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

Gianluca Interlandi gianluca at u.washington.edu
Fri Dec 6 01:08:37 CET 2013

Dear Mark,

Does GROMACS 5.0 have the ability to perform Monte Carlo steps?



On Thu, 5 Dec 2013, Mark Abraham wrote:

> 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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Gianluca Interlandi, PhD gianluca at u.washington.edu
                     +1 (206) 685 4435

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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