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 (81-100 of 127)

  1. Energy and Nanoscience A More Perfect Union

    29 Mar 2009 | | Contributor(s):: Mark Ratner

    Huge problems of energy and sustainability confront the science/engineering community, mankind, and our planet. The energy problem comes in many dimensions, including supply, demand, conservation, transportation, and storage. This overview will stress the nature of these problems, and offer a...

  2. Illinois Center for Cellular Mechanics: Discovery through the Computational Microscope

    11 Feb 2009 | | Contributor(s):: Klaus Schulten

    Computational MicroscopeAll-atom molecular dynamics simulations have become increasingly popular as a toolto investigate protein function and dynamics. However, researchers are usuallyconcerned about the short time scales covered by simulations, the apparentimpossibility to model large and...

  3. Illinois PHYS 466, Lecture 4: Molecular Dynamics

    05 Feb 2009 | | Contributor(s):: David M. Ceperley

    Molecular Dynamics What to choose in an integrator The Verlet algorithm Boundary Conditions in Space and time Reading assignment: Frenkel and Smit Chapter 4 Content: Characteristics of simulations The Verlet Algorithm Higher Order Methods? Quote from Berendsen Long-term stability of Verlet...

  4. Nanoparticle and Colloidal Simulations with Molecular Dynamics

    05 Dec 2008 | | Contributor(s):: Steve Plimpton

    Modeling nanoparticle or colloidal systems in a molecular dynamics (MD) code requires coarse-graining on several levels to achieve meaningful simulation times for study of rheological and other manufacturing properties. These include treating colloids as single particles, moving from explicit to...

  5. MSE 597G Lecture 4: Interatomic potentials I

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

    Interatomic potentials: pairwise potentials.

  6. MSE 597G Lecture 3: Statistical Mechanics II

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

    Basic physics: statistical mechanics, Algorithms: Integrating the equations of motion.

  7. MSE 597G An Introduction to Molecular Dynamics

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

    The goal of this short course is to provide an introduction to the theory and algorithms behind MD simulations, describe some of the most exciting recent developments in the field and exemplify with a few applications applications. The series also includes a tutorial on the nanoMATERIALS...

  8. 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.

  9. MSE 597G Lecture 5: Interatomic potentials II

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

    Embedded atom model for metals,Three body terms for semiconductors: Stillinger-Weber,Electrostatics and Covalent interactions.

  10. MSE 597G: An Introduction to Molecular Dynamics

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

  11. MSE 597G Lecture 6: Interatomic potentials III

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

    Reactive force fields,Parameterization of interatomic potentials

  12. MSE 597G Lecture 7: Advanced Techniques for Molecular Dynamics Simulations

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

    Thermostats and barostats,Linear methods for energy and force calculations,Coarse graining or mesodynamics,Validation and Verification.

  13. MSE 597G Lecture 2: Statistical Mechanics I

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

    Basic physics: statistical mechanics.

  14. MSE 597G Lecture 1: Classical Mechanics

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

    Basic physics: classical mechanics

  15. Ionic Selectivity in Channels: complex biology created by the balance of simple physics

    05 Jun 2008 | | Contributor(s):: Bob Eisenberg

    An important class of biological molecules—proteins called ionic channels—conduct ions (like Na+ , K+ , Ca2+ , and Cl− ) through a narrow tunnel of fixed charge (‘doping’). Ionic channels control the movement of electric charge and current across biological membranes and so play a role in...

  16. BNC Annual Research Review: An Introduction to PRISM and MEMS Simulation

    04 Jun 2008 | | Contributor(s):: Jayathi Murthy

    This presentation is part of a collection of presentations describing the projects, people, and capabilities enhanced by research performed in the Birck Center, and a look at plans for the upcoming year.

  17. MD Simulation

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

    Code to perform Molecular Dynamics (MD) Simulations

  18. Computational Nanoscience, Homework Assignment 3: Molecular Dynamics Simulation of Carbon Nanotubes

    14 Feb 2008 | | Contributor(s):: Elif Ertekin, Jeffrey C Grossman

    The purpose of this assignment is to perform molecular dynamics simulations to calculate various properties of carbon nanotubes using LAMMPS and Tersoff potentials.This assignment is to be completed following lectures 5 and 6 using the "LAMMPS" program in the Berkeley Computational Nanoscience...

  19. Computational Nanoscience, Homework Assignment 2: Molecular Dynamics Simulation of a Lennard-Jones Liquid

    14 Feb 2008 | | Contributor(s):: Elif Ertekin, Jeffrey C Grossman

    The purpose of this assignment is to perform a full molecular dynamics simulation based on the Verlet algorithm to calculate various properties of a simple liquid, modeled as an ensemble of identical classical particles interacting via the Lennard-Jones potential.This assignment is to be...

  20. Computational Nanoscience, Lecture 6: Pair Distribution Function and More on Potentials

    13 Feb 2008 | | Contributor(s):: Jeffrey C Grossman, Elif Ertekin

    In this lecture we remind ourselves what a pair distribution function is, how to compute it, and why it is so important in simulations. Then, we revisit potentials and go into more detail including examples of typical functional forms, relative energy scales, and what to keep in mind when...