Tags: molecular dynamics (MD)

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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.

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  1. Serge Raymond Maalouf

    https://nanohub.org/members/183454

  2. LAMMPS Data-File Generator

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

    The LAMMPS Data-File Generator generates LAMMPS data files to perform molecular dynamics simulations in LAMMPS using Dreiding or PCFF force field energy terms

  3. Atomistic Polymer Workflow Notebook

    Tools | 19 Oct 2017 | Contributor(s):: Benjamin P Haley

    Run PolymerModeler and nuSIMM tools to create atomistic polymer systems

  4. THERMAL CNT

    Tools | 23 May 2017 | Contributor(s):: Luca Bergamasco, Matteo Fasano, Eliodoro Chiavazzo, Pietro Asinari, Annalisa Cardellini, Matteo Morciano

    Compute thermal conductivity of single-walled carbon nano-tubes via NEMD method

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

    Presentation Materials | 26 Jul 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...

  6. Structure-Force Field Generator for Molecular Dynamics Simulations

    Online Presentations | 01 Aug 2017 | 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 principle simulations of large molecules are still not possible because the high computational time and...

  7. Multiscale Modelling of Nanoparticle Suspensions

    Online Presentations | 09 Jun 2017 | Contributor(s):: Pietro Asinari

    In the present work a multiscale modelling approach is implemented to relate the nanoscale phenomena to the macroscopic bulk properties of nano-suspensions. Specifically, Molecular Dynamics (MD) simulations and Brownian Dynamics (BD) are synergistically integrated to understand the mechanisms...

  8. Sumudu Tennakoon

    https://nanohub.org/members/172279

  9. Glass transition temperature notebook

    Tools | 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

  10. Vacancy Formation Energy with MD

    Tools | 03 May 2017 | Contributor(s):: Sam Reeve, Alejandro Strachan

    Calculate vacancy formation energy with molecular dynamics and various atomic interaction models

  11. PREPRINT: Molecular Modeling of the Microstructure Evolution during the Carbonization of PAN-Based Carbon Fibers

    Papers | 23 Mar 2017 | Contributor(s):: Alejandro Strachan, Saaketh Desai

    PREPRINTDevelopment of high strength carbon fibers (CFs) requires an understanding of the relationship between the processing conditions, microstructure and resulting properties. We developed a molecular model that combines kinetic Monte Carlo (KMC) and molecular dynamics (MD) techniques to...

  12. Danilo de Camargo Branco

    https://nanohub.org/members/165989

  13. Introduction to Molecular Dynamics Showcase

    Downloads | 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...

  14. Yang Zhong

    https://nanohub.org/members/162984

  15. Muhammad Ihsan Ul Haq

    https://nanohub.org/members/162682

  16. Molecular Dynamics (Mark Asta)

    Presentation Materials | 13 Jan 2017

  17. Fundamentals of Phonon Transport Modeling L1: Introduction

    Presentation Materials | 03 Jan 2017 | Contributor(s):: Alan McGaughey, Xiulin Ruan

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

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

    Presentation Materials | 03 Jan 2017 | Contributor(s):: Xiulin Ruan, Alan McGaughey

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

  19. Phani Ravi Teja Nunna

    https://nanohub.org/members/159739

  20. LAMMPS structure generator

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

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