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 (81-100 of 139)

  1. Lecture 10: Non Equilibrium MD

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

    Topics:Calculating transport coefficientShear flowPerturbation methods

  2. Lecture 9: Dynamic Properties

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

    Topics:Time correlation functionsEinstein relationsGreen-Kubo relations

  3. Lecture 8: Static Properties

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

    Topics:Thermodynamic propertiesEntropic propertiesStatic structure

  4. Lecture 7: Initialization and Equilibrium

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

    Topics:Initial positionsInitial velocitiesEvaluating equilibrium

  5. Lecture 6: Neighbor Lists

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

    Topics:Saving simulation timeVerlet listsCell lists

  6. Lecture 5: Boundary Conditions

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

    Topics:Fixed boundariesPeriodic boundary conditionsMinimum image distance

  7. Lecture 4: Temperature Control

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

    Topics:Velocity scalingHeat bath/reservoirStochastic methods

  8. Lecture 3: Integration Algorithms

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

    Topics:General guidelinesVerlet algorithmPredictor-corrector methods

  9. Lecture 2: Potential Energy Functions

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

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

  10. Lecture 1: Basic Concepts

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

    Topics:What is MDNewton’s lawBasic concepts and terminology

  11. Short Course on Molecular Dynamics Simulation

    13 Oct 2009 | | 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 the opportunities and limitations of Molecular Dynamics as a tool for scientific and engineering...

  12. MIT Tools for Energy Conversion and Storage

    13 Sep 2009 | | 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

  13. Energy and Nanoscience A More Perfect Union

    27 Mar 2009 | | Contributor(s):: Mark 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, transportation, and storage. This overview will stress the nature of these problems, and offer a few...

  14. Illinois Center for Cellular Mechanics: Discovery through the Computational Microscope

    09 Feb 2009 | | Contributor(s):: Klaus Schulten

    Computational MicroscopeAll-atom molecular dynamics simulations have become increasingly popular as a toolto investigate protein function and dynamics. However, researchers are usuallyconcerned about the short time scales covered by simulations, the apparentimpossibility to model large and...

  15. Illinois PHYS 466, Lecture 4: Molecular Dynamics

    05 Feb 2009 | | 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: Characteristics of simulations The Verlet Algorithm Higher Order Methods? Quote from Berendsen Long-term stability of Verlet...

  16. Nanoparticle and Colloidal Simulations with Molecular Dynamics

    05 Dec 2008 | | 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 manufacturing properties. These include treating colloids as single particles, moving from explicit to...

  17. MSE 597G Lecture 4: Interatomic potentials I

    14 Nov 2008 | | Contributor(s):: Alejandro Strachan

    Interatomic potentials: pairwise potentials.

  18. MSE 597G Lecture 3: Statistical Mechanics II

    14 Nov 2008 | | Contributor(s):: Alejandro Strachan

    Basic physics: statistical mechanics, Algorithms: Integrating the equations of motion.

  19. MSE 597G An Introduction to Molecular Dynamics

    13 Nov 2008 | | 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 with a few applications applications. The series also includes a tutorial on the nanoMATERIALS...

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

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

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