A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results

The oxDNA model of Deoxyribonucleic acid 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.

Automated summary

The oxDNA model is widely used in various fields and can be accessed through two open source packages. This article presents a set of example simulations with clear documentation, introducing how to simulate the model and reviewing its fundamental properties. It also outlines how simulation results can be interpreted and provides guidance on whether using oxDNA for simulating a system is worthwhile.