Abstract

Based on the analysis of modern tools for creating GRID-type information systems that are part of the European EGI “standard” – UMD repository (including new versions of Globus Toolkit, ARC, dCache, etc.), the applying of GRID systems for computational chemistry is briefly discussed. The GRID system created by the authors combines two clusters with Linux CentOS 7 and is based on software from UMD-4. The relevance and effectiveness of batch processing systems (we use Torque 4.2.10) in quantum chemical calculations is increased for mass calculations of docking complexes (including for drug modeling problems), for which an improved semiempirical method with more efficient approximations was proposed, implemented in the Fortran-95 LSSDOCK software package. For such calculations, new approximation methods have been developed, including for DFT functionals, and their software implementation is carried out. Converters of calculation results by LSSDOCK into a natural for GRID XML-based format CML version 3 are developed. Using the CML format based on dCache software, a single tree of a virtual GRID filesystem distributed between heterogeneous nodes is used to store the results of LSSDOCK calculations.

Highlights

  • The GRID system created by the authors combines

  • in quantum chemical calculations is increased for mass calculations of docking complexes

  • Using the CML format based on dCache software

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Summary

Introduction

GRID-система на основе европейских стандартов EGI для крупномасштабных расчетов по оригинальному ускоренному методу квантовой химии На основе анализа современных средств создания ИС GRID-типа, входящих в ставший европейским EGI-“стандартом” репозиторий UMD (включая новые версии Globus Toolkit, ARC, dCache и др.), кратко рассмотрено применение GRID-систем для задач вычислительной химии. Актуальность и эффективность применения систем пакетной обработки (у нас используется Torque 4.2.10) в квантовохимических расчетах повышается для массовых расчетов докинг-комплексов Разработаны конверторы результатов расчетов по LSSDOCK в естественный для GRID, основанный на XML, формат CML версии 3.

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