Suchergebnisse

Zeitschriftenartikel (13)

  1. 1.
    Zeitschriftenartikel
    Kutzner, C.; Páll, S.; Fechner, M.; Esztermann, A.; de Groot, B. L.; Grubmüller, H.: More bang for your buck: Improved use of GPU nodes for GROMACS 2018. Journal of Computational Chemistry 40 (27), S. 2418 - 2431 (2019)
  2. 2.
    Zeitschriftenartikel
    Igaev, M.; Kutzner, C.; Bock, L. V.; Vaiana, A. C.; Grubmüller, H.: Automated cryo-EM structure refinement using correlation-driven molecular dynamics. eLife 8 (2019)
  3. 3.
    Zeitschriftenartikel
    Briones, R.; Blau, C.; Kutzner, C.; de Groot, B. L.; Aponte-Santamaría, C.: GROmaρs: A GROMACS-based toolset to analyze density maps derived from molecular dynamics simulations. Biophysical Journal 116 (1), S. 4 - 11 (2019)
  4. 4.
    Zeitschriftenartikel
    Kutzner, C.; Köpfer, D.; Machtens, J. P.; de Groot, B. L.; Song, C.; Zachariae, U.: Insights into the function of ion channels by computational electrophysiology simulations. Biochimica et Biophysica Acta - Biomembranes 1858 (7, B), S. 1741 - 1752 (2016)
  5. 5.
    Zeitschriftenartikel
    Kutzner, C.; Páll, S.; Fechner, M.; Esztermann, A.; de Groot, B.; Grubmüller, H.: Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. Journal of Computational Chemistry 36 (26), S. 1990 - 2008 (2015)
  6. 6.
    Zeitschriftenartikel
    Kutzner, C.; Páll, S.; Fechner, M.; Esztermann, A.; De Groot, B.; Grubmueller, H.: Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. arXiv (2015)
  7. 7.
    Zeitschriftenartikel
    Michielssens, S.; van Erp, T. S.; Kutzner, C.; Ceulemans, A.; de Groot, B. L.: Molecular dynamics in principal component space. Journal of Physical Chemistry B 116 (29), S. 8350 - 8357 (2012)
  8. 8.
    Zeitschriftenartikel
    Kutzner, C.; Grubmüller, H.; de Groot, B. L.; Zachariae, U.: Computational Electrophysiology: The molecular dynamics of ion channel Permeation and selectivity in atomistic detail. Biophysical Journal 101 (4), S. 809 - 817 (2011)
  9. 9.
    Zeitschriftenartikel
    Kutzner, C.; Czub, J.; Grubmüller, H.: Keep it flexible: Driving macromolecular rotary motions in atomistic simulations with GROMACS. Journal of Chemical Theory and Computation 7 (5), S. 1381 - 1393 (2011)
  10. 10.
    Zeitschriftenartikel
    Risselada, H. J.; Kutzner, C.; Grubmüller, H.: Caught in the act: Visualization of SNARE-mediated fusion events in molecular detail. Chembiochem 12 (7), S. 1049 - 1055 (2011)
  11. 11.
    Zeitschriftenartikel
    Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E.: GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation 4 (3), S. 435 - 447 (2008)
  12. 12.
    Zeitschriftenartikel
    Sieber, J. J.; Willig, K. I.; Kutzner, C.; Gerding-Reimers, C.; Harke, B.; Donnert, G.; Rammner, B.; Eggeling, C.; Hell, S. W.; Grubmüller, H. et al.; Lang, T.: Anatomy and dynamics of a supramolecular membrane protein cluster. Science 317 (5841), S. 1072 - 1076 (2007)
  13. 13.
    Zeitschriftenartikel
    Kutzner, C.; van der Spoel, D.; Fechner, M.; Lindahl, E.; Schmitt, U. W.; de Groot, B. L.; Grubmueller, H.: Speeding up parallel GROMACS on high-latency networks. Journal of Computational Chemistry 28 (12), S. 2075 - 2084 (2007)

Buchkapitel (3)

  1. 14.
    Buchkapitel
    Páll, S.; Abraham, M. J.; Kutzner, C.; Hess, B.; Lindahl, E.: Tackling exascale software challenges in molecular dynamics simulations with GROMACS. In: Solving Software Challenges for Exascale: International Conference on Exascale Applications and Software, EASC 2014, Stockholm, Sweden, April 2-3, 2014, Revised Selected Papers, S. 3 - 27 (Hg. Markidis, S.; Laure, E.). Springer, Cham (2015)
  2. 15.
    Buchkapitel
    Kutzner, C.; Apostolov, R.; Hess, B.; Grubmüller, H.: Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC. In: Parallel Computing: Accelerating Computational Science and Engineering (CSE), S. 722 - 730 (Hg. Bader, M.; Bode, A.; Bungartz, H. J.). IOS Press, Amsterdam (2014)
  3. 16.
    Buchkapitel
    Kutzner, C.; van der Spoel, D.; Fechner, M.; Lindahl, E.; Schmitt, U. W.; de Groot, B. L.; Grubmueller, H.: Improved GROMACS scaling on ethernet switched clusters. In: Recent advances in parallel virtual machine and message passing interface. 13th European PVM/MPI User`s Group meeting, Bonn, Germany, September 17-20, 2006, S. 404 - 405 (Hg. Mohr, B.; Larsson, T. J.; Worringen, J.; Dongarra, J.). Springer, Berlin (2006)

Konferenzbeitrag (10)

  1. 17.
    Konferenzbeitrag
    Igaev, M.; Kutzner, C.; Bock, L. V.; Vaiana, A. C.; Grubmüller, H.: Automated cryo-EM structure refinement using correlation -driven molecular dynamics. Joint 12th EBSA European Biophysics Congress / 10th IUPAP International Conference on Biological Physics (ICBP), Madrid, Spain, 20. Juli 2019 - 24. Juli 2019. European Biophysics Journal 48 (Suppl 1), S. S126 - S126 (2019)
  2. 18.
    Konferenzbeitrag
    Briones, R.; Blau, C.; Kutzner, C.; de Groot, B. L.; Aponte-Santamaria, C.: Gromaps: A Gromacs-based toolset to analyse density maps derived from molecular dynamics simulations. 63rd Annual Meeting of the Biophysical-Society, Baltimore, MD, 02. März 2019 - 06. März 2019. Biophysical Journal (2019)
  3. 19.
    Konferenzbeitrag
    Vaiana, A. C.; Igaev, M.; Kutzner, C.; Grubmüller, H.: Fully automated correlation-based refinement of atomic models into high resolution cryo-EM density maps. 62nd Annual Meeting of the Biophysical-Society, San Francisco, CA, 17. Februar 2018 - 21. Februar 2018. Biophysical Journal 114 (3), S. 161a - 161a (2018)
  4. 20.
    Konferenzbeitrag
    Kohnke, B.; Ullmann, R. T.; Kutzner, C.; Beckmann, A.; Haensel, D.; Kabadshow, I.; Dachsel, H.; Hess, B.; Grubmüller, H.: A flexible, GPU - powered fast multipole method for realistic biomolecular simulations in Gromacs. 58th Annual Meeting of the Biophysical-Society, San Francisco, CA, 15. Februar 2014 - 19. Februar 2014. Biophysical Journal (2017)
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