GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

GENESIS (Generalized‐Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all‐atom force‐field models...

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Veröffentlicht in:Wiley interdisciplinary reviews. Computational molecular science Jg. 5; H. 4; S. 310 - 323
Hauptverfasser: Jung, Jaewoon, Mori, Takaharu, Kobayashi, Chigusa, Matsunaga, Yasuhiro, Yoda, Takao, Feig, Michael, Sugita, Yuji
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Hoboken, USA Wiley Periodicals, Inc 01.07.2015
Wiley Subscription Services, Inc
Schlagworte:
Algorithms
Atomic structure
Biophysics
Communication
Computer applications
Computer memory
Computer programs
Computer simulation
Computer software
Concurrent processing
Decomposition
Dynamics
Fast Fourier transformations
Flight simulators
Fourier transforms
Lipids
Macromolecules
Mathematical models
Mechanics
Molecular dynamics
Molecular modelling
Monte Carlo simulation
Parallel processing
Simulation
Simulators
Software Focus
Statistical mechanics
Supercomputers
ISSN:1759-0876, 1759-0884
Online-Zugang:Volltext
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Beschreibung
Zusammenfassung:GENESIS (Generalized‐Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all‐atom force‐field models as well as coarse‐grained Go‐like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large‐scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T‐REMD, REUS, multi‐dimensional REMD for both all‐atom and Go‐like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three‐dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real‐space and reciprocal‐space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310–323. doi: 10.1002/wcms.1220 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Computer and Information Science > Computer Algorithms and Programming Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Bibliographie:istex:5430CD401E00FEB8D3E293D263136585E1DE5C0C
ark:/67375/WNG-P0423B89-V
ArticleID:WCMS1220
Conflict of interest: The authors have declared no conflicts of interest for this article.
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These authors contributed equally to this work.
ISSN:1759-0876
1759-0884
DOI:10.1002/wcms.1220