GENESIS (MD software)
|Developer(s)||Computational Biophysics Research Team in RIKEN Center for Computational Science (R-CCS), Japan|
1.3.0 / 18 June 2018
|Type||Molecular dynamics simulation|
|License||GNU General Public License (GPL), version 2|
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 | edit source]
GENESIS package contains two molecular dynamics engines for different purposes: SPDYN and ATDYN. 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  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 | edit source]
Others articles of the Topic Free and open-source software : Koseven (framework), Phorum, AdoptOpenJDK, Ring (programming language), The Bug Genie, Grav (CMS), TOPCAT (software)
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References[edit | edit source]
- "GENESIS Downloads". Retrieved 2019-01-10.
- 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)
- 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)
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