[gmx-users] Netiquette on the gromacs user list?
mgoette at mpi-bpc.mpg.de
Thu Feb 23 11:23:32 CET 2006
I think, nearly everyone is trying to help others out.
Even, if a look in the manual would be wise before asking.
I can't feel this arrogance here...it's just, that there seem to be
1. don't understand, that GROMACS is not commercial and therefore the
support may be a bit worse than of commercial products.
2. expect to do MD without a deeper knowledge of the matter
3. don't see that helping via mailing-list is not that easy and requires
lots of informations concerning parameters, files, etc.
I think it's ok to tell those people, what they should do BEFORE they
try to calculate complicated things in general.
And especially the developers have to treat lot's of "simple" questions,
which can be solved by just reading the manual.
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
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
> 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.
More information about the gromacs.org_gmx-users