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.

Resources (81-100 of 121)

  1. MSE 597G An Introduction to Molecular Dynamics

    4.5 out of 5 stars 

    13 Nov 2008 | Courses | 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...

    https://nanohub.org/resources/5838

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

    0.0 out of 5 stars 

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

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

    https://nanohub.org/resources/5843

  3. MSE 597G Lecture 5: Interatomic potentials II

    0.0 out of 5 stars 

    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.

    https://nanohub.org/resources/5777

  4. MSE 597G: An Introduction to Molecular Dynamics

    0.0 out of 5 stars 

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

    https://nanohub.org/resources/5760

  5. MSE 597G Lecture 6: Interatomic potentials III

    0.0 out of 5 stars 

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

    Reactive force fields, Parameterization of interatomic potentials

    https://nanohub.org/resources/5778

  6. MSE 597G Lecture 7: Advanced Techniques for Molecular Dynamics Simulations

    0.0 out of 5 stars 

    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.

    https://nanohub.org/resources/5779

  7. MSE 597G Lecture 2: Statistical Mechanics I

    0.0 out of 5 stars 

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

    Basic physics: statistical mechanics.

    https://nanohub.org/resources/5765

  8. MSE 597G Lecture 1: Classical Mechanics

    0.0 out of 5 stars 

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

    Basic physics: classical mechanics

    https://nanohub.org/resources/5507

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

    3.5 out of 5 stars 

    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...

    https://nanohub.org/resources/4726

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

    0.0 out of 5 stars 

    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...

    https://nanohub.org/resources/4717

  11. MD Simulation

    5.0 out of 5 stars 

    31 Mar 2008 | Tools | Contributor(s): Sanket S Mahajan, Ganesh Subbarayan, Xufeng Wang

    Code to perform Molecular Dynamics (MD) Simulations

    https://nanohub.org/resources/mdsim

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

    5.0 out of 5 stars 

    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...

    https://nanohub.org/resources/4054

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

    5.0 out of 5 stars 

    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...

    https://nanohub.org/resources/4052

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

    5.0 out of 5 stars 

    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...

    https://nanohub.org/resources/4039

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

    5.0 out of 5 stars 

    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...

    https://nanohub.org/resources/4037

  16. BioMOCA Suite

    4.0 out of 5 stars 

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

    Simulates ion flow through a channel.

    https://nanohub.org/resources/BMCsuite

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

    5.0 out of 5 stars 

    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...

    https://nanohub.org/resources/4035

  18. Overview of Computational Nanoscience: a UC Berkeley Course

    5.0 out of 5 stars 

    01 Feb 2008 | Courses | Contributor(s): Jeffrey C Grossman, Elif Ertekin

    This course will provide students with the fundamentals of computational problem-solving techniques that are used to understand and predict properties of nanoscale systems. Emphasis will be placed...

    https://nanohub.org/resources/3944

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

    0.0 out of 5 stars 

    01 Feb 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...

    https://nanohub.org/resources/3951

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

    5.0 out of 5 stars 

    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...

    https://nanohub.org/resources/3940