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 (1-20 of 125)

  1. THERMAL CNT

    22 Aug 2017 | Tools | Contributor(s): Luca Bergamasco, Matteo Fasano, Eliodoro Chiavazzo, Pietro Asinari, Annalisa Cardellini, Matteo Morciano

    Compute thermal conductivity of single-walled carbon nano-tubes via NEMD method

    https://nanohub.org/resources/tcnt

  2. Applying Machine Learning to Computational Chemistry: Can We Predict Molecular Properties Faster without Compromising Accuracy?

    14 Aug 2017 | Presentation Materials | Contributor(s): Hanjing Xu, Pradeep Kumar Gurunathan

    Non-covalent interactions are crucial in analyzing protein folding and structure, function of DNA and RNA, structures of molecular crystals and aggregates, and many other processes in the fields...

    https://nanohub.org/resources/26904

  3. Structure-Force Field Generator for Molecular Dynamics Simulations

    07 Aug 2017 | Online Presentations | Contributor(s): Carlos Miguel Patiño, Lorena Alzate-Vargas, Alejandro Strachan

    Atomistic and molecular simulations have become an important research field due to the progress made in computer performance and the necessity of new and improved materials. Despite this, first...

    https://nanohub.org/resources/26959

  4. Multiscale Modelling of Nanoparticle Suspensions

    12 Jun 2017 | Online Presentations | Contributor(s): Pietro Asinari

    In the present work a multiscale modelling approach is implemented to relate the nanoscale phenomena to the macroscopic bulk properties of nano-suspensions. Specifically, Molecular Dynamics (MD)...

    https://nanohub.org/resources/26710

  5. Glass transition temperature notebook

    23 May 2017 | Tools | Contributor(s): Benjamin P Haley, Lorena Alzate-Vargas

    Calculate the glass transition temperature of an atomistic, amorphous system by running MD simulations in a notebook

    https://nanohub.org/resources/tgnb

  6. Vacancy Formation Energy with MD

    08 May 2017 | Tools | Contributor(s): Sam Reeve, Alejandro Strachan

    Calculate vacancy formation energy with molecular dynamics and various atomic interaction models

    https://nanohub.org/resources/mdvacancy

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

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

    PREPRINT Development of high strength carbon fibers (CFs) requires an understanding of the relationship between the processing conditions, microstructure and resulting properties. We developed...

    https://nanohub.org/resources/26089

  8. Introduction to Molecular Dynamics Showcase

    13 Feb 2017 | Downloads | 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 –...

    https://nanohub.org/resources/25866

  9. Fundamentals of Phonon Transport Modeling L1: Introduction

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

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

    https://nanohub.org/resources/25501

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

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

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

    https://nanohub.org/resources/25502

  11. LAMMPS structure generator

    07 Nov 2016 | Tools | Contributor(s): Benjamin P Haley

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

    https://nanohub.org/resources/struct2lammps

  12. OpenKIM Explorer

    28 Oct 2016 | Tools | Contributor(s): Benjamin P Haley, Dan Karls, Alejandro Strachan, Ryan S Elliott, Ellad B Tadmor

    Query the OpenKIM repository for names of interatomic Models for simulating selected materials

    https://nanohub.org/resources/kimexplorer

  13. Coarse Graining of Crystalline Cellulose

    24 Oct 2016 | Tools | Contributor(s): Kuo Tian, Mehdi Shishehbor, Pablo Daniel Zavattieri

    Bio-inspired Crystalline Nano-Cellulose coarse graining toolkit

    https://nanohub.org/resources/cgmcc

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

    22 Jan 2016 | Online Presentations | 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...

    https://nanohub.org/resources/22726

  15. MD simulations of shock loading

    29 Dec 2015 | Tools | 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

    https://nanohub.org/resources/mdshocks

  16. Molecular Exploration Tool

    10 Dec 2015 | Tools | Contributor(s): Xueying Wang, nicolas onofrio, Alejandro Strachan, David M Guzman

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

    https://nanohub.org/resources/molexpl

  17. Molecular Dynamics Showcase Builder

    09 Nov 2015 | Tools | 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.

    https://nanohub.org/resources/mdshowbuilder

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

    03 Nov 2015 | Online Presentations | 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...

    https://nanohub.org/resources/23041

  19. Introduction to Molecular Dynamics

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

    https://nanohub.org/resources/22694

  20. Nanomaterial Mechanics Explorer

    19 Aug 2015 | Tools | Contributor(s): Christopher Chow, Michael N Sakano, shuhui tang, Alexis Belessiotis, Sam Reeve, Mitchell Anthony Wood, Kiettipong Banlusan, Alejandro Strachan

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

    https://nanohub.org/resources/nanomatmech