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 139)

  1. Glass transition temperature notebook

    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

  2. Homework assignment: learning about elastic constants via molecular dynamics simulations

    17 Feb 2015 | | Contributor(s):: Alejandro Strachan, David Ray Johnson

    In this homework assignment students will use molecular dynamics to compute the elastic constants of metals using an embedded atom model to describe atomic interactions. They will deform  a single crystal along different directions and obtain c11, c12 and c44 elastic constants from the...

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

    09 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...

  4. 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...

  5. IMA 2013 UQ: Bayesian Calibration of Molecular Dynamics Simulations for Composite Materials Properties

    10 Feb 2014 | | Contributor(s):: Paul N. Patrone

    In this talk, I discuss ongoing research whose goal is to determine, via Bayesian inference, an ensemble of inputs that represents a class of commercially important amine-cured epoxies. We construct an analytical approximation (i.e. a surrogate or emulator) of the simulations, treating the input...

  6. IMA 2013 UQ: DFT-based Thermal Properties: Three Levels of Error Management

    10 Feb 2014 | | Contributor(s):: Kurt Lejaeghere

    It is often computationally expensive to predict finite-temperature properties of a crystal from density-functional theory (DFT). The temperature-dependent thermal expansion coefficient α, for example, is calculated from the phonon spectrum, and the melting temperature Tm can only be obtained...

  7. Introduction to Molecular Dynamics

    27 Aug 2015 | | Contributor(s):: Alejandro Strachan

  8. Introduction to Molecular Dynamics

    06 Apr 2015 | | Contributor(s):: Alejandro Strachan

    This short presentation will describe the idea behind MD simulations and demonstrate its use in real applications.

  9. Introduction to Molecular Dynamics Showcase

    10 Feb 2017 | | Contributor(s):: Chen-Yu Li, Karl Steven Decker (editor), Aleksei Aksimentiev

    In this tutorial, we will demonstrate how to use the MD showcase builder tool to create a showcase. We will start from the simplest example – creating a showcase from a PDB file – and move on to more complicated examples. We will also cover how to add a description, change...

  10. Introduction: molecular dynamics simulations

    09 Jan 2008 | | Contributor(s):: Alejandro Strachan

    This short presentation will describe the idea behind MD simulations and demonstrate its use in real applications.

  11. 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 biology...

  12. LAMMPS Data-File Generator

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

    This tool generates all necessary input files for LAMMPS simulations of molecular systems starting with an atomistic structure.

  13. LAMMPS driver tool for potential calibration

    15 Feb 2019 | | Contributor(s):: Saaketh Desai, Alejandro Strachan

    Calculates basic properties of interest with a given interatomic potential and is used to drive the calibration of the potential.

  14. LAMMPS Structure Analysis Toolkit

    07 Dec 2017 | | Contributor(s):: Nicholas J Finan, Saaketh Desai, Sam Reeve, Alejandro Strachan

    Perform structural analysis on trajectories in LAMMPS dump format

  15. LAMMPS structure generator

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

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

  16. Lecture 10: Non Equilibrium MD

    05 Jan 2010 | | Contributor(s):: Ashlie Martini

    Topics:Calculating transport coefficientShear flowPerturbation methods

  17. Lecture 1: Basic Concepts

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

    Topics:What is MDNewton’s lawBasic concepts and terminology

  18. Lecture 1: the theory behind molecular dynamics

    09 Jan 2008 | | Contributor(s):: Alejandro Strachan

    The first lecture will provide a brief description of classical mechanics and statistical mechanics necessary to understand the physics and approximations behind MD and how to correctly interpret and analyze its results. The power, range of applicability and limitations of MD will be discussed.

  19. Lecture 2: Potential Energy Functions

    05 Jan 2010 | | Contributor(s):: Ashlie Martini

    Topics:Pair potentialsCoulomb interactionsEmbedded atom modelIntra-molecular interactions (bond, angle, torsion)

  20. Lecture 2: total energy and force calculations

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

    This lecture will describe the various models used to describe the interactions between atoms in a wide range of materials including metals, ceramics and soft materials as well as new recent advances like reactive force fields. The key physics of widely used force fields will be described as well...