[gmx-users] FENE potential

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Dec 13 09:52:47 CET 2006


I do consider my reply right on the spot, since it showed that, in the
most current version of gromacs and the documentation thereof, there
was indeed a FENE bond type. If no additional information is given,
and none was given, we will assume that the query applies to the
latest version of Gromacs. You never stated that you used version 3.2,
in which case we would have pointed you to 3.3 anyway.
The presumption that we don't know what we're talking about is a bit
bold. I'll refrain from further comments on that.
If I were to 'do away with you' I wouldn't have answered in the first
place. I'm not paid to answer on the user list, but I do it of free
will, whenever I think that I can add something that maybe helpful to
someone posting a question. In your case, that meant giving a direct
pointer to the answer to your question, albeit together with a
statement expressing a feeling of annoyance I usually get when I have
the impression that the person asking a question has not done his/her
homework or ask us (the gromacs users) to do theirs. The frustration
was not solely due to you, but has been built up over the years that
I'm active on this user list.
Please do read the "How to ask smart questions" page if you haven't
done so already. It does give helpful suggestions for posting on a
user list and has helped me too.

Best regards,


On 12/12/06, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> > First of all in the gromacs manual 3.2, that i have on page 51 there is
> > the LJ and Buckingham potential  and in chapter 4.2.4 (page 58) the
> > harmonic potential is discussed, so page 51 and chapter 4.2.4 talk about
> > different things.
> That would be why it would be good for you to be looking in the current
> version of the manual, version 3.3, where 4.2.4 is on page 51 and refers
> to FENE. This makes it look like FENE was a new introduction in 3.3, and
> is a great general reason why people should be using current versions of
> software except with a clear scientific reason not to.
> Further, table 5.4 describes how to implement FENE in a topology.
> > Third Mark and Tsjerk you must be more careful, specific and polite in
> > your answers you give, especially when you don't know what you are talking
> > about, not try to get rid of someone, make sure first that you understand
> > and have the right answer, otherwise it is better not to
> > answer!
> Please check your assumptions here... we're expecting a basic level of
> competence in users attempting to solve their own problems. We both
> expressed our frustration at the regular occurrence of someone posting a
> query to this mailing list that is clearly covered in the available
> documentation. We're under no obligation to do anybody's work for them,
> and it annoys people when others expect them to do things for free when
> some basic attention would have prevented the need for the inquiry.
> Please have a look at "How to ask questions the smart way" here
> http://catb.org/esr/faqs/smart-questions.html, to see how questions like
> several you have posted here are likely to elicit less-than-helpful
> responses from knowledgeable users on groups such as this one.
> Both of our initial replies were more helpful than I think the care that
> went into the construction of your query merited. My initial reply
> suggested how to get a more useful response to your inquiry, and Tsjerk
> gave you a specific answer. I do concede that my subsequent reply to him
> was an unnecessary tongue-in-cheek cheap shot.
> Cheers,
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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