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Tags: molecular dynamics


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 (1-18 of 18)

  1. 1-D Chain Dispersions

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

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

  2. 2d Ideal Gas Molecular Dynamics

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

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

  3. Atomic Stick-Slip

    09 Nov 2009 | Tools | Contributor(s): Ashlie Martini, Jianguo Wu

    Molecular dynamics simulation of atomic stick-slip friction

  4. BioMOCA Suite

    04 Feb 2008 | Tools | Contributor(s): David Papke, Reza Toghraee, Umberto Ravaioli, Ankit Raj

    Simulates ion flow through a channel.

  5. Crack Propagation Simulation

    06 Aug 2014 | Tools | Contributor(s): hojin kim, Nilofer Rajpurkar, Benjamin P Haley, Alejandro Strachan

    Simulate crack propagations through materials under applied loads.

  6. Crystalline Cellulose - Atomistic Toolkit

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

    Crystalline Cellulose - Atomistic Toolkit

  7. MD Simulation

    31 Mar 2008 | Tools | Contributor(s): Sanket S Mahajan, Ganesh Subbarayan, Xufeng Wang

    Code to perform Molecular Dynamics (MD) Simulations

  8. Micelle

    24 Jul 2006 | Tools | Contributor(s): Kunal Shah, Patrick Chiu, Jing Xu, Susan Sinnott

    Parallel Molecular Dynamics (MD) code that models surfactant structures in water and at liquid/solid interfaces.

  9. MiniMol: Minimal Molecular Simulation Tool

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

    Perform simple molecular dynamics and statics simulations.

  10. MIT Tools for Energy Conversion and Storage

    13 Sep 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

  11. Molecular Dynamics Showcase

    06 Jul 2013 | Tools | Contributor(s): Michael McLennan, Chen-Yu Li, john stone, Aleksei Aksimentiev

    View interesting features of a molecular dynamics trajectory file

  12. Nano Heatflow

    25 Sep 2007 | Tools | Contributor(s): Joe Ringgenberg, P. Alex Greaney, daniel richards, Jeffrey C Grossman, Jeffrey B. Neaton, Justin Riley

    Study the transfer of energy between the vibrational modes of a carbon nanotube.

  13. nano-Materials Simulation Toolkit

    08 Aug 2006 | Tools | Contributor(s): Alejandro Strachan, Amritanshu Palaria, Ya Zhou, Janam Jhaveri

    Molecular Dynamics simulations of nano-materials

  14. Nanomaterial Mechanics Explorer

    30 Jun 2015 | Tools | Contributor(s): Michael N Sakano, shuhui tang, Alexis Belessiotis, Mitchell Anthony Wood, Sam Reeve, Alejandro Strachan

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

  15. nanoMATERIALS nanoscale heat transport

    03 Nov 2010 | 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

  16. Polymer Modeler

    28 Jun 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

  17. REBO

    24 Jul 2006 | Tools | Contributor(s): Wen-Dung Hsu, SeongJun Heo, Jing Xu, Susan Sinnott

    Reactive Empirical Bond-Order (REBO) potential is a many-body expression optimized for modeling covalently bonded materials, such as carbon and silicon, in large-scale atomistic simulations

  18. Temperature Accelerated Dynamics

    03 May 2011 | Tools | Contributor(s): Justin Riley, Markus J. Buehler

    Simulate temperature accelerated dynamics, a resource for nanoscience and nanotechnology, is supported by the National Science Foundation and other funding agencies. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.