Abstract

Classical molecular dynamics simulations are a common component of multi-modal analyses from scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a “black box” analysis technique. In this article, we describe an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open source software repository, which can be freely copied, modified, and redistributed by educators. The topic covered in this OER includes classical atomistic modelling, parameterising interatomic potentials, molecular dynamics simulations, typical sources of error, and some of the approaches to using simulations in the analysis of scattering data.
LanguageEnglish
Pages1-4
Number of pages4
JournalJournal of Applied Crystallography
Volume2019
Issue number52
DOIs
StatusPublished - 8 May 2019

Cite this

@article{c56eafdc6a174abda88ac8c3eb51073c,
title = "An introduction to classical molecular dynamics simulation for experimental scattering users",
abstract = "Classical molecular dynamics simulations are a common component of multi-modal analyses from scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a “black box” analysis technique. In this article, we describe an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open source software repository, which can be freely copied, modified, and redistributed by educators. The topic covered in this OER includes classical atomistic modelling, parameterising interatomic potentials, molecular dynamics simulations, typical sources of error, and some of the approaches to using simulations in the analysis of scattering data.",
author = "Andrew Mccluskey and Robert Grant and Adam Symington and Tim Snow and James Doutch and Benjamin Morgan and Stephen Parker and Karen Edler",
year = "2019",
month = "5",
day = "8",
doi = "10.5281/zenodo.2556826",
language = "English",
volume = "2019",
pages = "1--4",
journal = "Journal of Applied Crystallography",
issn = "0021-8898",
publisher = "International Union of Crystallography",
number = "52",

}

TY - JOUR

T1 - An introduction to classical molecular dynamics simulation for experimental scattering users

AU - Mccluskey, Andrew

AU - Grant, Robert

AU - Symington, Adam

AU - Snow, Tim

AU - Doutch, James

AU - Morgan, Benjamin

AU - Parker, Stephen

AU - Edler, Karen

PY - 2019/5/8

Y1 - 2019/5/8

N2 - Classical molecular dynamics simulations are a common component of multi-modal analyses from scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a “black box” analysis technique. In this article, we describe an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open source software repository, which can be freely copied, modified, and redistributed by educators. The topic covered in this OER includes classical atomistic modelling, parameterising interatomic potentials, molecular dynamics simulations, typical sources of error, and some of the approaches to using simulations in the analysis of scattering data.

AB - Classical molecular dynamics simulations are a common component of multi-modal analyses from scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a “black box” analysis technique. In this article, we describe an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open source software repository, which can be freely copied, modified, and redistributed by educators. The topic covered in this OER includes classical atomistic modelling, parameterising interatomic potentials, molecular dynamics simulations, typical sources of error, and some of the approaches to using simulations in the analysis of scattering data.

U2 - 10.5281/zenodo.2556826

DO - 10.5281/zenodo.2556826

M3 - Article

VL - 2019

SP - 1

EP - 4

JO - Journal of Applied Crystallography

T2 - Journal of Applied Crystallography

JF - Journal of Applied Crystallography

SN - 0021-8898

IS - 52

ER -