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.

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  1. FunUQ for MD

    22 Oct 2018 | Contributor(s):: Sam Reeve, Alejandro Strachan

    Functional uncertainty quantification for molecular dynamics

  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. LAMMPS Structure Analysis Toolkit

    01 Aug 2018 | | Contributor(s):: Nicholas J Finan, Saaketh Desai, Sam Reeve, Alejandro Strachan

    Perform structural analysis on trajectories in LAMMPS dump format

  4. Shobhit Sanjeev Chaturvedi

    https://nanohub.org/members/191633

  5. Sumit Kumar Sinha

    Completed my B.Tech (Mechanical engineering), M.tech (Design & Manufacturing) from National Institute of Technology Silchar, India & currently pursuing my Ph.D. from Malaviya National Institute of...

    https://nanohub.org/members/189614

  6. Dinesh Kumar

    https://nanohub.org/members/189551

  7. Serge Raymond Maalouf

    https://nanohub.org/members/183454

  8. 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.

  9. Atomistic Polymer Workflow Notebook

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

    Run PolymerModeler and nuSIMM tools to create atomistic polymer systems

  10. THERMAL CNT

    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

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

    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...

  12. Structure-Force Field Generator for Molecular Dynamics Simulations

    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...

  13. Multiscale Modelling of Nanoparticle Suspensions

    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...

  14. Sumudu Tennakoon

    https://nanohub.org/members/172279

  15. 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

  16. Vacancy Formation Energy with MD

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

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

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

    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...

  18. 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...

  19. Yang Zhong

    https://nanohub.org/members/162984

  20. Fundamentals of Phonon Transport Modeling L1: Introduction

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

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