[gmx-users] Netiquette on the gromacs user list?

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Feb 23 11:21:23 CET 2006

Yegor, Yegor, Yegor,

Though maybe not the most intuitive software around, Gromacs serves many
people on the globe in their attempts to understand the world around by
looking at the computed wiggling, bumping and such of atoms in all kinds of
systems. If it's a barely useful package, that can only be true from your
frame of reference, which, beyond doubt, is shared my the majority of
humanity, since these are more interested in playing Quake or other games
than they are in solving biological or physics puzzles.

If you are interested in doing MD, you have plenty of choices. NAMD, CHARMM,
AMBER, GROMOS, GROMACS, and many more. We by no means intend to force you in
using GROMACS. If it isn't what you expect from an MD package.., try another
one. But do expect that each of these packages requires understanding of the
principles of molecular simulations and takes a good deal of effort to get
the things you want to have done actually done.

Besides, just because you fail on a saturday afternoon to get a linker
modeled in gromacs and run your simulation with it, doesn't make the package
useless. Most people can live without that linker and just want 'normal'
proteins. Before adding such a linker, you require much more knowledge about
the package your using, with regards to topologies, force fields, etc, etc.
I understand your frustration with your attempts to get it done, as I've
been there before, but it won't be anything different for any of the other
packages. We're not doing magic here.

I'll try to summarize the last two paragraphs to interpret them from your
reference frame:
All molecular dynamics packages are barely useful.

If you are serious about doing MD, then try your best in understanding your
problem. Try hard to work out a solution and if you run into a problem with
your suggested solution, ask (without aiming your frustration to the
developers or the users of the list). Remember that all of us are trying to
do what no one has boldly done before, and therefore we'll all encounter
(have encountered) these roadblocks in one way or another.


On 2/23/06, Yegor Isakov <gromacs_problems at yahoo.com> wrote:
> That is not about any kind of etiquette. Despite enormous efforts of those
> developers the package is barely usefull, that is it.


Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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