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.


  • 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

You are running an old browser version which is not fully supported information system anymore. Some applications might not display correctly, some functions might not work as expected or might not work at all.