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

Molecular metadynamics is a method of accelerated exploration of free energy surface (i.e. possible shapes - conformations) of large molecules, typically proteins, by adding artificial "bias" energy to the simulation. However, the principal advantages of metadynamics are jeopardized by the computational complexity of the bias calculation. 

We developed an approximative method which speeds up the bias calculation dramatically while not affecting the overall precision of the method.

The method was implemented in Plumed and Gromacs software, it will be included in the 2017 release of Plumed. 

In 2015–2016, the work was supported by GACR project "Enhanced Sampling Simulations for Complex Systems", proj. no. 15-17269S.

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
• PAZÚRIKOVÁ, Jana, Aleš KŘENEK, Vojtěch SPIWOK a Mária ŠIMKOVÁ. Reducing the number of mean-square deviation calculations with floating close structure in metadynamics. Journal of Chemical Physics, Melville: American Institute of Physics, 2017, roč. 146, č. 11, s. "115101:1"-"115101:8". ISSN 0021-9606. doi:10.1063/1.4978296.

This work was supported by the projects OP RI CERIT Scientific Cloud LM2015085; GACR: Enhanced Sampling Simulations for Complex Systems 15-17269S.