[gmx-users] GROMACS 5.0-beta1 is released!
alexxy at omrb.pnpi.spb.ru
Thu Dec 5 21:23:06 CET 2013
Genbox segfaults in beta1 and git master
Mark Abraham писал 05-12-2013 23:22:
> 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
> work. While we try our hardest to keep the quality of GROMACS as high
> possible, we’re human, we overlook things while doing other things, and
> 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
> on the kinds of work that you do, and let us know what you think - good
> 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
> of you will need to update your version in order to build GROMACS. We
> 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* -
> 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
> 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++
> framework*, which we hope will provide a better platform for
> 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
> and the use of this scheme makes that easy and fast. In the long term,
> group cut-off scheme will be removed, but there is not yet a timetable
> * 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
> The implementation is still being enhanced, so for now neither
> calculations nor the Verlet cut-off scheme works with it, but we plan
> 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
> 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
> Xeon Phi, adding support for the new efficient TNG trajectory-file
> and more. If those sound interesting to you, please take a look at the
> in progress at http://gerrit.gromacs.org - early testers and reviewers
> 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
> 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
> suite at the links below.
> Happy testing!
> GROMACS development manager
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina,
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru
More information about the gromacs.org_gmx-users