[gmx-users] Problem with tabulated potentials

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 19 23:59:27 CEST 2010

On 20/04/2010 7:32 AM, Jhony Tolengo wrote:
> Hello Gromacs users,
> This is constructive criticism to some people on the list...

Suggesting that people have delusions of grandeur or need medication is 
not constructive criticism. That's abuse, and has no place on this list.

> Tabulated potentials are an advanced feature of Gromacs and the people
> who is looking for help on the mailing list (certainly not experienced)
> deserve a little respect, simply because they eventually will contribute
> to the human knowledge, like probably every single person that search
> answers on the list.

They get respect, but they will get more respect (and more help!) if 
they participate actively in their learning process. The advice here 
http://www.catb.org/%7Eesr/faqs/smart-questions.html is excellent 
reading for people participating on mailing lists.

> I'm saying this because of the dramatic answers that can be readed here:
> http://lists.gromacs.org/pipermail/gmx-users/2010-April/050256.html

There's nothing "dramatic" or "hysterical" there.

> Gromacs manual requieres: knowledge about molecular modeling in general
> and patience. More than a guide the manual is a challenge and specially
> the  tabulated potentials stuff. People often doesn't have time to learn
> a new programming languaje to see inside the code to understand how the
> machine works (this is the reason for a manual!). Because I usually work
> with high MW polymers, I know the feeling of discouragement when you're
> trying to use Gromacs for this kind of systems.

Doing good science is difficult and time-consuming and MD is typical 
here. Using advanced features of complex software is always 
time-consuming. GROMACS is excellent in that it makes it possible to use 
tabulated potentials without needing to write or understand code. 
Examples of such tables are provided in the code base.

If you really wish to give constructive criticism, what does the manual 
lack in regard to usage of tables? How should Gareth and Justin's web 
contribution be improved?


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