[gmx-users] GROMACS 5.0-beta1 is released!

Mark Abraham mark.j.abraham at gmail.com
Thu Dec 5 20:23:04 CET 2013

Hi GROMACS users,

The first beta release of GROMACS 5.0 is available! We are making this
available to you to get an early taste of how GROMACS 5.0 will look and
work, and most importantly to get feedback from you about how well things
work. While we try our hardest to keep the quality of GROMACS as high as
possible, we’re human, we overlook things while doing other things, and we
need your many pairs of eyes to help build a tool that we can all use to do
good science! We’d love it if you could try this new version of GROMACS out
on the kinds of work that you do, and let us know what you think - good and
bad! Please do not use this version for doing science you plan to publish -
it needs more testing before it’s reliable enough for that.

What new things can you expect? Here’s some of the big changes already

* GROMACS now uses a combination of *C++98* and C99, so you will need a
working C++ compiler that is intended to work with your C compiler

* Building GROMACS now requires *CMake version 2.8.8*, which will mean some
of you will need to update your version in order to build GROMACS. We don’t
like needing to get you to do that, but that’s the price of letting the
GROMACS developers focus more on writing code for reliable and fast MD
simulations, rather than maintaining a build system that works with 12
different feature sets of CMake 2.8.x

* GROMACS tools are now bundled together into *just two binaries* - mdrun
and gmx. The latter contains most of the tools familiar to you, perhaps
with new names, and a couple of new ones. For the time being, the install
procedure will also create symbolic links so that your old scripts will
keep working for a time, but these will go away at some future point

* A handful of the tools have been re-implemented using a* new C++ analysis
framework*, which we hope will provide a better platform for maintaining
and adding to their functionality in the future.

* The *Verlet cut-off scheme is now the default* in GROMACS. One of our
design principles is that GROMACS will do correct simulations by default,
and the use of this scheme makes that easy and fast. In the long term, the
group cut-off scheme will be removed, but there is not yet a timetable for

* You can now treat *Lennard-Jones interactions with PME*, which is
expected to provide a much better treatment of spatially heterogeneous
long-ranged dispersion interactions at cost comparable to that of a cutoff.
The implementation is still being enhanced, so for now neither free-energy
calculations nor the Verlet cut-off scheme works with it, but we plan to
finish those off soon.

* Enhanced testing suite, with *unit tests* for most new C++ code.

There’s lots of other new things, and old things removed - please see the
link to the release notes below for more details. All the content of
GROMACS 4.6.5 is present, apart from features that have been removed.

There’s quite a few other shiny features the hard-working GROMACS
developers are still polishing, including supporting the few remaining
algorithms missing from the Verlet cut-off scheme, adding support for Intel
Xeon Phi, adding support for the new efficient TNG trajectory-file format,
and more. If those sound interesting to you, please take a look at the work
in progress at http://gerrit.gromacs.org - early testers and reviewers of
code are always welcome!

If all goes to plan, we hope to ship the final 5.0 release in early
February, but that relies on people joining in and helping us test! We hope
you will consider making that contribution, so we we can continue to
deliver high-quality free simulation software.

You can find the code, manual, release notes, installation instructions and
suite at the links below.






Happy testing!

GROMACS development manager

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