[gmx-users] Netiquette on the gromacs user list?
Daan van Aalten
vdava at davapc1.bioch.dundee.ac.uk
Thu Feb 23 09:48:50 CET 2006
Sorry, but I have to agree with Mark Abraham here.
Although I haven't done much useful development myself apart from perhaps
PRODRG, the tone of some of the questions asked absolutely amazes me.
There seems to be no respect for the huge amount of work developers put
into a package like Gromacs - new people come in and "just expect it to
work" and if it doesn't then of course it's not their fault but that of
the developers. Gromacs is *free* and the developers have no formal
obligation whatsoever to help you in any way. I am sure everyone
involved with Gromacs is keen to continually improve the code and would
like to here about problems/bugs etc - but in properly worded E-mails,
giving constructive feedback, not some kind of shouting match.
I normally think that E-mails like that of Yegor Isakov don't even deserve
a response, but yours does as it is an important point of dicussion.
On Thu, 23 Feb 2006, Daniela S. Mueller wrote:
> On Thu, 2006-02-23 at 12:42 +1100, Mark Abraham wrote:
> > Yegor Isakov wrote:
> > You are much more likely to get a helpful response from the people who
> > know this software best (the programmers, who do read this list) if you
> > express a little less of your frustration, and imply less condemnation
> > of their software design choices, which you probably don't understand
> > yet anyway!
> though it might be unpleasant or even unjustified, frustrated reactions
> like these are in a way understandable.
> what i find less understandable and certainly a great deal less
> tolerable, is the arrogance and judgement of some users of this list
> towards others.
> also it would make helpful responses much likelier, if those unhelpful
> responses were omitted.
> > Check your assumptions - you haven't paid anybody for the right to rant
> > at them :-) You'd also do well to remember that GROMACS doesn't come
> > with a warranty of fitness for any purpose :-)
> > > I would be extremely pleased if anybody would tell me how could I foce
> > > that stupid pdb2gmx program to follow the path to the directory
> > > containing .itp files (~/share/top).
> > Setting the environment variable GMXLIB makes various GROMACS utilities
> > look there instead of the default, which is probably
> > $GMXDATA/gromacs/top. GMXDATA gets set when you run GMXRC which is
> > installed in the same place as the GROMACS binaries. You may need to
> > link the existing contents of $GMXDATA/gromacs/top/ to ~/share/top/ in
> > order to have everything work, as I couldn't get GMXLIB to accept a path.
> > I note that the manual mentions GMXLIB only in passing in a few of the
> > programs' man pages, and not at all in the Appendix section on
> > Environment variables. Usage of GMXRC is also not mentioned in the
> > installation section on the web page. Can either of both of these be
> > looked at, please?
> > > Although in the manual it was recomended to avoid modifying .rtp files,
> > > that is the only way I found to produce a topology "semi-automatically."
> > > Is there any other reasonable way to produce a topology? Is anywhere
> > > more intelegent converter of pdb files? Is anywhere a program that
> > > permits creating a stable bond between 2 atoms in a topolgy without
> > > blowing up the last one?
> > Construction of topologies for MM calculations is a process that
> > involves making judgements. Automating "sensible" defaults is an
> > extremely tricky business, given the multiplicity of force fields, the
> > kinds of kludgey PDB files that you can get hit with, and the
> > innumerability of the molecules people will want to use. Then of course,
> > a default someone thinks is sensible, someone else will think is
> > ludicrous, and they might both be right for different applications.
> > Basically you will need to do some work yourself if you are doing
> > something new... big surprise.
> > Mark
> Daniela S. Mueller
> biologist (Diplom, German degree)
> - Molecular Dynamics Group, UQ -
> School of Molecular and Microbial Sciences (SMMS)
> Chemistry Building (#68)
> University of Queensland
> Qld 4072, Brisbane
> Phone: +61-7-33653732
> Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm
> - MD group, RuG -
> Molecular Dynamics
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747 AG Groningen
> The Netherlands
> Website: http://www.rug.nl/gbb/md
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Dr. Daan van Aalten Wellcome Trust Senior Fellow / Reader
Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764
School of Life Sciences E-mail: see WWW page
Univ. of Dundee, Dundee DD1 5EH, UK WWW: http://davapc1.bioch.dundee.ac.uk
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