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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.

Resources (21-40 of 93)

  1. Atomic Picture of Plastic Deformation in Metals via Online Molecular Dynamics Simulations

    01 Jun 2011 | Courses | Contributor(s): Alejandro Strachan

    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/resources/8037

  2. Additional Tutorials on Selected Topics in Nanotechnology

    29 Mar 2011 | Workshops | Contributor(s): Gerhard Klimeck, Umesh V. Waghmare, Timothy S Fisher, N. S. Vidhyadhiraja

    Select tutorials in nanotechnology, a part of the 2010 NCN@Purdue Summer School: Electronics from the Bottom Up.

    http://nanohub.org/resources/11041

  3. OPV: Time Domain Ab Initio Studies of Organic-Inorganic Composites for Solar Cells

    31 Jan 2011 | Online Presentations | Contributor(s): Oleg Prezhdo

    This presentation was part of the "Organic Photovoltaics: Experiment and Theory" workshop at the 2010 Users' Meeting of the Molecular Foundry and the National Center for Electron Microscopy, both...

    http://nanohub.org/resources/10507

  4. Uncertainty Quantification of Molecular Dynamics Simulations

    31 Jan 2011 | Online Presentations | Contributor(s): Alejandro Strachan

    A full course, "Introduction to Uncertainty Quantification" is offered on memsHUB.org. ME597/AAE590: Introduction to Uncertainty Quantification NNSA Center for Prediction of Reliability,...

    http://nanohub.org/resources/10693

  5. 2010 NCN@Purdue Summer School: Electronics from the Bottom Up

    18 Jan 2011 | Workshops

    Electronics from the Bottom Up seeks to bring a new perspective to electronic devices – one that is designed to help realize the opportunities that nanotechnology presents.

    http://nanohub.org/resources/8878

  6. 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...

    http://nanohub.org/resources/9856

  7. 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

  8. 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 to...

    http://nanohub.org/resources/9684

  9. Polymer Modeler

    28 Jun 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

  10. 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

  11. Atomic Stick-Slip

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

    Molecular dynamics simulation of atomic stick-slip friction

    http://nanohub.org/resources/stickslip

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

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