GENESIS (MD software)
| Developer(s) | Computational Biophysics Research Team in RIKEN Center for Computational Science (R-CCS), Japan |
|---|---|
| Stable release | 1.3.0
/ 18 June 2018[1] |
| Written in | Fortran |
| Engine | |
| Operating system | GNU/Linux |
| Platform | Many |
| Available in | English |
| Type | Molecular dynamics simulation |
| License | GNU General Public License (GPL), version 2 |
| Website | www |
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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]
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References[edit]
- ↑ "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)
External links[edit]
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