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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
0.0 out of 5 stars
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 channels...
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...
5.0 out of 5 stars
31 Mar 2008 | Tools | Contributor(s): Sanket S Mahajan, Ganesh Subbarayan, Xufeng Wang
Code to perform Molecular Dynamics (MD) Simulations
Computational Nanoscience, Homework Assignment 3: Molecular Dynamics Simulation of Carbon Nanotubes
15 Feb 2008 | Teaching Materials | Contributor(s): Elif Ertekin, Jeffrey C Grossman
The purpose of this assignment is to perform molecular dynamics simulations to calculate various properties of carbon nanotubes using LAMMPS and Tersoff potentials.
This assignment is to be...
Computational Nanoscience, Homework Assignment 2: Molecular Dynamics Simulation of a Lennard-Jones Liquid
The purpose of this assignment is to perform a full molecular dynamics simulation based on the Verlet algorithm to calculate various properties of a simple liquid, modeled as an ensemble of...
Computational Nanoscience, Lecture 6: Pair Distribution Function and More on Potentials
15 Feb 2008 | Teaching Materials | Contributor(s): Jeffrey C Grossman, Elif Ertekin
In this lecture we remind ourselves what a pair distribution function is, how to compute it, and why it is so important in simulations. Then, we revisit potentials and go into more detail...
Computational Nanoscience, Lecture 5: A Day of In-Class Simulation: MD of Carbon Nanostructures
In this lecture we carry out simulations in-class, with guidance from the instructors. We use the LAMMPS tool (within the nanoHUB simulation toolkit for this course). Examples include...