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. Khatereh Kashmari

    https://nanohub.org/members/210632

  2. LAMMPS

    Tools | 27 Mar 2014 | Contributor(s):: Benjamin P Haley

    Run LAMMPS by uploading a data file and command script.

  3. LAMMPS Data File Generator Tool Demo

    Online Presentations | 15 Apr 2022 | Contributor(s):: Carlos Miguel Patiño

    A quick demonstration of the nanoHUB tool LAMMPS Data-File Generator. This was developed as part of the 2017 NCN URE program.

  4. 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

  5. LAMMPS driver tool for potential calibration

    Tools | 15 Feb 2019 | Contributor(s):: Saaketh Desai, Alejandro Strachan

    Calculates basic properties of interest with a given interatomic potential and is used to drive the calibration of the potential.

  6. LAMMPS Input Structure Generator for Functionally Graded Materials (FGM)

    Tools | 17 Nov 2019 | Contributor(s):: Md Shajedul Hoque Thakur, Mahmudul Islam, Abdullah Amin, Satyajit Mojumder, Md Mahbubul Islam

    Generates initial geometries of Functionally Graded Materials (FGM) for LAMMPS simulations

  7. LAMMPS Structure Analysis Toolkit

    Tools | 07 Dec 2017 | Contributor(s):: Nicholas J Finan, Saaketh Desai, Sam Reeve, Alejandro Strachan

    Perform structural analysis on trajectories in LAMMPS dump format

  8. 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

  9. Learning Module: Atomic Picture of Plastic Deformation in Metals

    Wiki

    The main goal of this learning module is to introduce students to the atomic-level processes responsible for plastic deformation in crystalline metals and help them develop a more intuitive...

    https://nanohub.org/wiki/LearningModulePlasticityMD

  10. Lecture 10: Non Equilibrium MD

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

    Topics:Calculating transport coefficientShear flowPerturbation methods

  11. Lecture 1: Basic Concepts

    Presentation Materials | 13 Nov 2009 | Contributor(s):: Ashlie Martini

    Topics:What is MDNewton’s lawBasic concepts and terminology

  12. Lecture 1: the theory behind molecular dynamics

    0.0 out of 5 stars 

    Online Presentations | 09 Jan 2008 | Contributor(s):: Alejandro Strachan

    The first lecture will provide a brief description of classical mechanics and statistical mechanics necessary to understand the physics and approximations behind MD and how to correctly interpret and analyze its results. The power, range of applicability and limitations of MD will be discussed.

  13. Lecture 2: Potential Energy Functions

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

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

  14. Lecture 2: total energy and force calculations

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    Online Presentations | 14 Jan 2008 | Contributor(s):: Alejandro Strachan

    This lecture will describe the various models used to describe the interactions between atoms in a wide range of materials including metals, ceramics and soft materials as well as new recent advances like reactive force fields. The key physics of widely used force fields will be described as well...

  15. Lecture 3: Integration Algorithms

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

    Topics:General guidelinesVerlet algorithmPredictor-corrector methods

  16. Lecture 3: simulation details and coarse grain approaches

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    Online Presentations | 09 Jan 2008 | Contributor(s):: Alejandro Strachan

    The last presentation will describe simulation techniques to simulate materials under isothermal and isobaric conditions. We will also describe coarse grain or mesodynamical approaches (where mesoparticles describe groups of atoms) focusing on recent advances in theory that enable...

  17. Lecture 4: Temperature Control

    0.0 out of 5 stars 

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

    Topics:Velocity scalingHeat bath/reservoirStochastic methods

  18. Lecture 5: Boundary Conditions

    0.0 out of 5 stars 

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

    Topics:Fixed boundariesPeriodic boundary conditionsMinimum image distance

  19. Lecture 6: Molecular Dynamics Simulation: Common Force Field Forms

    Online Presentations | 25 Jul 2024 | Contributor(s):: Ming Chen

    This lecture introduce a type of approximated potential energy function: force fields. A set of common function forms used for simulating molecular systems are discussed. 

  20. Lecture 6: Neighbor Lists

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

    Topics:Saving simulation timeVerlet listsCell lists