[gmx-users] GROMACS 5.0 official release
mark.j.abraham at gmail.com
Wed Jul 2 18:58:12 CEST 2014
On Jul 2, 2014 6:44 PM, "Ali Khan" <akk5r at virginia.edu> wrote:
> Hey Mark,
> This might be a a dumb question, but over the official release download
> links on the gromacs website, it still says: "Please note that these are
> not yet regarded as production quality, pending further testing, but the
> code is now feature-stable."
> Is this a typo because I thought the official release is production
Indeed, they are. I have fixed my copy-paste error, now. Sorry about that!
> Best Wishes,
> Ali Khan
> On Sun, Jun 29, 2014 at 4:53 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > 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
> > 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
> > 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
> > 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* -
> > 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!
> > * 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++
> > 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,
> > performance will only be slightly improved)
> > * GROMACS has removed support for particle decomposition - the
> > 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
> > features that have been removed.
> > You can find the code, manual, release notes, installation instructions
> > 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/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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