A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results

TL;DR

This paper introduces the oxDNA DNA model, providing guidance on when and how to simulate it, interpret results, and connect findings to larger-scale models, aiding researchers in biological, biophysical, and nanotechnological applications.

Contribution

It offers a comprehensive introduction, detailed exemplars, and interpretative guidance for using the oxDNA model effectively in various scientific contexts.

Findings

Provides clearly-documented exemplar simulations

Reviews fundamental properties of the oxDNA model

Guides interpretation of simulation results in broader models

Abstract

The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly-documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of -- and feed into our understanding of -- less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.