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 (1-13 of 13)

  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. 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.

  3. 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.

  4. Lecture 10: Non Equilibrium MD

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

    Topics:Calculating transport coefficientShear flowPerturbation methods

  5. Lecture 9: Dynamic Properties

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

    Topics:Time correlation functionsEinstein relationsGreen-Kubo relations

  6. Lecture 8: Static Properties

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

    Topics:Thermodynamic propertiesEntropic propertiesStatic structure

  7. Lecture 7: Initialization and Equilibrium

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

    Topics:Initial positionsInitial velocitiesEvaluating equilibrium

  8. Lecture 6: Neighbor Lists

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

    Topics:Saving simulation timeVerlet listsCell lists

  9. Lecture 5: Boundary Conditions

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

    Topics:Fixed boundariesPeriodic boundary conditionsMinimum image distance

  10. Lecture 4: Temperature Control

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

    Topics:Velocity scalingHeat bath/reservoirStochastic methods

  11. Lecture 3: Integration Algorithms

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

    Topics:General guidelinesVerlet algorithmPredictor-corrector methods

  12. Lecture 2: Potential Energy Functions

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

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

  13. Lecture 1: Basic Concepts

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

    Topics:What is MDNewton’s lawBasic concepts and terminology