Tags: molecular dynamics

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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.

Teaching Materials (1-10 of 10)

  1. 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

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

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    15 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

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

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    15 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

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

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    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

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

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    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

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

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    15 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

  7. Computational Nanoscience, Lecture 6: Pair Distribution Function and More on Potentials

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

    In this lecture we remind ourselves what a pair distribution function is, how to compute it, and why it is so important in simulations. Then, we revisit potentials and go into more detail...

    http://nanohub.org/resources/4039

  8. Homework assignment: learning about elastic constants via molecular dynamics simulations

    11 Mar 2015 | Teaching Materials | Contributor(s): Alejandro Strachan, David Ray Johnson

    In this homework assignment students will use molecular dynamics to compute the elastic constants of metals using an embedded atom model to describe atomic interactions. They will deform  a...

    http://nanohub.org/resources/21949

  9. Melting via molecular dynamics simulations

    10 Mar 2015 | Teaching Materials | Contributor(s): Alejandro Strachan

    In this assignment you will use MD simulations to study melting in metals using the nanoMATERIALS simulation tool in nanoHUB. You will build a supercell and heat it up to study its melting. You...

    http://nanohub.org/resources/22025

  10. REBO Nanofluidics Exercise

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    09 Jun 2004 | Teaching Materials | Contributor(s): Susan Sinnott, Hetal Patel

    Nanofluidics exercise showing the variation of energy and position of methane and butane molecules flowing through an opened carbon nanotube as the system temperature and the length of the...

    http://nanohub.org/resources/1270