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 139)

  1. PREPRINT: Molecular Modeling of the Microstructure Evolution during the Carbonization of PAN-Based Carbon Fibers

    23 Mar 2017 | | Contributor(s):: Alejandro Strachan, Saaketh Desai

    PREPRINTDevelopment of high strength carbon fibers (CFs) requires an understanding of the relationship between the processing conditions, microstructure and resulting properties. We developed a molecular model that combines kinetic Monte Carlo (KMC) and molecular dynamics (MD) techniques to...

  2. Introduction to Molecular Dynamics Showcase

    13 Feb 2017 | | Contributor(s):: Chen-Yu Li, Karl Steven Decker (editor), Aleksei Aksimentiev

    In this tutorial, we will demonstrate how to use the MD showcase builder tool to create a showcase. We will start from the simplest example – creating a showcase from a PDB file – and move on to more complicated examples. We will also cover how to add a description, change...

  3. Fundamentals of Phonon Transport Modeling L1: Introduction

    04 Jan 2017 | | Contributor(s):: Alan McGaughey, Xiulin Ruan

    Part of the 2016 IMECE Tutorial: Fundamentals of Phonon Transport Modeling: Formulation, Implementation, and Applications.

  4. Fundamentals of Phonon Transport Modeling L2: MD Simulation, Green Kubo, Direct Method

    04 Jan 2017 | | Contributor(s):: Xiulin Ruan, Alan McGaughey

    Part of the 2016 IMECE Tutorial: Fundamentals of Phonon Transport Modeling: Formulation, Implementation, and Applications.

  5. LAMMPS structure generator

    01 Nov 2016 | | Contributor(s):: Benjamin P Haley

    Convert a molecular structure file to a LAMMPS data file with force field parameters

  6. OpenKIM Explorer

    09 Jun 2015 | | Contributor(s):: Dan Karls, Benjamin P Haley, Alejandro Strachan, Ryan S Elliott, Ellad B Tadmor

    Run interatomic potentials from the OpenKIM Repository in LAMMPS

  7. Coarse Graining of Crystalline Cellulose

    29 Jul 2016 | | Contributor(s):: Kuo Tian, Mehdi Shishehbor, Pablo Daniel Zavattieri

    Bio-inspired Crystalline Nano-Cellulose coarse graining toolkit

  8. Polymer Synthesis and Characterization in the Cloud: a nanoHUB Classroom Experience

    31 Aug 2015 | | Contributor(s):: Coray Colina

    In this talk, I’ll share the experience of teaching a junior undergraduate computational course in materials science and engineering, with over 70 participants. Both molecular and continuum methods were studied and applied to relevant materials problems. Students were able to build and...

  9. MD simulations of shock loading

    11 Jun 2015 | | Contributor(s):: edwin alberto antillon, Mitchell Anthony Wood, Mathew Joseph Cherukara, Alejandro Strachan

    Use MD simulation to study shocks in various materials including metals and energetics

  10. Molecular Exploration Tool

    01 Aug 2014 | | Contributor(s):: Xueying Wang, nicolas onofrio, Alejandro Strachan, David M Guzman

    The tool can display the molecule structures and run Lammps simulations.

  11. Molecular Dynamics Showcase Builder

    09 Nov 2015 | | Contributor(s):: Michael McLennan, Nicholas K Kisseberth, George A. Howlett, Jim Slopsema, Aleksei Aksimentiev, Chen-Yu Li

    Tool to create showcases for the Molecular Dynamics Showcase viewer.

  12. Atomistic Modeling: Past, Present, and Future, MGI, ICME, etc.

    03 Nov 2015 | | Contributor(s):: Paul Saxe

    I will present a perspective on atomistic modeling — tools using quantum methods such as DFT, as well as molecular dynamics and Monte Carlo methods based on forcefields — over the past 30 years or so. While we are all caught up in the present, it is important to remember and realize...

  13. Introduction to Molecular Dynamics

    27 Aug 2015 | | Contributor(s):: Alejandro Strachan

  14. 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

  15. 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.

  16. 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....

  17. 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...

  18. 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...

  19. 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...

  20. 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...