High Performance Computing with Coarse Grained Model of Biological Macromolecules

Emilia Agnieszka Lubecka; Adam Kazimierz Sieradzan; Cezary Czaplewski; Paweł Krupa; Adam Liwo

doi:10.14529/jsfi180206

Authors

Emilia Agnieszka Lubecka Institute of Informatics Faculty of Mathematics, Physic and Informatics University of Gdansk, Poland
Adam Kazimierz Sieradzan Faculty of Chemistry University of Gdansk, Poland
Cezary Czaplewski Faculty of Chemistry University of Gdansk, Poland
Paweł Krupa Institute of Physics Polish Academy of Sciences, Warsaw, Poland
Adam Liwo Faculty of Chemistry University of Gdansk, Poland

DOI:

https://doi.org/10.14529/jsfi180206

Abstract

The Unified Coarse Grained Model of biological macromolecules (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.

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