Coarse-grained simulations of DNA and RNA systems with oxDNA and oxRNA models: Introductory tutorial

TL;DR

This tutorial introduces new users to the oxDNA coarse-grained model for simulating DNA and RNA systems, providing basic setup guidance and resources for further exploration in nanotechnology and biological research.

Contribution

It offers an accessible, step-by-step introduction to using the oxDNA model, filling a gap for beginners without prior experience.

Findings

Provides foundational setup examples for oxDNA

Guides new users to additional resources and reading

Facilitates entry into nucleic acid simulation studies

Abstract

We present a tutorial on setting-up the oxDNA coarse-grained model for simulations of DNA and RNA nanotechnology. The model is a popular tool used both by theorists and experimentalists to simulate nucleic acid systems both in biology and nanotechnology settings. The tutorial is aimed at new users asking "Where should I start if I want to use oxDNA". We assume no prior background in using the model. This tutorial shows basic examples that can get a novice user started with the model, and points the prospective user towards additional reading and online resources depending on which aspect of the model they are interested in pursuing.