Tags: molecular dynamics

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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.

Tools (1-20 of 26)

  1. Glass transition temperature notebook

    0.0 out of 5 stars 

    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

  2. Vacancy Formation Energy with MD

    0.0 out of 5 stars 

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

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

    https://nanohub.org/resources/mdvacancy

  3. LAMMPS structure generator

    0.0 out of 5 stars 

    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

  4. OpenKIM Explorer

    0.0 out of 5 stars 

    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

  5. Coarse Graining of Crystalline Cellulose

    0.0 out of 5 stars 

    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

  6. MD simulations of shock loading

    0.0 out of 5 stars 

    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

  7. Molecular Exploration Tool

    0.0 out of 5 stars 

    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

  8. Molecular Dynamics Showcase Builder

    0.0 out of 5 stars 

    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

  9. Nanomaterial Mechanics Explorer

    5.0 out of 5 stars 

    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

  10. Crack Propagation Simulation

    0.0 out of 5 stars 

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

    Simulate crack propagations through materials under applied loads.

    https://nanohub.org/resources/crackpropsim

  11. Molecular Dynamics Showcase

    0.0 out of 5 stars 

    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

    https://nanohub.org/resources/mdshowcase

  12. Crystalline Cellulose - Atomistic Toolkit

    0.0 out of 5 stars 

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

    Crystalline Cellulose - Atomistic Toolkit

    https://nanohub.org/resources/ccamt

  13. 2d Ideal Gas Molecular Dynamics

    0.0 out of 5 stars 

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

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

    https://nanohub.org/resources/smdc

  14. 1-D Chain Dispersions

    0.0 out of 5 stars 

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

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

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

  15. Temperature Accelerated Dynamics

    0.0 out of 5 stars 

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

    Simulate temperature accelerated dynamics

    https://nanohub.org/resources/tad

  16. nanoMATERIALS nanoscale heat transport

    0.0 out of 5 stars 

    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

    https://nanohub.org/resources/nmstthermal

  17. MiniMol: Minimal Molecular Simulation Tool

    0.0 out of 5 stars 

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

    Perform simple molecular dynamics and statics simulations.

    https://nanohub.org/resources/minimol

  18. Polymer Modeler

    3.5 out of 5 stars 

    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

    https://nanohub.org/resources/polymod

  19. Atomic Stick-Slip

    0.0 out of 5 stars 

    31 Mar 2010 | Tools | Contributor(s): Ashlie Martini, Jianguo Wu

    Molecular dynamics simulation of atomic stick-slip friction

    https://nanohub.org/resources/stickslip

  20. MIT Tools for Energy Conversion and Storage

    0.0 out of 5 stars 

    12 Oct 2009 | Tools | Contributor(s): Jeffrey C Grossman, Joo-Hyoung Lee, Varadharajan Srinivasan, Alexander S McLeod, Lucas Wagner

    Atomic-Scale Simulation Tools to Explore Energy Conversion and Storage Materials

    https://nanohub.org/resources/nanoenergytools