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.

Presentation Materials (1-16 of 16)

  1. Applying Machine Learning to Computational Chemistry: Can We Predict Molecular Properties Faster without Compromising Accuracy?

    14 Aug 2017 | Contributor(s):: Hanjing Xu, Pradeep Kumar Gurunathan

    Non-covalent interactions are crucial in analyzing protein folding and structure, function of DNA and RNA, structures of molecular crystals and aggregates, and many other processes in the fields of biology and chemistry. However, it is time and resource consuming to calculate such interactions...

  2. Combustion in Nanobubbles (generated from water electrolysis)

    27 Aug 2018 | | Contributor(s):: Shourya Jain, Li Qiao

    A long-pursued goal, which is also a grand challenge, in nanoscience and nanotechnology is to create nanoscale devices, machines and motors that can do useful work. However, loyal to the scaling law, combustion would be impossible at nanoscale be- cause the heat loss would profoundly dominate...

  3. Fundamentals of Phonon Transport Modeling L1: Introduction

    04 Jan 2017 | | Contributor(s):: Alan McGaughey, Xiulin Ruan

    Part of the 2016 IMECE Tutorial: Fundamentals of Phonon Transport Modeling: Formulation, Implementation, and Applications.

  4. Fundamentals of Phonon Transport Modeling L2: MD Simulation, Green Kubo, Direct Method

    04 Jan 2017 | | Contributor(s):: Xiulin Ruan, Alan McGaughey

    Part of the 2016 IMECE Tutorial: Fundamentals of Phonon Transport Modeling: Formulation, Implementation, and Applications.

  5. Lecture 10: Non Equilibrium MD

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

    Topics:Calculating transport coefficientShear flowPerturbation methods

  6. Lecture 1: Basic Concepts

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

    Topics:What is MDNewton’s lawBasic concepts and terminology

  7. Lecture 2: Potential Energy Functions

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

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

  8. Lecture 3: Integration Algorithms

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

    Topics:General guidelinesVerlet algorithmPredictor-corrector methods

  9. Lecture 4: Temperature Control

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

    Topics:Velocity scalingHeat bath/reservoirStochastic methods

  10. Lecture 5: Boundary Conditions

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

    Topics:Fixed boundariesPeriodic boundary conditionsMinimum image distance

  11. Lecture 6: Neighbor Lists

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

    Topics:Saving simulation timeVerlet listsCell lists

  12. Lecture 7: Initialization and Equilibrium

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

    Topics:Initial positionsInitial velocitiesEvaluating equilibrium

  13. Lecture 8: Static Properties

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

    Topics:Thermodynamic propertiesEntropic propertiesStatic structure

  14. Lecture 9: Dynamic Properties

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

    Topics:Time correlation functionsEinstein relationsGreen-Kubo relations

  15. Molecular Dynamics Simulation of Displacement Cascade in Molybdenum

    06 Dec 2018 | | Contributor(s):: Gyuchul Park, Alejandro Strachan

    Displacement cascade in molybdenum was conducted by using Molecular Dynamics (MD) Simulation method. LAMMPS tool was used to run the simulation at nanoHUB. Three primary questions were answered from the simulation:1. The number of displaced atoms/interstitials with respect to time when the...

  16. 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...