Find information on common issues.
Ask questions and find answers from other users.
Suggest a new site feature or improvement.
Check on status of your tickets.
Lecture 2: Potential Energy Functions
05 Jan 2010 | Presentation Materials | Contributor(s): Ashlie Martini
Embedded atom model
Intra-molecular interactions (bond, angle, torsion)
Lecture 1: Basic Concepts
What is MD
Basic concepts and terminology
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...
MIT Tools for Energy Conversion and Storage
0.0 out of 5 stars
12 Oct 2009 | Tools | 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
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,...
Illinois Center for Cellular Mechanics: Discovery through the Computational Microscope
11 Feb 2009 | Online Presentations | Contributor(s): Klaus Schulten
All-atom molecular dynamics simulations have become increasingly popular as a tool
to investigate protein function and dynamics. However, researchers are...
Illinois PHYS 466, Lecture 4: Molecular Dynamics
05 Feb 2009 | Online Presentations | Contributor(s): David M. Ceperley
What to choose in an integrator
The Verlet algorithm
Boundary Conditions in Space and time
Reading assignment: Frenkel and Smit Chapter 4
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 coarse-graining on several levels to achieve meaningful simulation times for study of rheological and other...
MSE 597G Lecture 4: Interatomic potentials I
14 Nov 2008 | Online Presentations | 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
4.5 out of 5 stars
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...
Running MD on the nanoHUB: The nano-MATERIALS Simulation Toolkit
13 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan
A quick demostration of the nanoHUB tool: nano-Materials Simulation Toolkit.
MSE 597G Lecture 5: Interatomic potentials II
Embedded atom model for metals,
Three body terms for semiconductors: Stillinger-Weber,
Electrostatics and Covalent interactions.
MSE 597G: An Introduction to Molecular Dynamics
MSE 597G Lecture 6: Interatomic potentials III
12 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan
Reactive force fields,
Parameterization of interatomic potentials
MSE 597G Lecture 7: Advanced Techniques for Molecular Dynamics Simulations
Thermostats and barostats,
Linear methods for energy and force calculations,
Coarse graining or mesodynamics,
Validation and Verification.
MSE 597G Lecture 2: Statistical Mechanics I
11 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan
Basic physics: statistical mechanics.
MSE 597G Lecture 1: Classical Mechanics
Basic physics: classical mechanics
Ionic Selectivity in Channels: complex biology created by the balance of simple physics
3.5 out of 5 stars
05 Jun 2008 | Online Presentations | Contributor(s): Bob Eisenberg
An important class of biological molecules—proteins called ionic channels—conduct ions (like Na+ , K+ , Ca2+ , and Cl− ) through a narrow tunnel of fixed charge (‘doping’). Ionic...
BNC Annual Research Review: An Introduction to PRISM and MEMS Simulation
04 Jun 2008 | Online Presentations | Contributor(s): Jayathi Murthy
This presentation is part of a collection of presentations describing the projects, people, and capabilities enhanced by research performed in the Birck Center, and a look at plans for the...