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 29)

  1. 1-D Chain Dispersions

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

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

  3. Atomic Stick-Slip

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

    Molecular dynamics simulation of atomic stick-slip friction

  4. Atomistic Polymer Workflow Notebook

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

    Run PolymerModeler and nuSIMM tools to create atomistic polymer systems

  5. BioMOCA Suite

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

    Simulates ion flow through a channel.

  6. 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

  7. Crack Propagation Simulation

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

    Simulate crack propagations through materials under applied loads.

  8. Crystalline Cellulose - Atomistic Toolkit

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

    Crystalline Cellulose - Atomistic Toolkit

  9. Glass transition temperature notebook

    22 May 2017 | | 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

  10. LAMMPS Data-File Generator

    01 Aug 2017 | | Contributor(s):: Carlos Miguel Patiño, Lorena Alzate-Vargas, Chunyu Li, Benjamin P Haley, Alejandro Strachan

    This tool generates all necessary input files for LAMMPS simulations of molecular systems starting with an atomistic structure.

  11. 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

  12. MD Simulation

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

    Code to perform Molecular Dynamics (MD) Simulations

  13. 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

  14. Micelle

    24 Jul 2006 | | 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.

  15. MiniMol: Minimal Molecular Simulation Tool

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

    Perform simple molecular dynamics and statics simulations.

  16. MIT Tools for Energy Conversion and Storage

    13 Sep 2009 | | 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

  17. Molecular Dynamics Showcase

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

    View interesting features of a molecular dynamics trajectory file

  18. 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.

  19. 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.

  20. Nano Heatflow

    25 Sep 2007 | | 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.