Please help us continue to improve nanoHUB operation and service by completing our survey - http://bit.ly/nH-survey14. Thank you - we appreciate your time. close

Support

Support Options

Submit a Support Ticket

 

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. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. MSE 597G: An Introduction to Molecular Dynamics

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

    http://nanohub.org/resources/5760

  8. 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

  9. 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

  10. 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

  11. MSE 597G Lecture 1: Classical Mechanics

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

    Basic physics: classical mechanics

    http://nanohub.org/resources/5507

  12. Ionic Selectivity in Channels: complex biology created by the balance of simple physics

    05 Jun 2008 | Online Presentations | Contributor(s): Bob Eisenberg

    An important class of biological molecules—proteins called ionic channels—conduct ions (like Na+ , K+ , Ca2+ , and Cl− ) through a narrow tunnel of fixed charge (‘doping’). Ionic channels...

    http://nanohub.org/resources/4726

  13. BNC Annual Research Review: An Introduction to PRISM and MEMS Simulation

    04 Jun 2008 | Online Presentations | Contributor(s): Jayathi Murthy

    This presentation is part of a collection of presentations describing the projects, people, and capabilities enhanced by research performed in the Birck Center, and a look at plans for the...

    http://nanohub.org/resources/4717

  14. Dynamics on the Nanoscale: Time-domain ab initio studies of quantum dots, carbon nanotubes and molecule-semiconductor interfaces

    31 Jan 2008 | Online Presentations | Contributor(s): Oleg Prezhdo

    Device miniaturization requires an understanding of the dynamical response of materials on the nanometer scale. A great deal of experimental and theoretical work has been devoted to characterizing...

    http://nanohub.org/resources/3951

  15. Lecture 2: total energy and force calculations

    14 Jan 2008 | Online Presentations | Contributor(s): Alejandro Strachan

    This lecture will describe the various models used to describe the interactions between atoms in a wide range of materials including metals, ceramics and soft materials as well as new recent...

    http://nanohub.org/resources/3678

  16. Lecture 1: the theory behind molecular dynamics

    09 Jan 2008 | Online Presentations | Contributor(s): Alejandro Strachan

    The first lecture will provide a brief description of classical mechanics and statistical mechanics necessary to understand the physics and approximations behind MD and how to correctly...

    http://nanohub.org/resources/3677

  17. Lecture 3: simulation details and coarse grain approaches

    09 Jan 2008 | Online Presentations | Contributor(s): Alejandro Strachan

    The last presentation will describe simulation techniques to simulate materials under isothermal and isobaric conditions. We will also describe coarse grain or mesodynamical approaches...

    http://nanohub.org/resources/3679

  18. Introduction: molecular dynamics simulations

    09 Jan 2008 | Online Presentations | Contributor(s): Alejandro Strachan

    This short presentation will describe the idea behind MD simulations and demonstrate its use in real applications.

    http://nanohub.org/resources/3676

  19. Computing the Horribleness of Soft Condensed Matter

    19 Oct 2007 | Online Presentations | Contributor(s): Eric Jakobsson

    A great triumph of computer simulations 40 years ago was to make the liquid state of matter understandable in terms of physical interactions between individual molecules. Prior to the first...

    http://nanohub.org/resources/3424

  20. Charge Transfer Across an Energy Transducing Integral Membrane Protein Complex

    31 May 2007 | Online Presentations | Contributor(s): William A. Cramer

    The cytochrome bc complexes of the mitochondrial respiratory and photosynthetic electron transport chains are hetero-oligomeric integral membrane proteins. These proteins are responsible for most...

    http://nanohub.org/resources/2679

nanoHUB.org, a resource for nanoscience and nanotechnology, is supported by the National Science Foundation and other funding agencies. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.