
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

Short Course on Molecular Dynamics Simulation
13 Oct 2009  Courses  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...
http://nanohub.org/resources/7570

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

Energy and Nanoscience A More Perfect Union
29 Mar 2009  Online Presentations  Contributor(s): Mark A. 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,...
http://nanohub.org/resources/6554

Illinois Center for Cellular Mechanics: Discovery through the Computational Microscope
11 Feb 2009  Online Presentations  Contributor(s): Klaus Schulten
Computational Microscope
Allatom molecular dynamics simulations have become increasingly popular as a tool
to investigate protein function and dynamics. However, researchers are...
http://nanohub.org/resources/6253

Illinois PHYS 466, Lecture 4: Molecular Dynamics
05 Feb 2009  Online Presentations  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:
...
http://nanohub.org/resources/6239

Nanoparticle and Colloidal Simulations with Molecular Dynamics
05 Dec 2008  Online Presentations  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...
http://nanohub.org/resources/5668

MSE 597G Lecture 4: Interatomic potentials I
14 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Interatomic potentials: pairwise potentials.
http://nanohub.org/resources/5776

MSE 597G Lecture 3: Statistical Mechanics II
14 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Basic physics: statistical mechanics, Algorithms: Integrating the equations of motion.
http://nanohub.org/resources/5775

MSE 597G An Introduction to Molecular Dynamics
13 Nov 2008  Courses  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...
http://nanohub.org/resources/5838

Running MD on the nanoHUB: The nanoMATERIALS Simulation Toolkit
13 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
A quick demostration of the nanoHUB tool: nanoMaterials Simulation Toolkit.
http://nanohub.org/resources/5843

MSE 597G Lecture 5: Interatomic potentials II
13 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Embedded atom model for metals,
Three body terms for semiconductors: StillingerWeber,
Electrostatics and Covalent interactions.
http://nanohub.org/resources/5777

MSE 597G: An Introduction to Molecular Dynamics
13 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
http://nanohub.org/resources/5760

MSE 597G Lecture 6: Interatomic potentials III
12 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Reactive force fields,
Parameterization of interatomic potentials
http://nanohub.org/resources/5778

MSE 597G Lecture 7: Advanced Techniques for Molecular Dynamics Simulations
12 Nov 2008  Online Presentations  Contributor(s): Alejandro Strachan
Thermostats and barostats,
Linear methods for energy and force calculations,
Coarse graining or mesodynamics,
Validation and Verification.
http://nanohub.org/resources/5779