AUTHOR=Sengar A. , Ouldridge T. E. , Henrich O. , Rovigatti L. , Šulc P. 

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

JOURNAL=Frontiers in Molecular Biosciences

VOLUME=Volume 8 - 2021

YEAR=2021

URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2021.693710

DOI=10.3389/fmolb.2021.693710

ISSN=2296-889X

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.