[gmx-users] [gmx-announce] GROMACS 5.0 official release

[Szilárd Páll]

Important note!

A small bug has slipped into the regression test script which causes
the "complex/nbnxn_vsites" test to fail in some cases. It happens
*only* when running the tests on a machine with supported GPUs using a
CUDA-enabled build (but you won't see it if you have exactly 6 GPUs
:).

So, when you run "make check" or manually run the regression tests
script on a GPU build, please ignore the "complex/nbnxn_vsites"
failure. Even better, rerun the test with forcing no GPUs to be used
e.g. with the CUDA_VISIBLE_DEVICES="" environment variable. This way
all tests will only use the CPU (in fact this is always recommended in
order to test both CPU and GPU kernels).

Cheers,
--
Szilárd


On Sun, Jun 29, 2014 at 10:53 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> Hi GROMACS users,
>
> The official release of GROMACS 5.0 is available!
>
> What new things can you expect?
>
>
> * 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.
>
>
> * The native GPU port available in GROMACS 4.6 supports a wider range of
> simulation types, and now requires CUDA 4.0
>
>
> * 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. The group cut-off
> scheme will be removed in a future version, so start planning 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. LJPME is
> supported for both cut-off schemes, and almost all kinds of simullations
>
> * GROMACS deploys the Random123 stateless random-number generator
>
>
> * GROMACS now uses the stochastic dynamics (sd1) integrator of Goga &
> Berendsen
>
>
> * 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!
>
> * There is support for the new TNG compressed trajectory format
>
> * GROMACS contains a feature for "computational electrophysiology"
> simulations, to simulate a steady-state ion concentration difference between
> compartments of a double membrane
>
>
> * GROMACS supports some special interactions for coarse-grained interactions
> with Martini force fields
>
> * GROMACS support for Interactive Molecular Dynamics (IMD)
>
>
> * 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.
>
>
> * There is an enhanced testing suite, with *unit tests* for most new C++
> code.
>
>
> * There is preliminary support for Intel Xeon Phi (only in native mode, and
> performance will only be slightly improved)
>
> * GROMACS has removed support for particle decomposition - the simulation
> types that required it are now limited to a single MPI rank (but perhaps
> multiple OpenMP threads)
>
>
> Please see the link to the release notes below for more details. All the
> content of GROMACS 4.6.6 (whose release is imminent) is present, apart from
> features that have been removed.
>
> 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.tar.gz
>
> ftp://ftp.gromacs.org/pub/manual/manual-5.0.pdf
>
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0
>
> http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0
>
> http://gerrit.gromacs.org/download/regressiontests-5.0.tar.gz
>
>
> Happy simulating!
>
>
> Mark Abraham
>
> GROMACS development manager
>
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