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.

Resources (121-129 of 129)

  1. Materials strength: does size matter? nanoMATERIALS simulation toolkit tutorial

    01 Feb 2007 | | Contributor(s):: Alejandro Strachan

    Molecular dynamics (MD) is a powerful technique to characterize the fundamental, atomic-level processes that govern materials behavior and is playing an important role in our understanding of the new phenomena that arises in nanoscale and nanostructured materials and result in their unique...

  2. Potassium Channels: Conduction, Selectivity, Blockage, Inactivation, and Gating

    03 Nov 2006 | | Contributor(s):: Benoit Roux, NCN at Northwestern University

    The determination of the structure of the KcsA K+ channel fromStreptomyces lividan has made it possible to investigate the functionof a biological channel at the atomic level. Because of its structuralsimilarity with eukaryotic K-channels, investigations of KcsA areexpected to help understand a...

  3. REBO

    24 Jul 2006 | | 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

  4. 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.

  5. Molecular Workbench: An Interface to the Molecular World

    25 Jun 2006 | | Contributor(s):: Charles Xie

    The Molecular Workbench software is a free, open-source modeling and authoring program specifically designed for use in science education. Powered by a set of real-time molecular simulation engines that compute and visualize the motion of particles interacting through force fields, in both 2D and...

  6. nano-Materials Simulation Toolkit

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

    Molecular Dynamics simulations of nano-materials

  7. Nanofluidics

    15 Jun 2004 | | Contributor(s):: Susan Sinnott

    Nanofluidics

  8. REBO Nanofluidics Exercise

    10 May 2006 | | Contributor(s):: Susan Sinnott, Hetal Patel

    Nanofluidics exercise showing the variation of energy and positionof methane and butane molecules flowing through an opened carbonnanotube as the system temperature and the length of the nanotubeare varied.

  9. Structure and Ion Permeation of the Gramicidin Channel using Molecular Dynamics

    12 Apr 2004 |

    Molecular dynamics (MD) has become an essential tool for obtaining microscopic insight into biological function. The gramicidin channel as an excellent benchmark system for this purpose. Using extensive MD simulations with explicit solvent and membrane, we determine the backbone structure and...