materialscloud:2019.0021/v2
Published June 17, 2019 | Version v2
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Reducing the Number of Mean-Square Deviation Calculations with Floating Close Structure in Metadynamics

Creators

  • 1. Institute of Computer Science, Masaryk University, Brno, Czech Republic
  • 2. Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague

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Description

Biomolecular simulations are computationally expensive. This limits their application in protein folding simulations, protein engineering, drug design and related fields. Enhanced sampling techniques such as metadynamics accelerates slow events in molecular simulation. This and other method apply artificial forces in directions of collective degrees of freedom (aka collective variables). Path collective variables and Property Map collective variables are defined using a series of reference structures of the studied molecular system. They require a huge number of mean square deviation calculations along the simulation. Close Structure algorithm reduces the number of these operations.

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References

Journal reference (Paper in which the Close Structure method for fast calculation of RMSD in Path and Property Map CVs is described)
J. Hozzova (nee Pazurikova), A. Krenek, V. Spiwok, M. Simkova, J. Chem. Phys. 146, 115101 (2017), doi: 10.1063/1.4978296

Preprint (Paper in which the Close Structure method for fast calculation of RMSD in Path and Property Map CVs is thoroughly tested)
J. Hozzova (nee Pazurikova), J. Olha, A. Krenek, V. Spiwok, arXiv:1801.02362