DataSheet1_A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results.pdf

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.

脱氧核糖核酸（Deoxyribonucleic acid，DNA）的oxDNA模型已被广泛应用于生物学、生物物理学及纳米技术领域的相关系统研究中。目前该模型可通过两个独立的开源软件包获取使用。本文提供了一套文档规范完备的示范性模拟实验，既可为该模型的模拟方法提供入门指引，也可作为对模型基础特性的综述回顾。我们阐释了如何依托大长度尺度下的简化模型解读模拟结果，并反过来深化对这类模型的认知，同时为判断使用oxDNA开展系统模拟是否具备研究价值提供参考依据。