Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins - Publikacja - MOST Wiedzy

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Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins

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We report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms to minimize the number of operations and to improve numerical stability, (iv) using OpenMP to parallelize those sections of the code for which distributed-memory parallelization involves unfavorable computing/communication time ratio, and (v) careful memory management to minimize simultaneous access of distant memory sections. The new code enables us to run molecular dynamics simulations of protein systems with size exceeding 100,000 amino-acid residues, reaching over 1 ns/day (1 μs/day in all-atom timescale) with 24 cores for proteins of this size. Parallel performance of the code and comparison of its performance with that of AMBER, GROMACS and MARTINI 3 is presented.

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Informacje szczegółowe

Kategoria:
Publikacja w czasopiśmie
Typ:
artykuły w czasopismach
Opublikowano w:
JOURNAL OF COMPUTATIONAL CHEMISTRY nr 44, strony 602 - 625,
ISSN: 0192-8651
Język:
angielski
Rok wydania:
2023
Opis bibliograficzny:
Sieradzan A., Sans‐duñó J., Lubecka E., Czaplewski C., Lipska A., Leszczyński H., Ocetkiewicz K., Proficz J., Czarnul P., Krawczyk H., Liwo A.: Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins// JOURNAL OF COMPUTATIONAL CHEMISTRY -Vol. 44,iss. 4 (2023), s.602-625
DOI:
Cyfrowy identyfikator dokumentu elektronicznego (otwiera się w nowej karcie) 10.1002/jcc.27026
Źródła finansowania:
  • COST_FREE
Weryfikacja:
Politechnika Gdańska

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