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.

Tools (1-20 of 28)

  1. Atomistic Polymer Workflow Notebook

    19 Oct 2017 | Tools | Contributor(s): Benjamin P Haley

    Run PolymerModeler and nuSIMM tools to create atomistic polymer systems

    http://nanohub.org/resources/polymerwfnb

  2. 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

    http://nanohub.org/resources/tcnt

  3. 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

    http://nanohub.org/resources/tgnb

  4. 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

    http://nanohub.org/resources/mdvacancy

  5. 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

    http://nanohub.org/resources/struct2lammps

  6. 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

    http://nanohub.org/resources/kimexplorer

  7. 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

    http://nanohub.org/resources/cgmcc

  8. 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

    http://nanohub.org/resources/mdshocks

  9. 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.

    http://nanohub.org/resources/molexpl

  10. 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.

    http://nanohub.org/resources/mdshowbuilder

  11. 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

    http://nanohub.org/resources/nanomatmech

  12. Crack Propagation Simulation

    13 Mar 2015 | Tools | Contributor(s): hojin kim, Nilofer Rajpurkar, Benjamin P Haley, Alejandro Strachan

    Simulate crack propagations through materials under applied loads.

    http://nanohub.org/resources/crackpropsim

  13. Molecular Dynamics Showcase

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

    View interesting features of a molecular dynamics trajectory file

    http://nanohub.org/resources/mdshowcase

  14. Crystalline Cellulose - Atomistic Toolkit

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

    Crystalline Cellulose - Atomistic Toolkit

    http://nanohub.org/resources/ccamt

  15. 2d Ideal Gas Molecular Dynamics

    27 Sep 2011 | Tools | Contributor(s): Terence Musho, Greg Walker

    Simulation of a 2d molecular gas with specified temperature boundary conditions

    http://nanohub.org/resources/smdc

  16. 1-D Chain Dispersions

    23 Sep 2011 | Tools | Contributor(s): Nicholas Roberts, Greg Walker

    1-D Chain of atoms, bases and layers to produce phonon dispersion

    http://nanohub.org/resources/1dchainmd

  17. Temperature Accelerated Dynamics

    13 Sep 2011 | Tools | Contributor(s): Justin Riley, Markus J. Buehler

    Simulate temperature accelerated dynamics

    http://nanohub.org/resources/tad

  18. nanoMATERIALS nanoscale heat transport

    31 Aug 2011 | Tools | Contributor(s): Keng-Hua Lin, Sean Sullivan, Mathew Joseph Cherukara, Alejandro Strachan, Tianli Feng, Xiulin Ruan, Bo Qiu

    Non-equilibrium MD simulations of heat transport in nano-materials

    http://nanohub.org/resources/nmstthermal

  19. MiniMol: Minimal Molecular Simulation Tool

    15 Aug 2011 | Tools | Contributor(s): Ellad B Tadmor, Ron Earle Miller, Ryan S Elliott

    Perform simple molecular dynamics and statics simulations.

    http://nanohub.org/resources/minimol

  20. Polymer Modeler

    25 Aug 2010 | Tools | Contributor(s): Benjamin P Haley, Nate Wilson, Chunyu Li, Andrea Arguelles, Eugenio Jaramillo, Alejandro Strachan

    Build thermoplastic polymer chains and run LAMMPS to relax the chains and study mechanical properties

    http://nanohub.org/resources/polymod