lecture 2: Potential Energy Functions
Presentation Materials | 05 Jan 2010 | Contributor(s):: Ashlie Martini
Topics:Pair potentialsCoulomb interactionsEmbedded atom modelIntra-molecular interactions (bond, angle, torsion)
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Lecture 1: Basic Concepts
Presentation Materials | 05 Jan 2010 | Contributor(s):: Ashlie Martini
Topics:What is MDNewton’s lawBasic concepts and terminology
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Short Course on Molecular Dynamics Simulation
Courses | 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...
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MIT Tools for Energy Conversion and Storage
Tools | 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
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Energy and Nanoscience A More Perfect Union
Online Presentations | 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...
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Illinois Center for Cellular Mechanics: Discovery through the Computational Microscope
Online Presentations | 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...
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Illinois PHYS 466, Lecture 4: Molecular Dynamics
Online Presentations | 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...
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Illinois MatSE485/Phys466/CSE485 - Atomic-Scale Simulation
Courses | 27 Jan 2009 | Contributor(s):: David M. Ceperley
THE OBJECTIVE is to learn and apply fundamental techniques used in (primarily classical) simulations in order to help understand and predict properties of microscopic systems in materials science, physics, chemistry, and biology. THE EMPHASIS will be on connections between the simulation...
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Nanoparticle and Colloidal Simulations with Molecular Dynamics
Online Presentations | 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...
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MSE 597G Lecture 4: Interatomic potentials I
Online Presentations | 14 Nov 2008 | Contributor(s):: Alejandro Strachan
Interatomic potentials: pairwise potentials.
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MSE 597G Lecture 3: Statistical Mechanics II
Online Presentations | 14 Nov 2008 | Contributor(s):: Alejandro Strachan
Basic physics: statistical mechanics, Algorithms: Integrating the equations of motion.
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MSE 597G An Introduction to Molecular Dynamics
Courses | 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...
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Running MD on the nanoHUB: The nano-MATERIALS Simulation Toolkit
Online Presentations | 13 Nov 2008 | Contributor(s):: Alejandro Strachan
A quick demostration of the nanoHUB tool: nano-Materials Simulation Toolkit.
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MSE 597G Lecture 5: Interatomic potentials II
Online Presentations | 13 Nov 2008 | Contributor(s):: Alejandro Strachan
Embedded atom model for metals,Three body terms for semiconductors: Stillinger-Weber,Electrostatics and Covalent interactions.
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MSE 597G: An Introduction to Molecular Dynamics
Online Presentations | 13 Nov 2008 | Contributor(s):: Alejandro Strachan
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MSE 597G Lecture 6: Interatomic potentials III
Online Presentations | 12 Nov 2008 | Contributor(s):: Alejandro Strachan
Reactive force fields,Parameterization of interatomic potentials