[gmx-users] Thanks to the developers heroic efforts!

Mirco Wahab mirco.wahab at chemie.tu-freiberg.de
Mon Jun 30 16:54:34 CEST 2014

I installed 5.0 on both Linux (GPU) and Windows (GPU)
and it seems to work very good.

Some remarks:
On 29.06.2014 22:53, Mark Abraham wrote:
> * The native GPU port available in GROMACS 4.6 supports a wider range of
> simulation types, and now requires CUDA 4.0

Should I read this 4.6 as 5.0?

> * 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!

Here on Linux, mdrun is a symlink to gmx, so there should be one binary?
On Windows, there is only one exe file 'gmx.exe' and (by default)
nothing else (no symlinks). So, on my systems, there is one binary
executeable per system installation.

> * There is support for the new TNG compressed trajectory format

And, the usual default compressed trajectory is now named
'traj_comp.xtc'instead of 'traj.xtc', but 'traj.xtc' is still
present. Maybe some people have to alter their shell scripts ;)

> * GROMACS supports some special interactions for coarse-grained
> interactions with Martini force fields

Is this documented somewhere? I couldn't find it in the

> * GROMACS support for Interactive Molecular Dynamics (IMD)

This, I think, is cool! Thumbs up for this (I'm still
figuring out how it works ...)

(unfortunaletly, the solution of the gtest problem on VS2012
didn't make it into the release - but the solution is easy to
explain for people who want to build the native windows

Thank you very much!



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