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GRID System Based on European EGI Standards for Large-Scale Calculations by the Original Accelerated Method of Quantum Chemistry

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Abstract

Based on the analysis of modern tools for the creation of GRID-type information systems incorporated into the UMD repository, which has become a European EGI “standard” (including new version of Globus Toolkit, ARC, dCache, etc.), the application of GRID systems for computational chemistry problems is briefly considered. The GRID system created by the authors is a combination of two Linux CentOS 7 clusters and based on the UMD-4 software. The relevance and efficiency of the application of batch processing systems (we use Torque 4.2.10) in quantum-chemical calculations are increased in the mass calculations of docking complexes (including drug design problems) and, for these purposes, an improved semiempirical method implemented with more efficient approximations in the LSSDOCL software in Fortran-95 has been proposed. New methods of approximation, including the methods for DFT functionals, have been developed for such calculations to perform their software implementation. The convertors of LSSDOCK calculation results into the XML based CML version 3 format, which is more natural for GRID, have been developed. Based on the CML format and the dCache software tools, the universal tree of a virtual GRID file system distributed between heterogeneous nodes for the storage of LSSDOCK calculation results has been implemented.

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FUNDING

This work was financially supported by the Russian Foundation for Basic Research within scientific project no. 18-07-00657.

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Authors and Affiliations

  1. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences, 119991, Moscow, Russia

    N. A. Anikin, A. Y. Muskatin & M. B. Kuzminsky

  2. Demidov Yaroslavl State University, 150003, Yaroslavl, Russia

    A. I. Rusakov

Authors
  1. N. A. Anikin
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  2. A. Y. Muskatin
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  3. M. B. Kuzminsky
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  4. A. I. Rusakov
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Corresponding authors

Correspondence to N. A. Anikin, A. Y. Muskatin, M. B. Kuzminsky or A. I. Rusakov.

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CONFLICT OF INTEREST

The authors declare that they have no conflicts of interest.

ADDITIONAL INFORMATION

Nikolay A. Anikin, orcid.org/0000-0002-5724-8969, PhD.

Alexander Y. Muskatin, orcid.org/0000-0002-3596-2782, PhD.

Mikhail B. Kuzminsky, orcid.org/0000-0002-3944-8203, PhD.

Alexandr I. Rusakov, orcid.org/0000-0001-8893-4577, PhD.

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Translated by E. Glushachenkova

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Anikin, N.A., Muskatin, A.Y., Kuzminsky, M.B. et al. GRID System Based on European EGI Standards for Large-Scale Calculations by the Original Accelerated Method of Quantum Chemistry. Aut. Control Comp. Sci. 54, 652–654 (2020). https://doi.org/10.3103/S0146411620070020

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  • DOI: https://doi.org/10.3103/S0146411620070020

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