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

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.