Tags: molecular dynamics


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.

Resources (1-20 of 127)

  1. 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.

  2. Atomistic Polymer Workflow Notebook

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

    Run PolymerModeler and nuSIMM tools to create atomistic polymer systems


    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

  4. 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...

  5. 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...

  6. 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...

  7. 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

  8. 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

  9. 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...

  10. 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...

  11. 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.

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

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

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

  13. LAMMPS structure generator

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

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

  14. OpenKIM Explorer

    09 Jun 2015 | | Contributor(s):: Benjamin P Haley, Dan Karls, Alejandro Strachan, Ryan S Elliott, Ellad B Tadmor

    Query the OpenKIM repository for names of interatomic Models for simulating selected materials

  15. Coarse Graining of Crystalline Cellulose

    29 Jul 2016 | | Contributor(s):: Kuo Tian, Mehdi Shishehbor, Pablo Daniel Zavattieri

    Bio-inspired Crystalline Nano-Cellulose coarse graining toolkit

  16. Polymer Synthesis and Characterization in the Cloud: a nanoHUB Classroom Experience

    31 Aug 2015 | | Contributor(s):: Coray Colina

    In this talk, I’ll share the experience of teaching a junior undergraduate computational course in materials science and engineering, with over 70 participants. Both molecular and continuum methods were studied and applied to relevant materials problems. Students were able to build and...

  17. MD simulations of shock loading

    11 Jun 2015 | | Contributor(s):: edwin alberto antillon, Mitchell Anthony Wood, Mathew Joseph Cherukara, Alejandro Strachan

    Use MD simulation to study shocks in various materials including metals and energetics

  18. Molecular Exploration Tool

    01 Aug 2014 | | Contributor(s):: Xueying Wang, nicolas onofrio, Alejandro Strachan, David M Guzman

    The tool can display the molecule structures and run Lammps simulations.

  19. Molecular Dynamics Showcase Builder

    09 Nov 2015 | | Contributor(s):: Michael McLennan, Nicholas K Kisseberth, George A. Howlett, Jim Slopsema, Aleksei Aksimentiev, Chen-Yu Li

    Tool to create showcases for the Molecular Dynamics Showcase viewer.

  20. Atomistic Modeling: Past, Present, and Future, MGI, ICME, etc.

    03 Nov 2015 | | Contributor(s):: Paul Saxe

    I will present a perspective on atomistic modeling — tools using quantum methods such as DFT, as well as molecular dynamics and Monte Carlo methods based on forcefields — over the past 30 years or so. While we are all caught up in the present, it is important to remember and realize...