UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales-Reference-Cited by-同舟云学术

UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales

Published:2023-06-01 Issue:6 Volume:39 Page:
ISSN:1367-4811
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Ocetkiewicz Krzysztof M¹^ORCID,Czaplewski Cezary¹²^ORCID,Krawczyk Henryk¹³^ORCID,Lipska Agnieszka G¹^ORCID,Liwo Adam¹²^ORCID,Proficz Jerzy¹^ORCID,Sieradzan Adam K¹²^ORCID,Czarnul Paweł³^ORCID

Affiliation:

1. Centre of Informatics Tricity Academic Supercomputer and Network (CI TASK), Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk , Gdańsk 80-233, Poland

2. Faculty of Chemistry, University of Gdańsk, Fahrenheit Union of Universities in Gdańsk , Gdańsk 80-309, Poland

3. Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Fahrenheit Union of Universities in Gdańsk , Gdańsk 80-233, Poland

Abstract

Abstract Summary The UNited RESisdue (UNRES) package for coarse-grained simulations, which has recently been optimized to treat large protein systems, has been implemented on Graphical Processor Units (GPUs). An over 100-time speed-up of the GPU code (run on an NVIDIA A100) with respect to the sequential code and an 8.5 speed-up with respect to the parallel Open Multi-Processing (OpenMP) code (run on 32 cores of 2 AMD EPYC 7313 Central Processor Units (CPUs)) has been achieved for large proteins (with size over 10 000 residues). Due to the averaging over the fine-grain degrees of freedom, 1 time unit of UNRES simulations is equivalent to about 1000 time units of laboratory time; therefore, millisecond time scale of large protein systems can be reached with the UNRES-GPU code. Availability and implementation The source code of UNRES-GPU along with the benchmarks used for tests is available at https://projects.task.gda.pl/eurohpcpl-public/unres.

Funder

National Science Centre

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad391/50657951/btad391.pdf

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