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

Mark Abraham mark.j.abraham at gmail.com
Tue Jul 1 10:53:16 CEST 2014

On Jun 30, 2014 4:56 PM, "Mirco Wahab" <mirco.wahab at chemie.tu-freiberg.de>
> 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?

Sorry, "... first available in GROMACS 4.6 now supports..."

>> * 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.

As Szilárd says, the ability to build two executables is present; my
wording was not quite precise. If there is a way to let CMake make symlinks
on Windows then we can do that, but the fact it has not worked suggests
there is not support for it. The symlinks are only temporary, for
compatibility, anyway.

>> * 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 ;)

I forget what's going on here (are you saying three trajectory files can be
written?), since we did it five months ago and nobody has noticed! The idea
is that because TNG format can contain either compressed or full-precision
trajectory data, the filename and not the extension must convey that
distinction to/from the user. So the old situation was not forward-thinking
enough, and can't be preserved.

>> * GROMACS supports some special interactions for coarse-grained
>> interactions with Martini force fields
> Is this documented somewhere? I couldn't find it in the
> 5.0-manual.

Yes, new parts in chapter 4.

>> * 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
> executeables.)

Indeed. There will be a cluster of such minor issues that we need to fix.
The more people test the beta and rc versions the better, but the line has
to go somewhere. Thanks very much for your past work keeping us honest on


> Thank you very much!
> Regards
> M.
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