Tags: molecular dynamics

Description

Molecular dynamics is a form of computer simulation in which atoms and molecules are allowed to interact for a period of time by approximations of known physics, giving a view of the motion of the particles. This kind of simulation is frequently used in the study of proteins and biomolecules, as well as in materials science. More information on Molecular dynamics can be found here.

All Categories (81-100 of 143)

  1. Atomic Picture of Plastic Deformation in Metals: Prelab Lecture

    24 Jan 2010 | Online Presentations | Contributor(s): Alejandro Strachan

    This lecture provides a detailed description of the activities the students will perform in the lab. We present a tutorial with step by step instructions on how to run MD simulations using the...

    http://nanohub.org/resources/8043

  2. Atomic Picture of Plastic Deformation in Metals: Lab Assignment Handout

    19 Jan 2010 | Teaching Materials | Contributor(s): Alejandro Strachan

    In this lab students will perform online molecular dynamics (MD) simulations of metallic nanowires deformed uniaxially and analyze the results...

    http://nanohub.org/resources/8140

  3. Lecture 10: Non Equilibrium MD

    05 Jan 2010 | Presentation Materials | Contributor(s): Ashlie Martini

    Topics: Calculating transport coefficient Shear flow Perturbation methods

    http://nanohub.org/resources/8125

  4. Lecture 9: Dynamic Properties

    05 Jan 2010 | Presentation Materials | Contributor(s): Ashlie Martini

    Topics: Time correlation functions Einstein relations Green-Kubo relations

    http://nanohub.org/resources/8124

  5. Lecture 8: Static Properties

    05 Jan 2010 | Presentation Materials | Contributor(s): Ashlie Martini

    Topics: Thermodynamic properties Entropic properties Static structure

    http://nanohub.org/resources/8123

  6. Lecture 7: Initialization and Equilibrium

    05 Jan 2010 | Presentation Materials | Contributor(s): Ashlie Martini

    Topics: Initial positions Initial velocities Evaluating equilibrium

    http://nanohub.org/resources/8122

  7. 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

  8. 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

  9. 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

  10. Lecture 3: Integration Algorithms

    05 Jan 2010 | Presentation Materials | Contributor(s): Ashlie Martini

    Topics: General guidelines Verlet algorithm Predictor-corrector methods

    http://nanohub.org/resources/8118

  11. Lecture 2: Potential Energy Functions

    05 Jan 2010 | Presentation Materials | Contributor(s): Ashlie Martini

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

    http://nanohub.org/resources/8117

  12. 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

  13. 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

  14. MIT Tools for Energy Conversion and Storage

    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

    http://nanohub.org/resources/nanoenergytools

  15. 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

  16. Illinois Center for Cellular Mechanics: Discovery through the Computational Microscope

    11 Feb 2009 | Online Presentations | Contributor(s): Klaus Schulten

    Computational Microscope All-atom molecular dynamics simulations have become increasingly popular as a tool to investigate protein function and dynamics. However, researchers are...

    http://nanohub.org/resources/6253

  17. 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

  18. 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...

    http://nanohub.org/resources/5668

  19. 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

  20. 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