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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 [http://physchem.ox.ac.uk/~doye/jon/ Doye] and [http://www-thphys.physics.ox.ac.uk/people/ArdLouis/ 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 [http://self-assembly.net/ 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 [http://en.wikipedia.org/wiki/DNA_nanotechnology 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 [http://lammps.sandia.gov/ LAMMPS] in the USER-CGDNA package, developed by [http://www.oliverhenrich.com/ Oliver Henrich] (with the help of Tom E. Ouldridge, F. Romano and L. Rovigatti). The package documentation can be found [https://lammps.sandia.gov/doc/Packages_details.html#pkg-user-cgdna here]. The code comes with any regular download from the central LAMMPS repository, and it is also available [https://github.com/ohenrich/cgdna here]. | |||
* [https://github.com/lorenzo-rovigatti/oxDNA/ Download] | |||
* [https://lorenzo-rovigatti.github.io/oxDNA/install.html Installation] | |||
* [[Features]] | |||
* [[DNA model introduction]] | |||
* [[RNA model introduction]] | |||
* [https://lorenzo-rovigatti.github.io/oxDNA/ Documentation] | |||
* [[Documentation|Old documentation]] | |||
* [[:Category:Examples|Examples]] | |||
* [[Tutorials]] | |||
* [[Publications]] | |||
* [[ | * [[External Resources]] | ||
* [[How To Write An Interaction]] | |||
* [[ | * [[Gallery of Journal Covers]] | ||
* [[Online talks]] | |||
* [[ | * [[Screenshots|Screenshots and movies]] | ||
* [[Gallery of studied systems]] | |||
* [[ | * [[License and Copyright]] | ||
* [[Previous version]] | |||
* [[ | * [[Contact information]] | ||
* [[oxDNA users and developers workshop 2019]] | |||
* [[oxDNA users and developers workshop 2024]] | |||
== News == | |||
* Code implementing [[DNA_model_introduction#oxDNA2|oxDNA2]], a new version of the oxDNA model, is now included in the latest release. See [https://doi.org/10.1063/1.4921957 ''J. Chem. Phys.'' '''142''', 234901 (2015)] for more information about the new model. | |||
* Follow the latest updates about oxDNA on our twitter account: [https://twitter.com/ox_dna ox_dna] | |||
* Youtube: More simulation movies can be found on the [https://www.youtube.com/channel/UCz3DCaoBsa9MvVSrVhyoU4A oxDNA] channel and video tutorials can be found on the [https://www.youtube.com/channel/UC4ClrQ8xMypSbDZG2QCehpA oxDNA tutorials] channel. | |||
* The [http://sourceforge.net/p/oxdna/discussion/ Discussion forum] for the old repository of the oxDNA code at sourceforge.net may provide answers to some common questions. | |||
* [[oxDNA users and developers workshop 2024]] Sept 2-5, 2024, Oxford. | |||
== | == 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. | |||
Latest revision as of 13:25, 25 April 2024
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.
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 oxDNA channel and video tutorials can be found on the oxDNA tutorials channel.
- The Discussion forum for the old repository of the oxDNA code at sourceforge.net may provide answers to some common questions.
- oxDNA users and developers workshop 2024 Sept 2-5, 2024, Oxford.
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.