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.

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

    14 Sep 2010 | | 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 constants and vibrational spectra of nano- structures and extended periodic materials.

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

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

  3. Polymer Modeler

    28 Jun 2010 | | 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

  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

    19 May 2010 | | 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 with a low energy branch of phonons that exhibits quadratic dispersion at long wave-lengths. Many...

  6. Atomic Stick-Slip

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

    Molecular dynamics simulation of atomic stick-slip friction

  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

    18 Dec 2009 | | 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 polycrystalline metals during tensile tests molecular dynamics simulations of materialsmechanical...

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

    18 Dec 2009 | | 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 nano-Materials Simulation Toolkit.This lecture is part of the learning module Atomic Picture of Plastic...

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

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

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

  11. Lecture 10: Non Equilibrium MD

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

    Topics:Calculating transport coefficientShear flowPerturbation methods

  12. Lecture 9: Dynamic Properties

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

    Topics:Time correlation functionsEinstein relationsGreen-Kubo relations

  13. Lecture 8: Static Properties

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

    Topics:Thermodynamic propertiesEntropic propertiesStatic structure

  14. Lecture 7: Initialization and Equilibrium

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

    Topics:Initial positionsInitial velocitiesEvaluating equilibrium

  15. Lecture 6: Neighbor Lists

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

    Topics:Saving simulation timeVerlet listsCell lists

  16. Lecture 5: Boundary Conditions

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

    Topics:Fixed boundariesPeriodic boundary conditionsMinimum image distance

  17. Lecture 4: Temperature Control

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

    Topics:Velocity scalingHeat bath/reservoirStochastic methods

  18. Lecture 3: Integration Algorithms

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

    Topics:General guidelinesVerlet algorithmPredictor-corrector methods

  19. Lecture 2: Potential Energy Functions

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

    Topics:Pair potentialsCoulomb interactionsEmbedded atom modelIntra-molecular interactions (bond, angle, torsion)

  20. Lecture 1: Basic Concepts

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

    Topics:What is MDNewton’s lawBasic concepts and terminology