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 127)

  1. Introduction to Molecular Dynamics

    11 Sep 2015 | | Contributor(s):: Alejandro Strachan

  2. Nanomaterial Mechanics Explorer

    30 Jun 2015 | | Contributor(s):: Sam Reeve, Christopher Chow, Michael N Sakano, shuhui tang, Alexis Belessiotis, Mitchell Anthony Wood, Kiettipong Banlusan, Saaketh Desai, Alejandro Strachan

    Simulate dislocation dynamics, crack propagation, nanowire tensile tests, and phase transitions

  3. Introduction to Molecular Dynamics

    06 Apr 2015 | | Contributor(s):: Alejandro Strachan

    This short presentation will describe the idea behind MD simulations and demonstrate its use in real applications.

  4. Reproducing results of "Thermal transport in SiGe superlattice thin films and nanowires"

    27 Mar 2015 | | Contributor(s):: Alejandro Strachan, Jonathan Mark Dunn

    In this document we show how to reproduce results in the paper "Thermal transport in SiGe superlattice thin films and nanowires", Keng-hua Lin, and Alejandro Strachan Physical Review B 87, 115302 (2011) using the nanoMATERIALS nanoscale heat transport tool in nanoHUB....

  5. MSE 498 Lesson 10: MD

    16 Mar 2015 | | 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 (e.g., VASP), molecular simulation (e.g., GROMACS), phase diagram modeling (e.g., Thermo-Calc), finite...

  6. MSE 498 Lesson 11: MD

    16 Mar 2015 | | 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 (e.g., VASP), molecular simulation (e.g., GROMACS), phase diagram modeling (e.g., Thermo-Calc), finite...

  7. MSE 498 Lesson 12: MD

    16 Mar 2015 | | 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 (e.g., VASP), molecular simulation (e.g., GROMACS), phase diagram modeling (e.g., Thermo-Calc), finite...

  8. MSE 498 Lesson 13: MD

    16 Mar 2015 | | 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 (e.g., VASP), molecular simulation (e.g., GROMACS), phase diagram modeling (e.g., Thermo-Calc), finite...

  9. MSE 498 Lesson 14: MD

    16 Mar 2015 | | 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 (e.g., VASP), molecular simulation (e.g., GROMACS), phase diagram modeling (e.g., Thermo-Calc), finite...

  10. MSE 498 Lesson 15: MD

    16 Mar 2015 | | 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 (e.g., VASP), molecular simulation (e.g., GROMACS), phase diagram modeling (e.g., Thermo-Calc), finite...

  11. Crack Propagation Simulation

    06 Aug 2014 | | Contributor(s):: hojin kim, Nilofer Rajpurkar, Benjamin P Haley, Alejandro Strachan

    Simulate crack propagations through materials under applied loads.

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

    17 Feb 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...

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

    10 Feb 2014 | | 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 construct an analytical approximation (i.e. a surrogate or emulator) of the simulations, treating the input...

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

    10 Feb 2014 | | 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 example, is calculated from the phonon spectrum, and the melting temperature Tm can only be obtained...

  16. Molecular Dynamics Showcase

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

    View interesting features of a molecular dynamics trajectory file

  17. [Illinois] Physics 550 Biomolecular Physics

    03 Sep 2013 | | 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 relation to other complex physical systems such as glasses; recent research in biomolecular physics; physical...

  18. Crystalline Cellulose - Atomistic Toolkit

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

    Crystalline Cellulose - Atomistic Toolkit

  19. Polymatic: A Simulated Polymerization Algorithm

    13 Mar 2013 | | 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 based on a number of defined bonding criteria. It works in conjunction with a simulation package to...

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

    03 Feb 2013 | | Contributor(s):: David M. Ceperley