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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]
Copyright of Journal of Computational Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
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DbLabel: Engineering Source
An: 161180334
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PubType: Academic Journal
PubTypeId: academicJournal
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  Data: Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins.
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  Data: <searchLink fieldCode="AR" term="%22Sieradzan%2C+Adam+K%2E%22">Sieradzan, Adam K.</searchLink><relatesTo>1,2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Sans‐Duñó%2C+Jordi%22">Sans‐Duñó, Jordi</searchLink><relatesTo>3</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Lubecka%2C+Emilia+A%2E%22">Lubecka, Emilia A.</searchLink><relatesTo>4</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Czaplewski%2C+Cezary%22">Czaplewski, Cezary</searchLink><relatesTo>1,2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Lipska%2C+Agnieszka+G%2E%22">Lipska, Agnieszka G.</searchLink><relatesTo>1,2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Leszczyński%2C+Henryk%22">Leszczyński, Henryk</searchLink><relatesTo>5</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Ocetkiewicz%2C+Krzysztof+M%2E%22">Ocetkiewicz, Krzysztof M.</searchLink><relatesTo>2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Proficz%2C+Jerzy%22">Proficz, Jerzy</searchLink><relatesTo>2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Czarnul%2C+Paweł%22">Czarnul, Paweł</searchLink><relatesTo>4</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Krawczyk%2C+Henryk%22">Krawczyk, Henryk</searchLink><relatesTo>2,4</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Liwo%2C+Adam%22">Liwo, Adam</searchLink><relatesTo>1,2</relatesTo> (AUTHOR)<i> adam@chem.univ.gda.pl</i>
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  Data: <searchLink fieldCode="JN" term="%22Journal+of+Computational+Chemistry%22">Journal of Computational Chemistry</searchLink>. 2/5/2023, Vol. 44 Issue 4, p602-625. 24p.
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  Data: 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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  Data: <i>Copyright of Journal of Computational Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1002/jcc.27026
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        Text: English
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      – SubjectFull: Dihedral angles
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      – SubjectFull: Proteins
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      – TitleFull: Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins.
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              Text: 2/5/2023
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              Y: 2023
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