Adun is a free biomolecular simulator developed at the Computational Biophysics and Biochemistry Laboratory, a part of the Research Unit on Biomedical Informatics of the UPF. It is distributed under the GNU General Public License.

See the Objectives page for an overview of what we aim to achieve with Adun and Features for what it can currently do.

Once you have installed the program a good place to start is the Quick-Start Guide. If you have any questions send us a mail at adun-users@gna.org or adun-dev@gna.org.

You can follow Adun developments through our news feed and commits feed. The Adun project page, giving access to our cvs repository, bug trackers etc., is hosted by Gna.org.

A detailed description of the Adun Framework can be found at

  • [2005,article] bibtex Go to document
    M. A. Johnston, I. F. Galván, and J. Villà-Freixa, "Framework-based design of a new all-purpose molecular simulation application: the Adun simulator.," J Comput Chem, vol. 26, iss. 15, pp. 1647-1659, 2005.
      author = {Michael A Johnston and Ignacio Fdez Galv\'an and Jordi Vill\`a-Freixa},
      title = {Framework-based design of a new all-purpose molecular simulation application: the Adun simulator.},
      journal = {J Comput Chem},
      year = {2005},
      volume = {26},
      pages = {1647--1659},
      number = {15},
      month = {Nov},
      abstract = {Here we present Adun, a new molecular simulator that represents a paradigm shift in the way scientific programs are developed. The traditional algorithm centric methods of scientific programming can lead to major maintainability and productivity problems when developing large complex programs. These problems have long been recognized by computer scientists; however, the ideas and techniques developed to deal with them have not achieved widespread adoption in the scientific community. Adun is the result of the application of these ideas, including pervasive polymorphism, evolutionary frameworks, and refactoring, to the molecular simulation domain. The simulator itself is underpinned by the Adun Framework, which separates the structure of the program from any underlying algorithms, thus giving a completely reusable design. The aims are twofold. The first is to provide a platform for rapid development and implementation of different simulation types and algorithms. The second is to decrease the learning barrier for new developers by providing a rigorous and well-defined structure. We present some examples on the use of Adun by performing simple free-energy simulations for the adiabatic charging of a single ion, using both free-energy perturbation and the Bennett's method. We also illustrate the power of the design by detailing the ease with which ASEP/MD, an elaborated mean field QM/MM method originally written in FORTRAN 90, was implemented into Adun.},
      doi = {10.1002/jcc.20312},
      institution = {Computational Biochemistry and Biophysics Laboratory, Research Group on Biomedical Informatics (GRIB), Institut Municipal d'Investigaci Mdica and Universitat Pompeu Fabra, C/Doctor Aiguader, 80 08003 Barcelona, Catalunya, Spain.},
      keywords = {Algorithms; Computer Simulation; Equipment Design; Models, Chemical; Software},
      owner = {jordivilla},
      pmid = {16175583},
      timestamp = {2010.03.14},
      url = {http://dx.doi.org/10.1002/jcc.20312}
  • [2007,article] bibtex Go to document
    M. A. Johnston and J. Villà-Freixa, "Enabling Data Sharing and Collaboration in Complex Systems Applications," LNBI, vol. 4360, pp. 124-140, 2007.
      author = {Johnston, M.A. and Vill\`a-Freixa, J.},
      title = {{Enabling Data Sharing and Collaboration in Complex Systems Applications}},
      journal = LNBI, year = {2007},
      volume = {4360},
      pages = {124--140},
      timestamp = {2008.12.02},
      url = {http://www.springerlink.com/content/9476700461j37732}
  • [2009,phdthesis] bibtex Go to document
    M. A. Johnston, "Development of a Molecular Simulator and its Application to Conformational Changes in Biomolecules," PhD Thesis , 2009.
      author = {Johnston, M. A.},
      title = {{Development of a Molecular Simulator and its Application to Conformational Changes in Biomolecules}},
      school = {Universitat Pompeu Fabra},
      year = {2009},
      abstract = {This thesis deals with the creation of a new open-source program and API for biomolecular simulation and its subsequent application to biological problems. The program, Adun, focuses on the key areas of biological free-energy calculations, rapid development and high-performance productivity. Methods such as SCAAS, EVB and switched Generalised-Born have been implemented to realise the first aim. The presence of these techniques, along with a multitude of others, verifies Adun's rapid development potential. All these features are united by an advanced graphical user interface which provides novel capabibilities such as inbuilt data management, and distributed datasharing and computation. Adun's ability to tackle biological problems is illustrated with an investigation of Ras dynamics and the development, implementation and testing of a novel method for determining transition paths. In addition to concretely demonstrating Adun's potential these studies also provide insight into the use of dynamic information in elucidating protein function. The current state of the program and the results of the two studies is discussed and indications of future aims and directions given. In addition personal thoughts on the role of computational biologists as developers of applications, for themselves and the wider scientific community, are provided},
      url = {http://www.tesisenxarxa.net/TDX-1015109-103730/}

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