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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 (1-20 of 92)

  1. 1-D Chain Dispersions

    01 Sep 2011 | Tools | Contributor(s): Nicholas Roberts, Greg Walker

    1-D Chain of atoms, bases and layers to produce phonon dispersion

    http://nanohub.org/resources/1dchainmd

  2. 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

  3. 2d Ideal Gas Molecular Dynamics

    01 Sep 2011 | Tools | Contributor(s): Terence Musho, Greg Walker

    Simulation of a 2d molecular gas with specified temperature boundary conditions

    http://nanohub.org/resources/smdc

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. Atomistic Material Science

    03 Nov 2011 | Courses | Contributor(s): Alejandro Strachan

    This course introduces first principles electronic structure calculations of materials properties and the concept of molecular dynamics (MD) simulations of materials focusing on the physics and...

    http://nanohub.org/resources/11916

  12. Atomistic Modeling of the Mechanical Properties of Nanostructured Materials

    16 Apr 2007 | Online Presentations | Contributor(s): SeongJun Heo, Susan Sinnott

    The mechanical properties of carbon nanotubes are studied by using classical molecular dynamics simulations. Especially, the effects of filling, temperature, and functionalization on CNT's...

    http://nanohub.org/resources/2604

  13. BioMOCA Suite

    04 Feb 2008 | Tools | Contributor(s): David Papke, Reza Toghraee, Umberto Ravaioli, Ankit Raj

    Simulates ion flow through a channel.

    http://nanohub.org/resources/BMCsuite

  14. 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

  15. 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

  16. Computational Nanoscience, Homework Assignment 2: Molecular Dynamics Simulation of a Lennard-Jones Liquid

    14 Feb 2008 | Teaching Materials | Contributor(s): Elif Ertekin, Jeffrey C Grossman

    The purpose of this assignment is to perform a full molecular dynamics simulation based on the Verlet algorithm to calculate various properties of a simple liquid, modeled as an ensemble of...

    http://nanohub.org/resources/4052

  17. Computational Nanoscience, Homework Assignment 3: Molecular Dynamics Simulation of Carbon Nanotubes

    14 Feb 2008 | Teaching Materials | Contributor(s): Elif Ertekin, Jeffrey C Grossman

    The purpose of this assignment is to perform molecular dynamics simulations to calculate various properties of carbon nanotubes using LAMMPS and Tersoff potentials. This assignment is to be...

    http://nanohub.org/resources/4054

  18. Computational Nanoscience, Lecture 2: Introduction to Molecular Dynamics

    30 Jan 2008 | Teaching Materials | Contributor(s): Jeffrey C Grossman, Elif Ertekin

    In this lecture, we present and introduction to classical molecular dynamics. Approaches to integrating the equations of motion (Verlet and other) are discussed, along with practical...

    http://nanohub.org/resources/3940

  19. Computational Nanoscience, Lecture 4: Geometry Optimization and Seeing What You're Doing

    13 Feb 2008 | Teaching Materials | Contributor(s): Jeffrey C Grossman, Elif Ertekin

    In this lecture, we discuss various methods for finding the ground state structure of a given system by minimizing its energy. Derivative and non-derivative methods are discussed, as well as the...

    http://nanohub.org/resources/4035

  20. Computational Nanoscience, Lecture 5: A Day of In-Class Simulation: MD of Carbon Nanostructures

    13 Feb 2008 | Teaching Materials | Contributor(s): Jeffrey C Grossman, Elif Ertekin

    In this lecture we carry out simulations in-class, with guidance from the instructors. We use the LAMMPS tool (within the nanoHUB simulation toolkit for this course). Examples include...

    http://nanohub.org/resources/4037

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.