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.

Teaching Materials (1-16 of 16)

  1. Atomic Picture of Plastic Deformation in Metals: Lab Assignment Handout

    19 Jan 2010 | | Contributor(s):: Alejandro Strachan

    In this lab students will perform online molecular dynamics (MD) simulations of metallic nanowires deformed uniaxially and analyze the results...

  2. Calculating heat of fusion of polyethylene using Polymer Modeler

    28 Jan 2019 | | Contributor(s):: Lorena Alzate-Vargas, Benjamin P Haley, Alejandro Strachan

    The main objective of this Learning Module is to determine the heat of fusion of a polytheylene sample using molecular dynamics.

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

    14 Feb 2008 | | 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 identical classical particles interacting via the Lennard-Jones potential.This assignment is to be...

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

    14 Feb 2008 | | 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 completed following lectures 5 and 6 using the "LAMMPS" program in the Berkeley Computational Nanoscience...

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

    30 Jan 2008 | | 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 considerations such as choice of timestep. A brief discussion of interatomic potentials (the pair potential and...

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

    13 Feb 2008 | | 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 importance of the starting guess and how to find or generate good initial structures. We also briefly...

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

    13 Feb 2008 | | 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 calculating the energy per atom of different fullerenes and nantubes, computing the Young's modulus of a nanotube...

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

    13 Feb 2008 | | 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 including examples of typical functional forms, relative energy scales, and what to keep in mind when...

  9. Dislocation structure and propagation with molecular dynamics

    20 Feb 2019 | | Contributor(s):: Sam Reeve, Alejandro Strachan

    In this computational lab you will learn about dislocations via online molecular dynamics (MD) simulations using nanoHUB. The simulations involve various types of dislocations in FCC and BCC crystals. During the learning module you will be able to:Distinguish edge and screw dislocations in...

  10. Ductile and brittle failure in metals with molecular dynamics

    20 Feb 2019 | | Contributor(s):: Sam Reeve, Alejandro Strachan

    In this computational lab you will perform online molecular dynamics (MD) simulations of nanoscale cracks under uniaxial tension through nanoHUB. Simulations with varying temperature and crystal structure will provide information to:Distinguish the atomistic mechanisms of ductile and...

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

    11 Mar 2015 | | 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 single crystal along different directions and obtain c11, c12 and c44 elastic constants from the...

  12. Martensitic transformations with molecular dynamics

    21 Feb 2019 | | Contributor(s):: Sam Reeve, Alejandro Strachan

    In this computational lab you will perform online molecular dynamics (MD) simulations through nanoHUB of martensitic transformations and analyze the results in order to:Describe the atomistic process of martensitic, solid-solid phase transitionsCompare different martensitic alloys,...

  13. Melting via molecular dynamics simulations

    10 Mar 2015 | | 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 can visualize the atomic configuration as the temperature is increased and after melting. From the...

  14. Melting with molecular dynamics

    21 Feb 2019 | | Contributor(s):: Sam Reeve, Alejandro Strachan

    In this computational lab you will perform online molecular dynamics (MD) simulations through nanoHUB to melt nickel samples and analyze the results in order to:Understand the process of melting at atomic scalesIdentify effects of surfaces and specimen sizeDescribe differences...

  15. Nanoscale tensile testing with molecular dynamics

    21 Feb 2019 | | Contributor(s):: Sam Reeve, Alejandro Strachan

    In this computational lab you will perform online molecular dynamics (MD) simulations through nanoHUB of single-crystal copper nanowires under uniaxial tension of varying orientations and analyze the results in order to:Observe how slip planes in single-crystal nanowires are formed and...

  16. REBO Nanofluidics Exercise

    10 May 2006 | | Contributor(s):: Susan Sinnott, Hetal Patel

    Nanofluidics exercise showing the variation of energy and positionof methane and butane molecules flowing through an opened carbonnanotube as the system temperature and the length of the nanotubeare varied.