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

Daniela S. Mueller D.S.Mueller at rug.nl
Thu Feb 23 04:37:40 CET 2006


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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