Coarse-grained simulation of DNA using LAMMPS : an implementation of the oxDNA model and its applications
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Published version
Author(s)
Henrich, Oliver
Gutiérrez Fosado, Yair Augusto
Curk, Tine
Ouldridge, Thomas E
Type
Journal Article
Abstract
During the last decade coarse-grained nucleotide models have emerged that allow us to study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.
Date Issued
2018-05-10
Date Acceptance
2018-04-19
Citation
European Physical Journal E. Soft Matter, 2018, 41 (5), pp.57-57
ISSN
1292-8941
Publisher
EDP Sciences
Start Page
57
End Page
57
Journal / Book Title
European Physical Journal E. Soft Matter
Volume
41
Issue
5
Copyright Statement
© The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Sponsor
The Royal Society
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/29748779
PII: 10.1140/epje/i2018-11669-8
Grant Number
UF150067
Subjects
Topical issue: Advances in Computational Methods for Soft Matter Systems
Publication Status
Published online
Coverage Spatial
France