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@article{Henrich:2018:epje/i2018-11669-8,
author = {Henrich, O and Gutiérrez, Fosado YA and Curk, T and Ouldridge, TE},
doi = {epje/i2018-11669-8},
journal = {European Physical Journal E. Soft Matter},
pages = {57--57},
title = {Coarse-grained simulation of DNA using LAMMPS : an implementation of the oxDNA model and its applications},
url = {http://dx.doi.org/10.1140/epje/i2018-11669-8},
volume = {41},
year = {2018}
}

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TY  - JOUR
AB  - 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.
AU  - Henrich,O
AU  - Gutiérrez,Fosado YA
AU  - Curk,T
AU  - Ouldridge,TE
DO  - epje/i2018-11669-8
EP  - 57
PY  - 2018///
SN  - 1292-8941
SP  - 57
TI  - Coarse-grained simulation of DNA using LAMMPS : an implementation of the oxDNA model and its applications
T2  - European Physical Journal E. Soft Matter
UR  - http://dx.doi.org/10.1140/epje/i2018-11669-8
UR  - https://www.ncbi.nlm.nih.gov/pubmed/29748779
UR  - http://hdl.handle.net/10044/1/59745
VL  - 41
ER  -

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