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README
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=====================================
GENESIS 2.1.4
=====================================
GENESIS website
===============
https://www.r-ccs.riken.jp/labs/cbrt/
- System requirements and installation guide: https://www.r-ccs.riken.jp/labs/cbrt/installation/
- Demo and tutorials: https://www.r-ccs.riken.jp/labs/cbrt/tutorials2022/
Project Leader: Yuji Sugita (RIKEN)
Current main developers:
Jaewoon Jung (RIKEN),
Shingo Ito (RIKEN),
Chigusa Kobayashi (RIKEN),
Takaharu Mori (RIKEN),
Hiraku Oshima (RIKEN),
Cheng Tan (RIKEN),
Diego Ugarte (RIKEN),
Kiyoshi Yagi (RIKEN).
Other developers/contributors for older versions:
Motoshi Kamiya (RIKEN),
Kento Kasahara (RIKEN/Osaka Univ.),
Yasuhiro Matsunaga (RIKEN/Saitama University)
Daisuke Matsuoka (RIKEN/RIST),
Osamu Miyashita (RIKEN),
Suyong Re (RIKEN/NIBIOHN),
Ai Shinobu (RIKEN),
Yosuke Sumiya (RIKEN),
Florence Tama (RIKEN/Nagoya University),
Shoji Takada (Kyoto Univ.),
Isseki Yu (RIKEN/Maebashi Institute of Technology).
Tadashi Ando (RIKEN),
Michael Feig (Michigan State University),
Raimondas Galvelis (RIKEN),
Ryuhei Harada (RIKEN),
Takashi Imai (RIKEN),
Yasuaki Komuro (RIKEN),
Yasuhito Karino (RIKEN),
Naoyuki Miyashita (RIKEN),
Wataru Nishima (RIKEN),
Donatas Surblys (RIKEN),
Koichi Tamura (RIKEN),
Kenta Yamada (RIKEN),
Takao Yoda (Nagahama Institute of Bio-Science and Technology),
Acknowledgments:
Norio Takase (Isogo Soft), Yasumasa Joti (RIKEN SPring8),
Akira Naruse (NVIDIA), Yukihiko Hirano (NVIDIA Japan),
Hikaru Inoue (Fujitsu Ltd.), Tomoyuki Noda (Fujitsu Ltd.),
Kiyotaka Sakamoto (Fujitsu Ltd.), Yoshinobu Akinaga (VINAS),
Yoshitake Sakae (RIST), Nobuhiko Kato (ASTOM R&D),
Toru Shiozaki (QSimulate), Klaas Gunst (QSimualte),
Hideyo Yoshida (JSOL Corporation), Kenta Chaki (JSOL Corporation),
Kazuhiro Hashiba (VINAS)
Copyright (C) 2014-2023 RIKEN. All Rights Reserved
What is GENESIS?
================
GENESIS (GENeralized-Ensemble SImulation System) is a suite of
computer programs for carrying out molecular dynamics simulations
of biomolecular systems.
GENESIS is free software, distributed under the GNU Lesser General Public
License version 3 or later. You can freely redistribute it and/or
modify it as a derived work under the terms of LGPL v3 or later.
If possible, however, it would be greatly appreciated if you send us
feedbacks. Your cooperation helps us to keep developing and managing
this official GENESIS, providing all other GENESIS users qualified
codes.
Citation Information
====================
J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita,
"GENESIS: A hybrid parallel and multi-scale molecular dynamics simulator
with enhanced sampling algorithms for biomolecular and cellular simulations",
WIREs Computational Molecular Science, 5, 310-323 (2015).
DOI: 10.1002/wcms.1220
C. Kobayashi, J. Jung, Y. Matsunaga, T. Mori, T. Ando, K. Tamura,
M. Kamiya, and Y. Sugita,
"GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced
sampling algorithms on multiple computational platforms",
J. Compute. Chem. 38, 2193-2206 (2017).
DOI: 10.1002/jcc.24874
Copyright Notices
=================
Copyright (C) 2014-2023 RIKEN.
GENESIS is free software; you can redistribute it and/or
modify it provided that the following conditions are met:
(1) All publications and commercial products using this software should cite
the above references, Jung et al (2015) and Kobayashi et al (2017).
(2) In addition, proper citations should be given for each specific
methods used. Visit the website,
https://www.r-ccs.riken.jp/labs/cbrt/citations/
to see how to cite the original papers.
(3) We ask the users to make their best effort to cite the papers in
the **main text**. Although it is permitted to cite some of the papers in
the supporting information / supplementary materials due to the limitation of
article length, the name of the software, GENESIS, and at least one of the
papers should appear in the main text.
GENESIS is released under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 3 of the License, or (at your option) any later version.
GENESIS is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with GENESIS -- see the file COPYING and COPYING.LESSER.
If not, see https://www.gnu.org/licenses/.
It should be mentioned this package contains the following softwares
for convenience. Please note that these are not covered by the license
under which a copy of GENESIS is licensed to you, while neither
composition nor distribution of any derivative work of GENESIS with
these software violates the terms of each license, provided that it meets
every condition of the respective licenses.
SIMD-oriented Fast Mersenne Twister (SFMT)
-------------------------------------------
SFMT is a new variant of Mersenne Twister (MT) introduced by Mutsuo
Saito and Makoto Matsumoto in 2006. The algorithm was reported at
MCQMC 2006. The routine is distributed under the New BSD License.
Copyright (c) 2006,2007 Mutsuo Saito, Makoto Matsumoto and Hiroshima University.
Copyright (c) 2012 Mutsuo Saito, Makoto Matsumoto,
Hiroshima University and The University of Tokyo.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
* Neither the names of Hiroshima University, The University of
Tokyo nor the names of its contributors may be used to endorse
or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
FFTE: A Fast Fourier Transform Package
--------------------------------------
FFTE (http://www.ffte.jp/) is written by Daisuke Takahashi (Tsukuba
University).
Copyright (C) 2000-2004, 2008-2011 Daisuke Takahashi (Tsukuba
University).
You may use, copy, modify this code for any purpose (include
commercial use) and without fee. You may distribute this ORIGINAL
package.
Complementary error function: erfc04
------------------------------------
A Complementary error function routine (erfc04) is written by SunSoft,
a Sun Microsystems, Inc. business.
Copyright (C) 1993 Sun Microsystems, Inc.
Developed at SunSoft, a Sun Microsystems, Inc. business.
Permission to use, copy, modify, and distribute this
software is freely granted, provided that this notice
is preserved (see at_energy_pme.fpp, and sp_energy_pme.fpp).
L-BFGS-B (version 3.0)
----------------------
L-BFGS-B (http://users.iems.northwestern.edu/~nocedal/lbfgsb.html)
is written by C. Zhu, R. Byrd, J. Nocedal and J. L. Morales.
This software is freely available, but we expect that all publications
describing work using this software, or all commercial products using
it, quote at least one of the references given below. This software is
released under the "New BSD License" (aka "Modified BSD License" or
"3-clause license").
R. H. Byrd, P. Lu and J. Nocedal.
A Limited Memory Algorithm for Bound Constrained Optimization,
(1995), SIAM Journal on Scientific and Statistical Computing,
16, 5, pp. 1190-1208.
C. Zhu, R. H. Byrd and J. Nocedal.
L-BFGS-B: Algorithm 778: L-BFGS-B, FORTRAN routines for large scale
bound constrained optimization
(1997), ACM Transactions on Mathematical Software,
Vol 23, Num. 4, pp. 550-560.
J.L. Morales and J. Nocedal.
L-BFGS-B: Remark on Algorithm 778: L-BFGS-B, FORTRAN routines for
large scale bound constrained optimization
(2011), ACM Transactions on Mathematical Software,
Vol 38, Num. 1, Article No. 7.
JSON-Fortran (version 8.2.5)
----------------------------
JSON-Fortran (https://github.com/jacobwilliams/json-fortran)
developed by J. Williams, is a user-friendly, thread-safe, and object-oriented
API for reading and writing JSON files, written in modern Fortran
The JSON-Fortran source code and related files and documentation are distributed
under a permissive free software license (BSD-style). See the LICENSE file
(src/lib/json-fortran/LICENSE) for more details.