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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 .

Of course we will do our utmost to help you with any problems, but PLEASE 

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 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 if you are interested.

                       Good luck with your simulations!

                              The GROMACS Crew

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