UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 06 2023
01 06 2023
Historique:
received:
03
04
2023
revised:
05
06
2023
accepted:
19
06
2023
medline:
30
6
2023
pubmed:
20
6
2023
entrez:
20
6
2023
Statut:
ppublish
Résumé
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. The source code of UNRES-GPU along with the benchmarks used for tests is available at https://projects.task.gda.pl/eurohpcpl-public/unres.
Identifiants
pubmed: 37338530
pii: 7203798
doi: 10.1093/bioinformatics/btad391
pmc: PMC10307937
pii:
doi:
Substances chimiques
Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© The Author(s) 2023. Published by Oxford University Press.
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