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 (21-40 of 118)

  1. MSE 498 Lesson 15: MD

    17 Mar 2015 | Online Presentations | Contributor(s): Andrew Ferguson

    This new course will give students hands-on experience with popular computational materials science and engineering software through a series of projects in: electronic structure calculation...

    http://nanohub.org/resources/22079

  2. Crack Propagation Simulation

    13 Mar 2015 | Tools | Contributor(s): hojin kim, Nilofer Rajpurkar, Benjamin P Haley, Alejandro Strachan

    Simulate crack propagations through materials under applied loads.

    http://nanohub.org/resources/crackpropsim

  3. 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

  4. 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

  5. IMA 2013 UQ: Bayesian Calibration of Molecular Dynamics Simulations for Composite Materials Properties

    28 May 2014 | Online Presentations | Contributor(s): Paul N. Patrone

    In this talk, I discuss ongoing research whose goal is to determine, via Bayesian inference, an ensemble of inputs that represents a class of commercially important amine-cured epoxies. We...

    http://nanohub.org/resources/20312

  6. IMA 2013 UQ: DFT-based Thermal Properties: Three Levels of Error Management

    02 Apr 2014 | Online Presentations | Contributor(s): Kurt Lejaeghere

    It is often computationally expensive to predict finite-temperature properties of a crystal from density-functional theory (DFT). The temperature-dependent thermal expansion coefficient α, for...

    http://nanohub.org/resources/20311

  7. Molecular Dynamics Showcase

    14 Oct 2013 | Tools | Contributor(s): Michael McLennan, Chen-Yu Li, john stone, Aleksei Aksimentiev, George A. Howlett

    View interesting features of a molecular dynamics trajectory file

    http://nanohub.org/resources/mdshowcase

  8. [Illinois] Physics 550 Biomolecular Physics

    05 Sep 2013 | Courses | Contributor(s): Klaus Schulten, Taekjip Ha

        Physical concepts governing the structure and function of biological macromolecules; general properties, spatial structure, energy levels, dynamics and functions, and...

    http://nanohub.org/resources/19299

  9. Crystalline Cellulose - Atomistic Toolkit

    05 Aug 2013 | Tools | Contributor(s): Mateo Gómez Zuluaga, Robert J. Moon, Fernando Luis Dri, Pablo Daniel Zavattieri

    Crystalline Cellulose - Atomistic Toolkit

    http://nanohub.org/resources/ccamt

  10. Polymatic: A Simulated Polymerization Algorithm

    26 Mar 2013 | Downloads | Contributor(s): Lauren Abbott, Coray Colina

    Polymatic is a set of codes for structure generation of amorphous polymers by a simulated polymerization algorithm. The main task of Polymatic is to perform polymerization steps within a system...

    http://nanohub.org/resources/17278

  11. [Illinois] PHYS466 2013 Lecture 4: Molecular Dynamics I

    06 Feb 2013 | Online Presentations | Contributor(s): David M. Ceperley

    Professor Ceperley received his BS in physics from the University of Michigan in 1971 and his Ph.D. in physics from Cornell University in 1976. After one year at the University of Paris and a...

    http://nanohub.org/resources/16719

  12. [Illinois] Beckman Graduate Seminar: Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations

    18 Dec 2012 | Online Presentations | Contributor(s): Hang Yu

    Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in...

    http://nanohub.org/resources/16098

  13. [Illinois] CSE Seminar Series: Advances in First-principles Computational Materials Science

    20 Nov 2012 | Online Presentations | Contributor(s): Elif Ertekin

    Title: Advances in first-principles computational materials science Subtitle: Things we can calculate now, that we couldn't when I was in grad school. The capability to rationally design new...

    http://nanohub.org/resources/15919

  14. [Illinois] Molecular Dynamics Software (NAMD)

    09 Jul 2012 | Online Presentations | Contributor(s): Emad Tajkhorshid

    http://nanohub.org/resources/14318

  15. [Illinois] Molecular Dynamics

    19 Jun 2012 | Online Presentations | Contributor(s): Emad Tajkhorshid

    http://nanohub.org/resources/14317

  16. MD Simulations of Gas Flows in Nano-Channels and Interface Thermal Resistance Between Simple Liquids and Solids

    31 May 2012 | Online Presentations | Contributor(s): Ali Beskok

    This talk focuses on our group’s recent research on molecular dynamics simulations of gas flows in nano-scale confined geometries, and interface thermal resistance between simple liquids and...

    http://nanohub.org/resources/14133

  17. 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

  18. Tutorial 1: Atomistic Material Science - ab initio simulations of materials

    03 Nov 2011 | Online Presentations | Contributor(s): Alejandro Strachan

    This lecture introduces first principles electronic structure calculations of materials properties. It describes the approximations made to the many-body Schrodinger equation in Hartree Fock and...

    http://nanohub.org/resources/11917

  19. Tutorial 2: Atomistic Material Science - Molecular Dynamics simulations of materials

    03 Nov 2011 | Online Presentations | Contributor(s): Alejandro Strachan

    This lecture introduces the concept of molecular dynamics (MD) simulations of materials focusing on the physics and approximations underlying the simulations and interpretation of their results.

    http://nanohub.org/resources/11918

  20. 2d Ideal Gas Molecular Dynamics

    27 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