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

[Szilárd Páll]

On Fri, Dec 6, 2013 at 7:37 AM, Yorquant Wang <wangykoo at gmail.com> wrote:
> 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
> simulation.

No, it was planned, but it did not make it.

--
Szilárd


>
> best,
> cheers
>
> Yorquant Wang
> SJTU
> 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
>> --
>> Gromacs Users mailing list
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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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