Eur. Phys. J. E (2018) 41: 57
https://doi.org/10.1140/epje/i2018-11669-8

Regular Article

Coarse-grained simulation of DNA using LAMMPS

An implementation of the oxDNA model and its applications

¹ Department of Physics, SUPA, University of Strathclyde, G4 0NG, Glasgow, Scotland, UK
² School of Physics and Astronomy, University of Edinburgh, EH9 3FD, Edinburgh, Scotland, UK
³ CAS Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190, Beijing, China
⁴ Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
⁵ Department of Bioengineering, Imperial College London, SW7 2AZ, London, UK
⁶ Centre of Synthetic Biology, Imperial College London, SW7 2AZ, London, UK

^* e-mail: oliver.henrich@strath.ac.uk

Received: 20 February 2018
Accepted: 19 April 2018
Published online: 10 May 2018

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.