Tags: molecular dynamics (MD)

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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.

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  1. Nanoparticle Shape Lab

    Tools | 10 Jan 2020 | Contributor(s):: JCS Kadupitiya, Nicholas E. Brunk, Vikram Jadhao

    Simulates the low-energy shapes of nanocontainers over a wide range of solution conditions

  2. LAMMPS Input Structure Generator for Functionally Graded Materials (FGM)

    Tools | 27 Nov 2019 | Contributor(s):: Md Shajedul Hoque Thakur, Mahmudul Islam, Abdullah Amin, Satyajit Mojumder, Md Mahbubul Islam

    Generates initial geometries of Functionally Graded Materials (FGM) for LAMMPS simulations

  3. Materials Science Modules with Molecular Dynamics

    Series | 25 Nov 2019 | Contributor(s):: Sam Reeve, Alejandro Strachan

    This module uses the Nanomaterial Mechanics Explorer: https://nanohub.org/tools/nanomatmech

  4. Yang Hu

    https://nanohub.org/members/260238

  5. NPT Simulator

    Tools | 29 Aug 2019 | Contributor(s):: Julian C Umeh, Thomas A Manz

    Calculate density and total energy of gas molecules using NPT ensemble

  6. Radial Distribution Function Calculator

    Tools | 25 Jul 2019 | Contributor(s):: Julian C Umeh, Thomas A Manz

    This tools calculates the radial distribution function of gas molecules

  7. Md Shajedul Hoque Thakur

    https://nanohub.org/members/232908

  8. Gas Diffusion Coefficient in Metal Organic Frameworks

    Tools | 28 May 2019 | Contributor(s):: Julian Chinonso Umeh, Thomas A Manz

    Calculates gas self diffusion coefficient in metal organic frameworks

  9. Structural Analysis for Molecular Dynamics Trajectories

    Presentation Materials | 03 Mar 2019 | Contributor(s):: Nicholas J Finan, Saaketh Desai, Sam Reeve, Alejandro Strachan

    This tool reads in LAMMPS trajectories and performs the following analysis: Radial Distribution Function (RDF), X-Ray Diffraction (XRD), Vibrational Density of States, and  (More to Come!). By default the tool requires trajectory files to be input by the user however there are some...

  10. LAMMPS driver tool for potential calibration

    Tools | 24 Feb 2019 | Contributor(s):: Saaketh Desai, Alejandro Strachan

    Calculates basic properties of interest with a given interatomic potential and is used to drive the calibration of the potential.

  11. Thomas A Manz

    Tom Manz is a Chemical & Materials Engineering faculty at New Mexico State University. His research group develops new computational chemistry methods and physical interaction models. He is the...

    https://nanohub.org/members/222347

  12. Martensitic Transformations with Molecular Dynamics

    Teaching Materials | 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 transitions Compare different martensitic alloys,...

  13. Melting with Molecular Dynamics

    Teaching Materials | 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 scales Identify effects of surfaces and specimen size Describe differences...

  14. Nanoscale Tensile Testing with Molecular Dynamics

    Teaching Materials | 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...

  15. Dislocation Structure and Propagation with Molecular Dynamics

    Teaching Materials | 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.

  16. Ductile and Brittle Failure in Metals with Molecular Dynamics

    Teaching Materials | 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...

  17. Rajmohan Muthaiah

    https://nanohub.org/members/222059

  18. Sanda Moldovean

    https://nanohub.org/members/221982

  19. Chris Jones

    https://nanohub.org/members/221455

  20. Nanoparticle Assembly Lab

    Tools | 28 Jan 2019 | Contributor(s):: Nicholas Brunk, JCS Kadupitiya, Masaki Uchida, Douglas, Trevor, Vikram Jadhao

    Simulate assembly of nanoparticles into aggregates in physiological conditions.