High performance computing with coarse grained model of biological macromolecules

Emilia Lubecka , Adam Sieradzan , Cezary Czaplewski , Paweł Krupa , Józef Adam Liwo

Abstract

The Unified Coarse Grained Model of biological acromolecules (UCGM) that is being developed in our laboratory is a model designed to carry out large-scale simulations of biological macromolecules. The simplified chain representation used in the model allows to obtain 3-4 orders of magnitude extention of the time-scale of simulations, compared to that of all-atom simulations. Unlike most of the other coarse-grained force fields, UCGM is a physics-based force field, independent of structural databases and applicable to treat non-standard systems. In this communication, the efficiency and scalability of the new version of UCGM package with Fortran 90, with two parallelization levels: coarse-grained and fine-grained, is reported for systems with various size and oligomeric state. The performance was tested in the canonical- and replica exchange MD mode, with small- and moderate-size proteins and protein complexes (20 to 1,636 amino-acid residues), as well as with large systems such as, e.g., human proteosome 20S with size over 6,200 aminoacid residues, which show the advantage of using coarse-graining. It is demonstrated that, with using massively parallel architectures, and owing to the physics-based nature of UCGM, real-time simulations of the behavior of subcellular systems are feasible.
Author Emilia Lubecka (FMPI / II)
Emilia Lubecka,,
- Institute of Informatics
, Adam Sieradzan (FCh / DTCh / LMM)
Adam Sieradzan,,
- Laboratory of Molecular Modeling
, Cezary Czaplewski (FCh / DTCh / LSP)
Cezary Czaplewski,,
- Laboratory of Simulation of Polymers
, Paweł Krupa
Paweł Krupa,,
-
, Józef Adam Liwo (FCh / DTCh / LMM)
Józef Adam Liwo,,
- Laboratory of Molecular Modeling
Journal seriesSupercomputing Frontiers and Innovations, ISSN 2409-6008, e-ISSN 2313-8734, (0 pkt)
Issue year2018
Vol5
No2
Pages63-75
Publication size in sheets0.6
Keywords in EnglishUnified Coarse Grained Model, UNRES force field, molecular dynamics simulations, fine-grained parallelization, coarse-grained parallelization
DOIDOI:10.14529/jsfi180206
URL http://superfri.org/superfri/article/download/171/266
Languageen angielski
LicenseJournal (articles only); published final; Uznanie Autorstwa - Użycie Niekomercyjne (CC-BY-NC); with publication
Score (nominal)5
ScoreMinisterial score = 0.0, 24-09-2018, ArticleFromJournal
Ministerial score (2013-2016) = 5.0, 24-09-2018, ArticleFromJournal - czasopismo zagraniczne spoza list
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