Tags: molecular dynamics (MD)

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.

All Categories (1-20 of 227)

  1. Parsimonious Neural Networks Learn Classical Mechanics and Can Teach It

    15 May 2020 | | Contributor(s):: Saaketh Desai, Alejandro Strachan

    We combine neural networks with genetic algorithms to find parsimonious models that describe the time evolution of a point particle subjected to an external potential. The genetic algorithm is designed to find the simplest, most interpretable network compatible with the training data. The...

  2. Hands-on Unsupervised Learning using Dimensionality Reduction via Matrix Decomposition (2nd offering)

    30 Apr 2020 | | Contributor(s):: Michael N Sakano, Alejandro Strachan

    This tutorial introduces unsupervised machine learning algorithms through dimensionality reduction via matrix decomposition techniques in the context of chemical decomposition of reactive materials in a Jupyter notebook on nanoHUB.org. The tool used in this demonstration...

  3. Hands-on Unsupervised Learning using Dimensionality Reduction via Matrix Decomposition (1st offering)

    29 Apr 2020 | | Contributor(s):: Michael N Sakano, Alejandro Strachan

    This tutorial introduces unsupervised machine learning algorithms through dimensionality reduction via matrix decomposition techniques in the context of chemical decomposition of reactive materials in a Jupyter notebook on nanoHUB.org. The tool used in this demonstration...

  4. Unsupervised learning using dimensionality reduction via matrix decomposition

    14 Apr 2020 | | Contributor(s):: Michael N Sakano, Alejandro Strachan

    Learn PCA and NMF via chemistry example

  5. Rohit Goswami

    https://nanohub.org/members/282063

  6. Sourav Sahoo

    https://nanohub.org/members/281706

  7. Aleksander Joachim Tomanek

    https://nanohub.org/members/274940

  8. Nanoparticle Shape Lab

    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

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

    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

  10. Materials Science Modules with Molecular Dynamics

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

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

  11. Yang Hu

    https://nanohub.org/members/260238

  12. Md Shajedul Hoque Thakur

    https://nanohub.org/members/232908

  13. Structural Analysis for Molecular Dynamics Trajectories

    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...

  14. LAMMPS driver tool for potential calibration

    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.

  15. 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 transitions Compare different martensitic alloys,...

  16. 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 scales Identify effects of surfaces and specimen size Describe differences...

  17. 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...

  18. 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.

  19. 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...

  20. Rajmohan Muthaiah

    https://nanohub.org/members/222059