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.

Resources (121-139 of 139)

  1. Ripples and Warping of Graphene: A Theoretical Study

    08 Jun 2010 | | Contributor(s):: Umesh V. Waghmare

    We use first-principles density functional theory based analysis to understand formation of ripples in graphene and related 2-D materials. For an infinite graphene, we show that ripples are linked with a low energy branch of phonons that exhibits quadratic dispersion at long wave-lengths. Many...

  2. Running MD on the nanoHUB: The nano-MATERIALS Simulation Toolkit

    13 Nov 2008 | | Contributor(s):: Alejandro Strachan

    A quick demostration of the nanoHUB tool: nano-Materials Simulation Toolkit.

  3. Short Course on Molecular Dynamics Simulation

    13 Oct 2009 | | Contributor(s):: Ashlie Martini

    This set of ten presentations accompanied a graduate level course on Molecular Dynamics simulation. The specific objective of the course (and the presentations) is to provide:1. Awareness of the opportunities and limitations of Molecular Dynamics as a tool for scientific and engineering...

  4. Structural Analysis for Molecular Dynamics Trajectories

    03 Mar 2019 | | Contributor(s):: Nicholas J Finan, Saaketh Desai, Sam Reeve, Alejandro Strachan

    This tool reads in LAMMPS trajectories and performs the following analysis: Radial Distribution Function (RDF), X-Ray Diffraction (XRD), Vibrational Density of States, and  (More to Come!). By default the tool requires trajectory files to be input by the user however there are some...

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

    12 Apr 2004 | | Contributor(s):: Toby Allen

    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...

  6. Structure-Force Field Generator for Molecular Dynamics Simulations

    01 Aug 2017 | | Contributor(s):: Carlos Miguel Patiño, Lorena Alzate-Vargas, Alejandro Strachan

    Atomistic and molecular simulations have become an important research field due to the progress made in computer performance and the necessity of new and improved materials. Despite this, first principle simulations of large molecules are still not possible because the high computational time and...

  7. Temperature Accelerated Dynamics

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

    Simulate temperature accelerated dynamics


    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

  9. Tutorial 1: Atomistic Material Science - ab initio simulations of materials

    25 Aug 2011 | | Contributor(s):: Alejandro Strachan

    This lecture introduces first principles electronic structure calculations of materials properties.It describes the approximations made to the many-body Schrodinger equation in Hartree Fock and Density Functional Theory and numerical approximations used in computer simulations.

  10. Tutorial 2: Atomistic Material Science - Molecular Dynamics simulations of materials

    25 Aug 2011 | | Contributor(s):: Alejandro Strachan

    This lecture introduces the concept of molecular dynamics (MD) simulations of materials focusing on the physics and approximations underlying the simulations and interpretation of their results.

  11. Tutorial 3: Materials Simulation by First-Principles Density Functional Theory

    14 Sep 2010 | | Contributor(s):: Umesh V. Waghmare

    This two-part lecture will provide an introduction to first-principles density functional theory based methods for simulation of materials, with a focus on determination of interatomic force constants and vibrational spectra of nano- structures and extended periodic materials.

  12. Tutorial 3b: Materials Simulation by First-Principles Density Functional Theory II

    09 Sep 2010 | | Contributor(s):: Umesh V. Waghmare

  13. Vacancy Formation Energy with MD

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

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

  14. [Illinois] Beckman Graduate Seminar: Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations

    17 Dec 2012 | | Contributor(s):: Hang Yu

    Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in cellular morphogenesis, for example curving planar membranes into tubular membranes. However, it is...

  15. [Illinois] CSE Seminar Series: Advances in First-principles Computational Materials Science

    20 Nov 2012 | | Contributor(s):: Elif Ertekin

    Title: Advances in first-principles computational materials scienceSubtitle: Things we can calculate now, that we couldn't when I was in grad school.The capability to rationally design new materials with tailored properties and functionality on a computer remains a grand challenge whose success...

  16. [Illinois] Molecular Dynamics

    19 Jun 2012 | | Contributor(s):: Emad Tajkhorshid

  17. [Illinois] Molecular Dynamics Software (NAMD)

    19 Jun 2012 | | Contributor(s):: Emad Tajkhorshid

  18. [Illinois] PHYS466 2013 Lecture 4: Molecular Dynamics I

    03 Feb 2013 | | Contributor(s):: David M. Ceperley

  19. [Illinois] Physics 550 Biomolecular Physics

    03 Sep 2013 | | Contributor(s):: Klaus Schulten, Taekjip Ha

      Physical concepts governing the structure and function of biological macromolecules; general properties, spatial structure, energy levels, dynamics and functions, and relation to other complex physical systems such as glasses; recent research in biomolecular physics; physical...