Tags: molecular dynamics (MD)

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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 (21-40 of 54)

  1. LAMMPS Data-File Generator

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

    The LAMMPS Data-File Generator generates LAMMPS data files to perform molecular dynamics simulations in LAMMPS using Dreiding or PCFF force field energy terms

  2. Atomistic Polymer Workflow Notebook

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

    Run PolymerModeler and nuSIMM tools to create atomistic polymer systems

  3. THERMAL CNT

    Tools | 23 May 2017 | 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

  4. Glass transition temperature notebook

    Tools | 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

  5. Vacancy Formation Energy with MD

    Tools | 03 May 2017 | Contributor(s):: Sam Reeve, Alejandro Strachan

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

  6. LAMMPS structure generator

    Tools | 01 Nov 2016 | Contributor(s):: Benjamin P Haley

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

  7. OpenKIM Explorer

    Tools | 09 Jun 2015 | Contributor(s):: Dan Karls, Benjamin P Haley, Alejandro Strachan, Ryan S Elliott, Ellad B Tadmor

    Run interatomic potentials from the OpenKIM Repository in LAMMPS

  8. Coarse Graining of Crystalline Cellulose

    Tools | 29 Jul 2016 | Contributor(s):: Kuo Tian, Mehdi Shishehbor, Pablo Daniel Zavattieri

    Bio-inspired Crystalline Nano-Cellulose coarse graining toolkit

  9. LegoGen

    Tools | 05 Feb 2016 | Contributor(s):: Scott Michael Louis Slone, Chris Maffeo, AbderRahman N Sobh, Aleksei Aksimentiev

    Tool workflow for building DNA Brick structures automatically.

  10. MD simulations of shock loading

    Tools | 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

  11. Molecular Exploration Tool

    Tools | 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.

  12. Molecular Dynamics Showcase Builder

    Tools | 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.

  13. Nanomaterial Mechanics Explorer

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

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

  14. Crack Propagation Simulation

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

    Simulate crack propagations through materials under applied loads.

  15. LAMMPS

    Tools | 27 Mar 2014 | Contributor(s):: Benjamin P Haley

    Run LAMMPS by uploading a data file and command script.

  16. Molecular Dynamics Showcase

    Tools | 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

  17. Crystalline Cellulose - Atomistic Toolkit

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

    Crystalline Cellulose - Atomistic Toolkit

  18. Two-temperature Non-equilibrium Molecular Dynamics Simulator

    Tools | 26 Jul 2012 | Contributor(s):: Yan Wang, Xin Jin, Xiulin Ruan

    Simulate electron-phonon coupled thermal transport across metal-nonmetal interface

  19. 2d Ideal Gas Molecular Dynamics

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

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

  20. 1-D Chain Dispersions

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

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