An introduction to classical molecular dynamics simulation for experimental scattering users
McCluskey, Andrew R. ; Grant, James ; Symington, Adam R. ; Snow, Tim ; Doutch, James ; Morgan, Benjamin J. ; Parker, Stephen C. and Edler, Karen J. LU
(2019)
In Journal of Applied Crystallography
52(3).
p.665-668
- Abstract
Classical molecular dynamics simulations are a common component of multi-modal analyses of 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. This article describes 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... (More)
Classical molecular dynamics simulations are a common component of multi-modal analyses of 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. This article describes 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 topics covered in this OER include classical atomistic modelling, parameterizing interatomic potentials, molecular dynamics simulations, typical sources of error and some of the approaches to using simulations in the analysis of scattering data.
(Less)
- author
- McCluskey, Andrew R.
; Grant, James
; Symington, Adam R.
; Snow, Tim
; Doutch, James
; Morgan, Benjamin J.
; Parker, Stephen C.
and Edler, Karen J.
LU
- publishing date
- 2019-06
- type
- Contribution to journal
- publication status
- published
- keywords
- classical simulation, multimodal analysis, open educational resources, scattering
- in
- Journal of Applied Crystallography
- volume
- 52
- issue
- 3
- pages
- 4 pages
- publisher
- International Union of Crystallography
- external identifiers
-
- scopus:85065532926
- ISSN
- 0021-8898
- DOI
- 10.1107/S1600576719004333
- language
- English
- LU publication?
- no
- additional info
- Publisher Copyright: © 2019 Andrew R. McCluskey et al. Journal of Applied Crystallography published by IUCr Journals.
- id
- baa7dfc0-2e82-487c-94fa-78a2aea1782a
- date added to LUP
- 2023-01-18 09:06:32
- date last changed
- 2023-02-03 11:19:08
@article{baa7dfc0-2e82-487c-94fa-78a2aea1782a,
abstract = {{<p>Classical molecular dynamics simulations are a common component of multi-modal analyses of 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. This article describes 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 topics covered in this OER include classical atomistic modelling, parameterizing interatomic potentials, molecular dynamics simulations, typical sources of error and some of the approaches to using simulations in the analysis of scattering data.</p>}},
author = {{McCluskey, Andrew R. and Grant, James and Symington, Adam R. and Snow, Tim and Doutch, James and Morgan, Benjamin J. and Parker, Stephen C. and Edler, Karen J.}},
issn = {{0021-8898}},
keywords = {{classical simulation; multimodal analysis; open educational resources; scattering}},
language = {{eng}},
number = {{3}},
pages = {{665--668}},
publisher = {{International Union of Crystallography}},
series = {{Journal of Applied Crystallography}},
title = {{An introduction to classical molecular dynamics simulation for experimental scattering users}},
url = {{http://dx.doi.org/10.1107/S1600576719004333}},
doi = {{10.1107/S1600576719004333}},
volume = {{52}},
year = {{2019}},
}