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 (41-60 of 132)

  1. 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

  2. [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...

  3. 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

  4. Polymatic: A Simulated Polymerization Algorithm

    13 Mar 2013 | | Contributor(s):: Lauren Abbott, Coray Colina

    Polymatic is a set of codes for structure generation of amorphous polymers by a simulated polymerization algorithm. The main task of Polymatic is to perform polymerization steps within a system based on a number of defined bonding criteria. It works in conjunction with a simulation package to...

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

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

  6. [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...

  7. [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...

  8. [Illinois] Molecular Dynamics Software (NAMD)

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

  9. [Illinois] Molecular Dynamics

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

  10. MD Simulations of Gas Flows in Nano-Channels and Interface Thermal Resistance Between Simple Liquids and Solids

    30 May 2012 | | Contributor(s):: Ali Beskok

    This talk focuses on our group’s recent research on molecular dynamics simulations of gas flows in nano-scale confined geometries, and interface thermal resistance between simple liquids and solids. Gas flow research demonstrates the importance of wall force field effects that penetrate...

  11. Atomistic Material Science

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

    This course introduces first principles electronic structure calculations of materials properties and the concept of molecular dynamics (MD) simulations of materials focusing on the physics and approximations underlying the simulations and interpretation of their results.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. Temperature Accelerated Dynamics

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

    Simulate temperature accelerated dynamics

  17. Development of the ReaxFF reactive force fields and applications to combustion, catalysis and material failure

    29 Jul 2011 | | Contributor(s):: Adri van Duin

    This lecture will describe how the traditional, non-reactive FF-concept can be extended for application including reactive events by introducing bond order/bond distance concepts. Furthermore, it will address how these reactive force fields can be trained against QM-data, thus greatly enhancing...

  18. nanoMATERIALS nanoscale heat transport

    03 Nov 2010 | | 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

  19. 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.

  20. Atomic Picture of Plastic Deformation in Metals via Online Molecular Dynamics Simulations

    18 Dec 2009 | | Contributor(s):: Alejandro Strachan

    The main goal of this learning module is to introduce students to the atomic-level processes responsible for plastic deformation in crystalline metals and help them develop a more intuitive understanding of how materials work at molecular scales. The module consists of: i) Two introductory...