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GENESIS (MD software)

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GENESIS
Developer(s)Computational Biophysics Research Team in RIKEN Center for Computational Science (R-CCS), Japan
Stable release
1.3.0 / 18 June 2018; 2 years ago (2018-06-18)[1]
Written inFortran
Engine
    Operating systemGNU/Linux
    PlatformMany
    Available inEnglish
    TypeMolecular dynamics simulation
    LicenseGNU General Public License (GPL), version 2
    Websitewww.r-ccs.riken.jp/labs/cbrt/

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    GENeralized-Ensemble SImulation System (GENESIS) is a molecular dynamics software mainly designed for large scale simulations of biological systems containing proteins, lipids, glycans, nucleic acids etc. It was developed in RIKEN Center for Computational Science (R-CCS), Japan.

    Features[edit]

    GENESIS package contains two molecular dynamics engines for different purposes: SPDYN and ATDYN[2]. Both engines use hybrid (MPI + OpenMP) parallelism, support CPU and GPU, and share similar data structures, subroutines, and modules. SPDYN (Spatial decomposition dynamics) is developed for simulations of large systems (such as 100 million of atoms) with a speed comparable or higher than many other simulation programs by employing spatial decomposition and new parallel algorithm [3] to increase the performance. On the other hand, ATDYN (Atomic decomposition dynamics) is very efficient for smaller systems with a code easy to understand and modify.

    See also[edit]


    Other articles of the topic Free and open-source software : Ring (programming language), Uftp-server, Tigris.org, DominoCMS, DMCMS, Enguage, ChessFriend-Fire
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    • Comparison of software for molecular mechanics modeling
    • Molecular design software

    References[edit]

    1. "GENESIS Downloads". Retrieved 2019-01-10.
    2. J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita (2015). "GENESIS: a hybrid‐parallel and multi‐scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations". WIREs Comput. Mol. Sci. 5: 310–323.CS1 maint: Multiple names: authors list (link)
    3. J. Jung, T. Mori, and Y. Sugita (2013). "Efficient lookup table using a linear function of inverse distance squared". J. Comput. Chem. 34: 2412–2420.CS1 maint: Multiple names: authors list (link)

    External links[edit]


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