[gmx-users] GROMACS 5.0 official release

Mark Abraham mark.j.abraham at gmail.com
Sun Jun 29 22:53:45 CEST 2014

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

* GROMACS deploys the Random123 stateless random-number generator

* GROMACS now uses the stochastic dynamics (sd1) integrator of Goga &

* 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++

* 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.






Happy simulating!

Mark Abraham
GROMACS development manager

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