oxDNA: coarse-grained simulations of nucleic acids made simple

The fields of DNA and RNA nanotechnology have progressed from pioneering, proof-of-principle experiments to fully-fledged applications in material science, biology and medicine. These applications exploit the intrinsic programmability of nucleic acids to generate nano- and even micro-scale structures with tailored properties. However, the design of the DNA/RNA sequences that self-assemble into a desired structure is not straightforward and often relies on expensive trial-and-error experimental protocols. A complementary approach is provided by computer simulations, which can model biomacromolecules at different levels of detail, ranging from atomistic to continuous, and can be leveraged to investigate the whole range of time- and length-scales relevant for applications. Here we present oxDNA, a software package that has been designed to efficiently run coarse-grained simulations of DNA and RNA and also features an analysis suite aimed at post-processing the analysis of oxDNA/oxRNA trajectories.