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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.

All Categories (61-80 of 209)

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. MIT Tools for Energy Conversion and Storage

    13 Sep 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. MSE 597G An Introduction to Molecular Dynamics

    13 Nov 2008 | Courses | Contributor(s): Alejandro Strachan

    The goal of this short course is to provide an introduction to the theory and algorithms behind MD simulations, describe some of the most exciting recent developments in the field and exemplify...

    http://nanohub.org/resources/5838

  15. Running MD on the nanoHUB: The nano-MATERIALS Simulation Toolkit

    13 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan

    A quick demostration of the nanoHUB tool: nano-Materials Simulation Toolkit.

    http://nanohub.org/resources/5843

  16. MSE 597G Lecture 5: Interatomic potentials II

    13 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan

    Embedded atom model for metals, Three body terms for semiconductors: Stillinger-Weber, Electrostatics and Covalent interactions.

    http://nanohub.org/resources/5777

  17. MSE 597G: An Introduction to Molecular Dynamics

    13 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan

    http://nanohub.org/resources/5760

  18. MSE 597G Lecture 6: Interatomic potentials III

    12 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan

    Reactive force fields, Parameterization of interatomic potentials

    http://nanohub.org/resources/5778

  19. MSE 597G Lecture 7: Advanced Techniques for Molecular Dynamics Simulations

    12 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan

    Thermostats and barostats, Linear methods for energy and force calculations, Coarse graining or mesodynamics, Validation and Verification.

    http://nanohub.org/resources/5779

  20. MSE 597G Lecture 2: Statistical Mechanics I

    11 Nov 2008 | Online Presentations | Contributor(s): Alejandro Strachan

    Basic physics: statistical mechanics.

    http://nanohub.org/resources/5765

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