This Debian-packaged version of GROMACS was assembled by Nicholas Breen and others from the original sources at http://www.gromacs.org/ . GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2014, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. A detailed list of Gromacs contributors is available at http://www.gromacs.org/About_Gromacs/People ============================================ GROMACS is free software, distributed under the GNU Lesser General Public License (LGPL) Version 2.1. See section 1 for details. GROMACS includes optional code covered by several different licences as described below. The GROMACS package in its entirety may be copied, modified or distributed according to the conditions described in section 1. However, in the interests of clarity and completeness, some individual parts of GROMACS that can be used under their respective licenses are also noted here. This file contains the licenses for the following bodies of code: 1. GROMACS 2. Trajectory file reading using VMD plugins 3. Internal FFT (fftpack) 4. The memtestG80 library 5. thread_mpi 6. Blas 7. Lapack 8. Subset of Boost C++ library 9. Google Test and Google Mock 10. Sun XDR implementation (External Data Representation) 11. Sun FDLIBM (Freely Distributable Maths Library) 12. Random123 13. md5 Our chosen method for packaging distributions (CPack) only permits a package to have a single license file, so we are unfortunately forced to combine all of this information into a single license file. Sorry about that. ============================================ 1. GROMACS ========== As our use of the LGPL conveys upon a licensee the option to redistribute the library under the terms of the plain GPL, we must include a copy of that GPL for their reference. On Debian systems, the full text of the LGPL v2.1 can be found in '/usr/share/common-licenses/LGPL-2.1', and the full text of the GPL v2 can be found in '/usr/share/common-licenses/GPL-2'. Copyright: Copyright (c) 1991-2001, University of Groningen, The Netherlands. Copyright (c) 2001-2014, The GROMACS development team. The Debian packaging, consisting of files in the debian/ directory, is copyright (C) 2005-2014 Nicholas Breen and the Debichem Team, and is licensed under the GPL v2 or (at your discretion) any later version, as referenced above. As an exclusion, copyright for files in the debian/man/ subdirectory are held by the GROMACS development team under the same licensing conditions as GROMACS proper. 2. Trajectory file reading using VMD plugins ============================================ Files: src/external/vmd_molfile/ src/gromacs/fileio/vmdio.c (C) Copyright 1995-2009 The Board of Trustees of the University of Illinois All Rights Reserved Developed by: Theoretical and Computational Biophysics Group University of Illinois at Urbana-Champaign http://www.ks.uiuc.edu/ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the Software), to deal with the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimers in the documentation and/or other materials provided with the distribution. Neither the names of Theoretical and Computational Biophysics Group, University of Illinois at Urbana-Champaign, nor the names of its contributors may be used to endorse or promote products derived from this Software without specific prior written permission. THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE. 3. Internal FFT (ffpack) ======================== Files: src/external/fftpack/fftpack.c Copyright (c) 2005-2011, NumPy Developers. 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 name of the NumPy Developers nor the names of any 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. fftpack.c : A set of FFT routines in C. Algorithmically based on Fortran-77 FFTPACK by Paul N. Swarztrauber (Version 4, 1985). 4. The memtestG80 library ========================= Files: src/gromacs/gmxlib/gpu_utils/memtestG80_core.* The memtestG80 library, written by Imran Haque, is Copyright 2009 Stanford University, covered by the LGPL license. It may be used under the following terms: IN NO EVENT SHALL STANFORD UNIVERSITY BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF STANFORD UNIVERSITY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. STANFORD UNIVERSITY SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING DOCUMENTATION PROVIDED HEREUNDER IS PROVIDED "AS IS". Folding@home HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. Restrictions: You may use this software on a computer system only if you own the system or have the written permission of the owner. You may not alter the software or associated data files. Certain builds of this software incorporate by linkage code from the libintl and libiconv libraries, which are covered by the Library GNU General Public License, available at http://www.gnu.org/licenses/lgpl-3.0.txt or on this system at '/usr/share/common-licenses/LGPL-3'. 5. thread_mpi ============= Files: src/external/thread_mpi/ Copyright (c) 2009-2012, Sander Pronk & Erik Lindahl. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1) Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2) 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. 3) Neither the name of the 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 US ''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 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. If you want to redistribute modifications, please consider that scientific software is very special. Version control is crucial - bugs must be traceable. We will be happy to consider code for inclusion in the official distribution, but derived work should not be called official thread_mpi. 6. Blas ======= These files are semi-automatic translations by f2c from the original netlib BLAS library. The source has been modified to (mostly) use modern C formatting, and to get rid of compiler warnings. Any errors in doing this should be blamed on the Gromacs developers, and not the reference BLAS implementation. The reference BLAS implementation is available from http://www.netlib.org/blas BLAS does not come with a formal named "license", but a general statement that "The reference BLAS is a freely-available software package. It is available from netlib via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software packages (and has been). We only ask that proper credit be given to the authors." While the rest of Gromacs is LGPL, we think it's only fair to give you the same rights to our modified BLAS files as the original netlib versions, so do what you want with them. However, be warned that we have only tested that they to the right thing in the cases used in Gromacs (primarily full & sparse matrix diagonalization), so in most cases it is a much better idea to use the full reference implementation. Erik Lindahl, 2008-10-07. 7. Lapack ========= These files are semi-automatic translations by f2c from the original netlib LAPACK library. The source has been modified to (mostly) use modern C formatting, and to get rid of compiler warnings. Any errors in doing this should be blamed on the Gromacs developers, and not the reference LAPACK implementation. The reference LAPACK implementation is available from http://www.netlib.org/lapack LAPACK does not come with a formal named "license", but a general statement saying: "The reference LAPACK is a freely-available software package. It is available from netlib via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software packages (and has been). We only ask that proper credit be given to the authors." While the rest of Gromacs is LGPL, we think it's only fair to give you the same rights to our modified LAPACK files as the original netlib versions, so do what you want with them. However, be warned that we have only tested that they to the right thing in the cases used in Gromacs (primarily full & sparse matrix diagonalization), so in most cases it is a much better idea to use the full reference implementation. Erik Lindahl, 2008-10-07. 8. Subset of Boost C++ library ============================== Files: src/external/boost/boost/* Boost Software License - Version 1.0 - August 17th, 2003 Permission is hereby granted, free of charge, to any person or organization obtaining a copy of the software and accompanying documentation covered by this license (the "Software") to use, reproduce, display, distribute, execute, and transmit the Software, and to prepare derivative works of the Software, and to permit third-parties to whom the Software is furnished to do so, all subject to the following: The copyright notices in the Software and this entire statement, including the above license grant, this restriction and the following disclaimer, must be included in all copies of the Software, in whole or in part, and all derivative works of the Software, unless such copies or derivative works are solely in the form of machine-executable object code generated by a source language processor. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 9. Google Test and Google Mock =============================== Files: src/external/gmock-1.7.0/* Copyright 2008, Google Inc. 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 name of Google Inc. 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. 10. Sun Extensible Data Representation routines (XDR) ===================================================== Files: src/gromacs/fileio/gmx_system_xdr.c Sun RPC is a product of Sun Microsystems, Inc. and is provided for unrestricted use provided that this legend is included on all tape media and as a part of the software program in whole or part. Users may copy or modify Sun RPC without charge, but are not authorized to license or distribute it to anyone else except as part of a product or program developed by the user. SUN RPC IS PROVIDED AS IS WITH NO WARRANTIES OF ANY KIND INCLUDING THE WARRANTIES OF DESIGN, MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE, OR ARISING FROM A COURSE OF DEALING, USAGE OR TRADE PRACTICE. Sun RPC is provided with no support and without any obligation on the part of Sun Microsystems, Inc. to assist in its use, correction, modification or enhancement. SUN MICROSYSTEMS, INC. SHALL HAVE NO LIABILITY WITH RESPECT TO THE INFRINGEMENT OF COPYRIGHTS, TRADE SECRETS OR ANY PATENTS BY SUN RPC OR ANY PART THEREOF. In no event will Sun Microsystems, Inc. be liable for any lost revenue or profits or other special, indirect and consequential damages, even if Sun has been advised of the possibility of such damages. Sun Microsystems, Inc. 2550 Garcia Avenue Mountain View, California 94043 11. Sun FDLIBM (Freely Distributable Maths Library) =================================================== Files: src/gromacs/math/utilities.c Copyright (C) 1993 by Sun Microsystems, Inc. All rights reserved. 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. 12. Random123 ============================================ Copyright 2010-2012, D. E. Shaw Research. 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 name of D. E. Shaw Research 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. 13. md5 ============================================ Copyright (C) 1999, 2002 Aladdin Enterprises. All rights reserved. This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. L. Peter Deutsch ghost@aladdin.com