Coarse-grained simulation of DNA using LAMMPS: an implementation of the oxDNA model and its applications

Oliver Henrich, Yair Augusto Gutiérrez Fosado, Tine Curk, Thomas E. Ouldridge

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.
LanguageEnglish
Article number57
Number of pages16
JournalEuropean Physical Journal E
Volume41
Issue number5
Early online date10 May 2018
DOIs
Publication statusE-pub ahead of print - 10 May 2018

Fingerprint

DNA
deoxyribonucleic acid
Single-Stranded DNA
simulation
Molecular Dynamics Simulation
nucleotides
Molecular dynamics
Structural properties
Nucleotides
RNA
Software
entry
molecular dynamics
computer programs
Research

Keywords

  • oxDNA
  • LAMMPS
  • molecular code

Cite this

Henrich, Oliver ; Gutiérrez Fosado, Yair Augusto ; Curk, Tine ; Ouldridge, Thomas E. . / Coarse-grained simulation of DNA using LAMMPS : an implementation of the oxDNA model and its applications. In: European Physical Journal E . 2018 ; Vol. 41, No. 5.
@article{645ca9a8435943ebb1bce8fde20ef69c,
title = "Coarse-grained simulation of DNA using LAMMPS: an implementation of the oxDNA model and its applications",
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.",
keywords = "oxDNA, LAMMPS, molecular code",
author = "Oliver Henrich and {Guti{\'e}rrez Fosado}, {Yair Augusto} and Tine Curk and Ouldridge, {Thomas E.}",
year = "2018",
month = "5",
day = "10",
doi = "10.1140/epje/i2018-11669-8",
language = "English",
volume = "41",
journal = "European Physical Journal E - Soft Matter",
issn = "1292-8941",
number = "5",

}

Coarse-grained simulation of DNA using LAMMPS : an implementation of the oxDNA model and its applications. / Henrich, Oliver; Gutiérrez Fosado, Yair Augusto; Curk, Tine; Ouldridge, Thomas E. .

In: European Physical Journal E , Vol. 41, No. 5, 57, 10.05.2018.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Coarse-grained simulation of DNA using LAMMPS

T2 - European Physical Journal E - Soft Matter

AU - Henrich, Oliver

AU - Gutiérrez Fosado, Yair Augusto

AU - Curk, Tine

AU - Ouldridge, Thomas E.

PY - 2018/5/10

Y1 - 2018/5/10

N2 - 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.

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.

KW - oxDNA

KW - LAMMPS

KW - molecular code

UR - https://arxiv.org/pdf/1802.07145

UR - https://link.springer.com/journal/volumesAndIssues/10189

U2 - 10.1140/epje/i2018-11669-8

DO - 10.1140/epje/i2018-11669-8

M3 - Article

VL - 41

JO - European Physical Journal E - Soft Matter

JF - European Physical Journal E - Soft Matter

SN - 1292-8941

IS - 5

M1 - 57

ER -