
Glass transition temperature notebook
22 May 2017   Contributor(s):: Benjamin P Haley, Lorena AlzateVargas
Calculate the glass transition temperature of an atomistic, amorphous system by running MD simulations in a notebook

Homework assignment: learning about elastic constants via molecular dynamics simulations
17 Feb 2015   Contributor(s):: Alejandro Strachan, David Ray Johnson
In this homework assignment students will use molecular dynamics to compute the elastic constants of metals using an embedded atom model to describe atomic interactions. They will deform a single crystal along different directions and obtain c11, c12 and c44 elastic constants from the...

Illinois Center for Cellular Mechanics: Discovery through the Computational Microscope
09 Feb 2009   Contributor(s):: Klaus Schulten
Computational MicroscopeAllatom 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 Longterm stability of Verlet...

IMA 2013 UQ: Bayesian Calibration of Molecular Dynamics Simulations for Composite Materials Properties
10 Feb 2014   Contributor(s):: Paul N. Patrone
In this talk, I discuss ongoing research whose goal is to determine, via Bayesian inference, an ensemble of inputs that represents a class of commercially important aminecured epoxies. We construct an analytical approximation (i.e. a surrogate or emulator) of the simulations, treating the input...

IMA 2013 UQ: DFTbased Thermal Properties: Three Levels of Error Management
10 Feb 2014   Contributor(s):: Kurt Lejaeghere
It is often computationally expensive to predict finitetemperature properties of a crystal from densityfunctional theory (DFT). The temperaturedependent thermal expansion coefficient α, for example, is calculated from the phonon spectrum, and the melting temperature Tm can only be obtained...

Introduction to Molecular Dynamics
27 Aug 2015   Contributor(s):: Alejandro Strachan

Introduction to Molecular Dynamics
06 Apr 2015   Contributor(s):: Alejandro Strachan
This short presentation will describe the idea behind MD simulations and demonstrate its use in real applications.

Introduction to Molecular Dynamics Showcase
10 Feb 2017   Contributor(s):: ChenYu Li, Karl Steven Decker (editor), Aleksei Aksimentiev
In this tutorial, we will demonstrate how to use the MD showcase builder tool to create a showcase. We will start from the simplest example – creating a showcase from a PDB file – and move on to more complicated examples. We will also cover how to add a description, change...

Introduction: molecular dynamics simulations
09 Jan 2008   Contributor(s):: Alejandro Strachan
This short presentation will describe the idea behind MD simulations and demonstrate its use in real applications.

Ionic Selectivity in Channels: complex biology created by the balance of simple physics
05 Jun 2008   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 control the movement of electric charge and current across biological membranes and so play a role in biology...

LAMMPS DataFile Generator
01 Aug 2017   Contributor(s):: Carlos Miguel Patiño, Lorena AlzateVargas, Chunyu Li, Benjamin P Haley, Alejandro Strachan
This tool generates all necessary input files for LAMMPS simulations of molecular systems starting with an atomistic structure.

LAMMPS driver tool for potential calibration
15 Feb 2019   Contributor(s):: Saaketh Desai, Alejandro Strachan
Calculates basic properties of interest with a given interatomic potential and is used to drive the calibration of the potential.

LAMMPS Structure Analysis Toolkit
07 Dec 2017   Contributor(s):: Nicholas J Finan, Saaketh Desai, Sam Reeve, Alejandro Strachan
Perform structural analysis on trajectories in LAMMPS dump format

LAMMPS structure generator
01 Nov 2016   Contributor(s):: Benjamin P Haley
Convert a molecular structure file to a LAMMPS data file with force field parameters

Lecture 10: Non Equilibrium MD
05 Jan 2010   Contributor(s):: Ashlie Martini
Topics:Calculating transport coefficientShear flowPerturbation methods

Lecture 1: Basic Concepts
13 Nov 2009   Contributor(s):: Ashlie Martini
Topics:What is MDNewton’s lawBasic concepts and terminology

Lecture 1: the theory behind molecular dynamics
09 Jan 2008   Contributor(s):: Alejandro Strachan
The first lecture will provide a brief description of classical mechanics and statistical mechanics necessary to understand the physics and approximations behind MD and how to correctly interpret and analyze its results. The power, range of applicability and limitations of MD will be discussed.

Lecture 2: Potential Energy Functions
05 Jan 2010   Contributor(s):: Ashlie Martini
Topics:Pair potentialsCoulomb interactionsEmbedded atom modelIntramolecular interactions (bond, angle, torsion)

Lecture 2: total energy and force calculations
14 Jan 2008   Contributor(s):: Alejandro Strachan
This lecture will describe the various models used to describe the interactions between atoms in a wide range of materials including metals, ceramics and soft materials as well as new recent advances like reactive force fields. The key physics of widely used force fields will be described as well...