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Welcome to the official version of GROMACS! There are no significant changes to the installation or use between version 3.1 and 3.0, so if you're already used to 3.0 you can just go ahead and update. A lot of things changed with version 3.0, though. Not only is the code significantly faster, but we also introduced a completely new installation process and licensed the package under the GPL (see the COPYING file). If you are familiar with unix, it should be fairly trivial to compile and install GROMACS. Installation instructions are available in the INSTALL file, and a more extended step-by-step guide can be found on http://www.gromacs.org . Of course we will do our utmost to help you with any problems, but PLEASE READ THE INSTALLATION INSTRUCTIONS BEFORE CONTACTING US! There are also several other online resources available from the homepage, and special information for developers. We recommend all users to subscribe at least to the gmx-announce list - there is almost no traffic at all, but you get notice of new versions or severe bugs, and it gives us a possibility to keep track of the number of users since no signature is required anymore. If you are a developer, or change the source for any other reason, check out http://www.gromacs.org/developer for details on using automake & autoconf! * * * * * GROMACS is free software, distributed under the GNU General Public License. However, scientific software is a little special compared to most other programs. Both you, we, and all other GROMACS users depend on the quality of the code, and when we find bugs (every piece of software has them) it is crucial that we can correct it and say that it was fixed in version X of the file or package release. For the same reason, it is important that you can reproduce other people's result from a certain GROMACS version. The easiest way to avoid this kind of problems is to get your modifications included in the main distribution. We'll be happy to consider any decent code. If it's a separate program it can probably be included in the contrib directory straight away (not supported by us), but for major changes in the main code we appreciate if you first test that it works with MPI, double precision, fortran code, etc. If you still want to distribute a modified version or use part of GROMACS in your own program, remember that the entire modified must be licensed under GPL, and that it must clearly be labeled as derived work. It should not use the name "official GROMACS", and make sure support questions are directed to you instead of the GROMACS developers. Sorry for the hard wording, but it is meant to protect YOUR reseach results! * * * * * The development of GROMACS is mainly funded by academic research grants. To help us fund development, we humbly ask that you cite the GROMACS papers: * GROMACS: A message-passing parallel molecular dynamics implementation H.J.C. Berendsen, D. van der Spoel and R. van Drunen Comp. Phys. Comm. 91, 43-56 (1995) * GROMACS 3.0: A package for molecular simulation and trajectory analysis Erik Lindahl, Berk Hess and David van der Spoel J. Mol. Mod. 7, 306-317 (2001) There are a lot of cool features we'd like to include in future versions, but our resources are limited. All kinds of donations are welcome, both in form of code, hardware and funding! Industrial users who choose to pay for a license pro bono (it is still GPL and can be redistributed freely) or contribute in other ways are listed as GROMACS supporters on our webpages. Don't hesitate to contact us at firstname.lastname@example.org if you are interested. Good luck with your simulations! The GROMACS Crew