Speedup of molecular metadynamics

Department of Biochemistry and Microbiology, Institute of Chemical Technology, Prague

Modified Plumed + Gromacs implementation was deeply analyzed and due to rewriting critical code sections significant speedup was achieved. Opportunities for parallel processing are also opened. The achieved results were submitted as a journal paper.

Results

  • Spiwok V, Oborský P, Pazúriková J, Křenek A, Králová B. Nonlinear vs. linear biasing in Trp-cage folding simulations. Journal of the chemical society. Faraday transactions II, Journal of chemical physics, London: Chemical society, 2015
  • Filipovič J, Pazúriková J, Křenek A, Spiwok V. Accelerated RMSD Calculation for Molecular Metadynamics. In José Évora-Gómez and José Juan Hernandéz-Cabrera. Proceedings of the 2016 European Simulation and Modelling Conference. Ghent, Belgie: EUROSIS - ETI, 2016

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