A NEW NEWSGROUP? bionet.molecular.modelling

Dr. Mrigank mrigank at imtech.ernet.in
Thu Apr 28 02:34:33 EST 1994

In article <Pine.3.89.9404201250.A21568-0100000 at fox.cce.usp.br>, szeinfel at FOX.CCE.USP.BR (Rafael N Szeinfeld) writes:

> 	I think these newsgroup would fit the biosci structure only if it 
> major goal where to discuss the ideas behind all these programs where i 
> mean not only the algorhitms but also the physical and chemical aspects 
> or better supositions you're doing when you use these programs. I used 
> for some time Quanta 3.3 and WHATIF and these programs where black boxes 
> to me even though I'm physicist & biochemisist with a strong background 
> in FORTRAN programing. 

I think what you say is right. It should apart from discussing the programs
should also discuss applications of the program, idea's behind the program
but then that is upto us. bcos it is we who will post. 

I think this BLACK BOX stuff is more true with non specialists. I always, if
get the source, try to have a look at it. May be also due to complusion as so
far I had to implement the software on wiered systems. But i do not like
to work with black boxes as not only it serve little purpose, you do not
use the software efficiently.

A charter of the group should be made and posted in announce with may be Stas
Philippe as discussion leader, as it was his idea if he is willing. 
> 	My felling is that who make the program knows nothing about the
> physics and chemistry behind it and who tells the first guy what to do
> cannot undestand what he made and then the black box is born. 

It may be true for many commercial ventures, but academic software are often
made or atleast with active participation with specialist. Do you say that
Kollman, Case or Singh knew a little about basics of  AMBER? or Brooks/Karplus
little about CHARMm? 
Dr. Mrigank                       \/Phone  +91 172 45004 x216, +91 172 44252
Institute of Microbial Technology /\Email:  mrigank at imtech.ernet.in
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