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 (1-14 of 14)

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

    14 Aug 2017 | Presentation Materials | 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...

    http://nanohub.org/resources/26904

  2. Structure-Force Field Generator for Molecular Dynamics Simulations

    07 Aug 2017 | Presentation Materials | Contributor(s): Carlos Miguel Patiño, Lorena Alzate-Vargas, Alejandro Strachan

    Atomistic and molecular simulations have become an important research field due to the progress made in computer performance and the necessity of new and improved materials. Despite this, first...

    http://nanohub.org/resources/26959

  3. Fundamentals of Phonon Transport Modeling L1: Introduction

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

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

    http://nanohub.org/resources/25501

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

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

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

    http://nanohub.org/resources/25502

  5. Lecture 10: Non Equilibrium MD

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

    Topics: Calculating transport coefficient Shear flow Perturbation methods

    http://nanohub.org/resources/8125

  6. Lecture 9: Dynamic Properties

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

    Topics: Time correlation functions Einstein relations Green-Kubo relations

    http://nanohub.org/resources/8124

  7. Lecture 8: Static Properties

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

    Topics: Thermodynamic properties Entropic properties Static structure

    http://nanohub.org/resources/8123

  8. Lecture 7: Initialization and Equilibrium

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

    Topics: Initial positions Initial velocities Evaluating equilibrium

    http://nanohub.org/resources/8122

  9. Lecture 6: Neighbor Lists

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

    Topics: Saving simulation time Verlet lists Cell lists

    http://nanohub.org/resources/8121

  10. Lecture 5: Boundary Conditions

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

    Topics: Fixed boundaries Periodic boundary conditions Minimum image distance

    http://nanohub.org/resources/8120

  11. Lecture 4: Temperature Control

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

    Topics: Velocity scaling Heat bath/reservoir Stochastic methods

    http://nanohub.org/resources/8119

  12. Lecture 3: Integration Algorithms

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

    Topics: General guidelines Verlet algorithm Predictor-corrector methods

    http://nanohub.org/resources/8118

  13. Lecture 2: Potential Energy Functions

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

    Topics: Pair potentials Coulomb interactions Embedded atom model Intra-molecular interactions (bond, angle, torsion)

    http://nanohub.org/resources/8117

  14. Lecture 1: Basic Concepts

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

    Topics: What is MD Newton’s law Basic concepts and terminology

    http://nanohub.org/resources/7795