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 151)

  1. Tutorial 3: Materials Simulation by First-Principles Density Functional Theory

    14 Sep 2010 | Courses | Contributor(s): Umesh V. Waghmare

    This two-part lecture will provide an introduction to first-principles density functional theory based methods for simulation of materials, with a focus on determination of interatomic force...

    http://nanohub.org/resources/9716

  2. Tutorial 3b: Materials Simulation by First-Principles Density Functional Theory II

    14 Sep 2010 | Online Presentations | Contributor(s): Umesh V. Waghmare

    This lecture is part of the 2010 NCN@Purdue Summer School: Electronics from the Bottom Up. “Electronics from the Bottom Up” is an educational initiative designed to bring a new perspective...

    http://nanohub.org/resources/9684

  3. Polymer Modeler

    25 Aug 2010 | Tools | Contributor(s): Benjamin P Haley, Nate Wilson, Chunyu Li, Andrea Arguelles, Eugenio Jaramillo, Alejandro Strachan

    Build thermoplastic polymer chains and run LAMMPS to relax the chains and study mechanical properties

    http://nanohub.org/resources/polymod

  4. Francisco Murphy

    Studying biochemistry and molecular biology Want to do a master

    http://nanohub.org/members/45284

  5. Ripples and Warping of Graphene: A Theoretical Study

    08 Jun 2010 | Online Presentations | Contributor(s): Umesh V. Waghmare

    We use first-principles density functional theory based analysis to understand formation of ripples in graphene and related 2-D materials. For an infinite graphene, we show that ripples are linked...

    http://nanohub.org/resources/9010

  6. Atomic Stick-Slip

    31 Mar 2010 | Tools | Contributor(s): Ashlie Martini, Jianguo Wu

    Molecular dynamics simulation of atomic stick-slip friction

    http://nanohub.org/resources/stickslip

  7. Learning Module: Atomic Picture of Plastic Deformation in Metals

    The main goal of this learning module is to introduce students to the atomic-level processes responsible for plastic deformation in crystalline metals and help them develop a more intuitive...

    http://nanohub.org/wiki/LearningModulePlasticityMD

  8. Atomic Picture of Plastic Deformation in Metals: Overview Lecture

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

    The lecture describes the objectives of the learning module and provides the necessary background for the activities. We briefly discuss the following topics: mechanical response of macroscopic...

    http://nanohub.org/resources/8038

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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