Frenkel-Kontarova Model

11 Jul 2011 | Tools | Contributor(s): Calvin J Mwesigwa, Ashlie Martini

Simulate movement of simple molecules over a 2D potential energy landscape due to external forcing using the Frenkel-Kontarova model

Protein Contact Maps

22 Oct 2010 | Tools | Contributor(s): Benjamin Rafferty, Zachary Carl Flohr, Ashlie Martini

Create and view protein contact maps and distance maps.

Addressing Molecular Dynamics Time-scale Issues to Study Atomic-scale Friction

12 Oct 2010 | Online Presentations | Contributor(s): Ashlie Martini

This presentation will include an introduction to several accelerated molecular dynamics methods. However, particular focus will be given to parallel replica (ParRep) dynamics in which atomistic simulations are run parallel in time to extend their total duration. The ParRep method is based on the …

Atomic Stick-Slip

09 Nov 2009 | Tools | Contributor(s): Ashlie Martini, Jianguo Wu

Molecular dynamics simulation of atomic stick-slip friction

Lecture 10: Non Equilibrium MD

05 Jan 2010 | Notes | Contributor(s): Ashlie Martini

Topics: Calculating transport coefficient Shear flow Perturbation methods

Lecture 9: Dynamic Properties

05 Jan 2010 | Notes | Contributor(s): Ashlie Martini

Topics: Time correlation functions Einstein relations Green-Kubo relations

Lecture 8: Static Properties

05 Jan 2010 | Notes | Contributor(s): Ashlie Martini

Topics: Thermodynamic properties Entropic properties Static structure

Lecture 7: Initialization and Equilibrium

05 Jan 2010 | Notes | Contributor(s): Ashlie Martini

Topics: Initial positions Initial velocities Evaluating equilibrium

Lecture 6: Neighbor Lists

05 Jan 2010 | Notes | Contributor(s): Ashlie Martini

Topics: Saving simulation time Verlet lists Cell lists

Lecture 5: Boundary Conditions

05 Jan 2010 | Notes | Contributor(s): Ashlie Martini

Topics: Fixed boundaries Periodic boundary conditions Minimum image distance

Lecture 4: Temperature Control

05 Jan 2010 | Notes | Contributor(s): Ashlie Martini

Topics: Velocity scaling Heat bath/reservoir Stochastic methods

Lecture 3: Integration Algorithms

05 Jan 2010 | Notes | Contributor(s): Ashlie Martini

Topics: General guidelines Verlet algorithm Predictor-corrector methods

Lecture 2: Potential Energy Functions

05 Jan 2010 | Notes | Contributor(s): Ashlie Martini

Topics: Pair potentials Coulomb interactions Embedded atom model Intra-molecular interactions (bond, angle, torsion)

Lecture 1: Basic Concepts

13 Nov 2009 | Notes | Contributor(s): Ashlie Martini

Topics: What is MD Newton’s law Basic concepts and terminology

Short Course on Molecular Dynamics Simulation

11 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 the opportunities and limitations of Molecular Dynamics as a tool for scientific and engineering …

Forced Protein Unfolding

01 Jun 2009 | Tools | Contributor(s): Ashlie Martini, Benjamin Rafferty, Zachary Carl Flohr

Molecular dynamics simulation of forced protein unfolding