Coarse-Grained Simulation of DNA using LAMMPS

TL;DR

This paper introduces a LAMMPS implementation of the oxDNA coarse-grained DNA model, enabling large-scale simulations and practical applications, especially for single-stranded DNA, with improved performance and accessibility.

Contribution

It presents the first integration of oxDNA into LAMMPS, enhancing usability, performance, and extending research capabilities in DNA modeling.

Findings

Improved parallel performance of oxDNA in LAMMPS

Facilitates large-scale DNA simulations

Enables new research on single-stranded DNA

Abstract

During the last decade coarse-grained nucleotide models have emerged that allow us to 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.