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

Krzysztof M Ocetkiewicz; Cezary Czaplewski; Henryk Krawczyk; Agnieszka G Lipska; Adam Liwo; Jerzy Proficz; Adam K Sieradzan; Paweł Czarnul

doi:10.1093/bioinformatics/btad391

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

Bioinformatics. 2023 Jun 1;39(6):btad391. doi: 10.1093/bioinformatics/btad391.

Authors

Krzysztof M Ocetkiewicz¹, Cezary Czaplewski^{1

2}, Henryk Krawczyk^{1

3}, Agnieszka G Lipska¹, Adam Liwo^{1

2}, Jerzy Proficz¹, Adam K Sieradzan^{1

2}, Paweł Czarnul³

Affiliations

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

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Physics
Protein Conformation
Proteins* / chemistry
Software*

Substances

Proteins