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.
Keywords: biophysics; coarse-grained modelling; deoxyribonucleic acid; molecular simulation (molecular modeling); nanotechnology.
Copyright © 2021 Sengar, Ouldridge, Henrich, Rovigatti and Šulc.