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oxDNA

oxDNA is a simulation code originally developed to implement the coarse-grained DNA model introduced by T. E. Ouldridge, J. P. K. Doye and A. A. Louis. It has been since reworked and it is now an extensible simulation+analysis framework. It natively supports simulations of DNA (oxDNA and oxDNA2) and RNA (oxRNA) on both CPUs and NVIDIA GPUs.

The code implements Monte Carlo and Molecular Dynamics. The developers are L. Rovigatti, F. Romano, P. Šulc, B. Snodin, F. Randisi and T. E. Ouldridge in the Doye and Louis groups at the University of Oxford. Additionally, Molecular Dynamics simulations modeling DNA-linked nanoparticles have been implemented by J. Hendricks, T. Fochtman, and B. Walcutt in the Patitz group at the University of Arkansas.

The oxDNA and oxRNA models are intended to provide a physical representation of the thermodynamic and mechanical properties of single- and double-stranded DNA and RNA, as well as the transition between the two. At the same time, the representation of DNA and RNA is sufficiently simple to allow access to assembly processes which occur on long timescales, beyond the reach of atomistic simulations. Basic examples include duplex formation from single strands, and the folding of a self-complementary single strand into a hairpin. These are the underlying processes of the fast-growing field of DNA nanotechnology and RNA nanotechnology, as well as many biophysical uses of DNA/RNA, allowing the model to be used to understand these fascinating systems.

There also exists an implementation of the oxDNA and oxDNA2 models for LAMMPS in the USER-CGDNA package, developed by Oliver Henrich (with the help of Tom E. Ouldridge, F. Romano and L. Rovigatti). The package documentation can be found here. The code comes with any regular download from the central LAMMPS repository, and it is also available here.

• Download and Installation

• Features

• DNA model introduction

• RNA model introduction

• Documentation

• Examples

• How To Write An Interaction

• Publications

• Tutorials

• External Resources

• Gallery of Journal Covers

• Online talks

• Screenshots and movies

• Gallery of studied systems

• License and Copyright

• Previous version

• Contact information

• oxDNA users and developers workshop

News

• Code implementing oxDNA2, a new version of the oxDNA model, is now included in the latest release. See J. Chem. Phys. 142, 234901 (2015) for more information about the new model.
• Follow the latest updates about oxDNA on our twitter account: ox_dna
• Youtube: More simulation movies can be found on the oxDNAchannel] and video tutorials can be found on the oxDNA tutorials channel.
• You can post questions about the installation and usage of our code to the newly created Discussion forum for oxDNA at sourceforge.net

Acknowledgments

We thank our co-workers C. Matek, R. Harrison and W. Smith for having contributed bits of code and/or material for the examples and our webmasters Russell Jones and Greg Agacinski for maintaining the website.