Welcome to the official version of GROMACS! If you are familiar with Unix, it should be fairly trivial to compile and install GROMACS. GROMACS uses only the CMake build sytem, and our installation guide can be found at http://manual.gromacs.org/documentation/current/install-guide/index.html 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. If you are a developer, or change the source for any other reason, check out http://www.gromacs.org/Developer_Zone. * * * * * GROMACS is free software, distributed under the GNU Lesser General Public License, version 2.1 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 (and without) MPI, threads, double precision, etc. If you still want to distribute a modified version or use part of GROMACS in your own program, remember that the entire project must be licensed according to the requirements of the LGPL v2.1 license under which you received this copy of GROMACS. We request 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) DOI: https://doi.org/10.1016/0010-4655(95)00042-E * GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl J. Chem. Theory Comput. 4 (2008) pp. 435-447 DOI: https://doi.org/10.1021/ct700301q * GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, Erik Lindahl. Bioinformatics 29 (2013) pp. 845-54 DOI: https://doi.org/10.1093/bioinformatics/btt055 * Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS Szilárd Páll, Mark J. Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale, Lecture Notes for Computer Science, 8759 (2015) pp. 3–27 DOI: https://doi.org/10.1007/978-3-319-15976-8_1 * GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl, SoftwareX, 1, (2015), 19-25 DOI: https://doi.org/10.1016/j.softx.2015.06.001 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 LGPL and can be redistributed freely) or contribute in other ways are listed as GROMACS supporters on our webpages. Don't hesitate to contact us if you are interested. Good luck with your simulations! The GROMACS Crew
Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.
Minor improvements to the format:
- Make the annotations to Tab. 13 readable
- Fix "Order of parameters and their units" column of Tab. 14 for SETTLE (math-mode)
- Fix bond entry 3 in urea topology
- Fix amber99.ff/tip3p include in urea topology
Introduce new helper function to help maintainers keep test names to a uniform maximum length
Shortened pdb2gmx, FEP, and replica-exchange test names to conform to new maximum length. Added the helper function to other tests whose reference data files have long names.
- Roll back accidental atom->particle rename in exclusion blocks of GROMACS.
- Make the transpose(...) function inline to remove the compilation time warning.