License and Copyright

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oxDNA is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. You can also find it on the GNU web site:

http://www.gnu.org/copyleft/gpl.html

A copy of the GNU General Public License version 3 can be found in the source tarball.

Referencing

We kindly ask you to reference oxDNA and its authors in any publication for which oxDNA was used. Since you are not legally required to do so, it is up to your common sense to decide whether you want to comply with this request or not.

You can cite us in this way:

  • P. Šulc, F. Romano, T. E. Ouldridge, L. Rovigatti, J. P. K. Doye, A. A. Louis, J. Chem. Phys. 137, 135101 (2012)

or, if you use BibTeX,

@Article{oxDNA,
  author = {Petr \v{S}ulc and Flavio Romano and Thomas E. Ouldridge and Lorenzo Rovigatti and Jonathan P. K. Doye and Ard A. Louis},
  title = {Sequence-dependent thermodynamics of a coarse-grained DNA model},
  publisher = {AIP},
  year = {2012},
  journal = {The Journal of Chemical Physics},
  volume = {137},
  number = {13},
  eid = {135101},
  numpages = {14},
  pages = {135101},
  keywords = {biology computing; DNA; melting point; molecular biophysics; molecular configurations; thermodynamics},
  url = {http://link.aip.org/link/?JCP/137/135101/1},
  doi = {10.1063/1.4754132}
}

If you use the CUDA backend, please cite at least

  • L. Rovigatti, P. Šulc, I. Z. Reguly,Flavio Romano, J. Comput. Chem. 36, 1 (2015)
@article {oxDNA_edge,
author = {Rovigatti, Lorenzo and Šulc, Petr and Reguly, István Z. and Romano, Flavio},
title = {A comparison between parallelization approaches in molecular dynamics simulations on GPUs},
journal = {Journal of Computational Chemistry},
volume = {36},
number = {1},
issn = {1096-987X},
url = {http://dx.doi.org/10.1002/jcc.23763},
doi = {10.1002/jcc.23763},
pages = {1--8},
keywords = {graphics processing unit, parallelization, molecular dynamics, soft matter},
year = {2015},
}


and, if you use the oxRNA model as well, please also cite

  • P. Šulc, F. Romano, T. E. Ouldridge, J. P. K. Doye, A. A. Louis: A nucleotide-level coarse-grained model of RNA, J. Chem. Phys. 140, 235102 (2014)
@Article{oxRNA,
   author = "\v{S}ulc, Petr and Romano, Flavio and Ouldridge, Thomas E. and Doye, Jonathan P. K. and Louis, Ard A.",
   title = "A nucleotide-level coarse-grained model of RNA",
   journal = "The Journal of Chemical Physics",
   year = "2014",
   volume = "140",
   number = "23", 
   eid = 235102,
}