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

Henrich, Oliver and Gutiérrez Fosado, Yair Augusto and Curk, Tine and Ouldridge, Thomas E. (2018) Coarse-grained simulation of DNA using LAMMPS : an implementation of the oxDNA model and its applications. European Physical Journal E, 41 (5). 57. ISSN 1292-8941

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    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.