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MDDriver: Driving Molecular Dynamics codes by coupling with a CPU intensive visualization module.
Grasseau & Baaden 2007.

Latest News (updated 20/9/2011)

  • a paper about fast and efficient visualization appeared in Journal of Computational Chemistry (reference below)
  • new interactive molecular visualization now working with MDDriver - stay tuned
  • a paper about constructing a model of the RecA nucleofilament is now online in Nucleic Acids Research (reference below)
  • a paper about interactively locating ion binding sites has been published in Pac Symp Biocomp (see full reference below)
  • MDDriver now working with Gromacs 4.x !
  • MDDriver 0.99 ready, version 1.0 about to be released!
  • The FVNano/MDDriver team was present at GGMM’2009 with posters, demos and a talk
  • A paper about MDDriver was published in J Comp Chem and can be accessed from this website
  • Our interactive simulations approach was featured in International Science Grid, Image of the week - Molecular dynamics on DEISA: lipids, licorice and lines
  • The MDDriver team was present at VRST’2008 and VRIPHYS’08 with posters, demos and a short paper

Related Websites

Webpage clipping The MDDriver project has served as prototype for designing the FVNano application that is currently in development

Related Publications

  • M. Chavent, A. Vanel, A. Tek, B. Levy, S. Robert, B. Raffin and M. Baaden: "GPU-accelerated atom and dynamic bond visualization using HyperBalls, a unified algorithm for balls, sticks and hyperboloids", J. Comput. Chem., 2011, 32, 2924
  • A. Saladin, C. Amourda, P. Poulain, N. Férey, M. Baaden, M. Zacharias, O. Delalande and C. Prévost : "Modeling the Early Stage of DNA Sequence Recognition within RecA Nucleoprotein Filaments", NAR, 2010, online (http://nar.oxfordjournals.org/cgi/content/full/gkq459).
  • O. Delalande, N. Férey, B. Laurent, M. Guéroult, B. Hartmann and M. Baaden: "Multi-resolution and multi-physics approach for interactively locating functionally linked ion binding sites by steering small molecules into electrostatic potential maps using a haptic device", Pac. Symp. Biocomput., 2010, 205-15.
  • O. Delalande, N. Férey, G. Grasseau and M. Baaden : "Complex Molecular Assemblies at hand via Interactive Simulations", Journal of Computational Chemistry 30, 2009, 2375-2387
  • N. Férey, O. Delalande, G. Grasseau and M. Baaden : "A VR framework for interacting with molecular simulations", 2008, in Proceedings of the 2008 ACM symposium on Virtual reality software and technology, edited by E. Kruiff, pp. 91-94, ACM, Bordeaux, France.
  • N. Férey, O. Delalande, G. Grasseau and M. Baaden : "From Interactive to Immersive Molecular Dynamics", 2008, in Proceedings of the International Workshop on Virtual Reality and Physical Simulation (VRIPHYS'08), edited by F. Faure and M. Teschner, pp. 89-96, Eurographics, Grenoble, France.

You can also access my complete list of publications with links to the download locations.

Poster selection

Poster clipping Poster clipping Poster clipping

Task 1: Implementing IMD in Gromacs - completed!

Interactive Molecular Dynamics (IMD) is one particular method where a simulation is coupled with an interactive visualisation in order to drive the system towards the relevant degrees of freedom. In order to be able to carry out IMD simulations, one needs to couple the simulation code with an interactive visualisation tool like VMD.

VMD communicates with the simulation using a protocol that is called IMD, too. This protocol is implemented in a handful of simulation programs amongst which NAMD. The goal of this task is to implement the IMD protocol into Gromacs.

Task 2: Implementing other simulation engines

If you want to use your simulation software with MDDriver, please give it a try! We’ll be glad to assist you as far as time allows.

Task 3: Integrating MDDriver in FVNano

The initial MDDriver project is now continued and largely expanded in the FVNano project.

Support

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Copyright

The MDDriver logo is copyright 2007 by Marc Baaden. It is licensed under the creative commons license (see page footer for details).