| 词条 | Draft:GENESIS (MD software) |
| 释义 |
{{Infobox software | name = GENESIS | logo = | screenshot = | caption = | author = | developer = Computational Biophysics Research Team in RIKEN Center for Computational Science (R-CCS), Japan | released = | latest release version = 1.3.0 | latest release date = {{Start date and age|2018|06|18|df=yes}}[1] | status = Active | programming language = Fortran | operating system = GNU/Linux | platform = Many | size = | language = English | genre = Molecular dynamics simulation | license = GNU General Public License (GPL), version 2 | website = {{URL|https://www.r-ccs.riken.jp/labs/cbrt/}} }} 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. FeaturesGENESIS 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{{Portal|Free and open-source software}}{{Columns-list|colwidth=30em|
}} References1. ^{{cite web |url= https://www.r-ccs.riken.jp/labs/cbrt/download/ |title= GENESIS Downloads |accessdate= 2019-01-10}} 2. ^{{cite journal|author=J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita |year=2015 |title=GENESIS: a hybrid‐parallel and multi‐scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations |journal=WIREs Comput. Mol. Sci. |volume=5 |pages=310-323|url=https://onlinelibrary.wiley.com/doi/full/10.1002/wcms.1220 }} 3. ^{{cite journal|author=J. Jung, T. Mori, and Y. Sugita |year=2013 |title=Efficient lookup table using a linear function of inverse distance squared |journal=J. Comput. Chem. |volume=34 |pages=2412-2420|url=https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.23404 }} External links
|
| 随便看 |
|
开放百科全书收录14589846条英语、德语、日语等多语种百科知识，基本涵盖了大多数领域的百科知识，是一部内容自由、开放的电子版国际百科全书。