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

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Title: Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins.
Authors: Sieradzan, Adam K.1,2 (AUTHOR), Sans‐Duñó, Jordi3 (AUTHOR), Lubecka, Emilia A.4 (AUTHOR), Czaplewski, Cezary1,2 (AUTHOR), Lipska, Agnieszka G.1,2 (AUTHOR), Leszczyński, Henryk5 (AUTHOR), Ocetkiewicz, Krzysztof M.2 (AUTHOR), Proficz, Jerzy2 (AUTHOR), Czarnul, Paweł4 (AUTHOR), Krawczyk, Henryk2,4 (AUTHOR), Liwo, Adam1,2 (AUTHOR) adam@chem.univ.gda.pl
Source: Journal of Computational Chemistry. 2/5/2023, Vol. 44 Issue 4, p602-625. 24p.
Subjects: Molecular dynamics, Dihedral angles, Proteins
Abstract: 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. [ABSTRACT FROM AUTHOR]
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Database: Engineering Source
Description
Abstract: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. [ABSTRACT FROM AUTHOR]
ISSN:01928651
DOI:10.1002/jcc.27026