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

Yorquant Wang wangykoo at gmail.com
Fri Dec 6 07:37:31 CET 2013

Hi Mark!
    Does the new released GMX5.0.x surpport AXV2.0 instruction set? You
know, MD simulations involve many integer calculations,and AVX2 instruction set
which widens the Integer register to 256 bit can greetly speed up the


Yorquant Wang
Shanghai China

2013/12/6 Mark Abraham <mark.j.abraham at gmail.com>

> 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
> present:
> * 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
> that.
> * 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
> test
> suite at the links below.
> ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0-beta1.tar.gz
> ftp://ftp.gromacs.org/pub/manual/manual-5.0-beta1.pdf
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0-beta1
> http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0
> http://gromacs.googlecode.com/files/regressiontests-5.0-beta1.tar.gz
> Happy testing!
> Mark
> GROMACS development manager
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Yukun Wang
PhD candidate
Institute of Natural Sciences && College of Life Science, Shanghai Jiao
Tong University
Cell phone: 13621806236.
China Shanghai

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