[gmx-users] that is not about abuse

Mark Abraham Mark.Abraham at anu.edu.au
Thu Feb 23 12:28:56 CET 2006

Yegor Isakov wrote:
> That is not about abuse. Sorry if you were abused. I think you should 
> not be so sensitive. I spent a lot of my time on running that package. I 
> express my critisism.  You should be pleased - I expressed my interest 
> in that. When you will make this package commercial may be you will 
> encounter my remarks (look, I do not ask a share in your future 
> buisiness ;^) ).

Criticism is (and should be) welcome - but the use of adjectives like 
"stupid", "semi-automatically", "intelligent" and "reasonable" in the 
contexts they were used could be considered abusive, and were not 
necessary to describe the problem you were experiencing.

You may have noticed that in one of my replies describing the use of 
GMXLIB I noted my opinion that the manual didn't describe its use 
clearly, and suggested that it be considered for an update. This is the 
kind of useful criticism that has a place on this list.

I'm an outsider to the GROMACS development team, but I think it will be 
a good many years yet before MD codes like GROMACS will be able to 
consider a "commercial" release. First there is the problem of small 
market, and second that of the required expertise in the users. 
Doubtless there are others.

As an example from elsewhere in the field of computational chemistry, 
the ab initio quantum chemistry code Gaussian has been commercial for at 
least one decade and probably more like two decades. It has a 
nice-looking GUI called Gaussview which greatly simplifies the task of 
doing simple calculations and visualization - but it's just a front end 
for producing the same kind of text input files to control complex 
computational frameworks that is also common with MD. If you wanted to 
use a custom basis set with the current Gaussian release - a procedure 
vaguely comparable with introducing a -S(C=O)- linking group for peptide 
MD in my opinion - you would be forced to construct a text file full of 
seemingly-meaningless numbers following a strict file format described 
deep in a many-hundred page manual - and then to work out problems 
yourself as they arise. All this in market-leader commercial software 
costing thousands of dollars when all you are doing is a calculation of 
the same type using a starting point the original authors didn't have 
the scope to support.

Computational chemistry is difficult because of its scope, and its 
software is correspondingly difficult to use effectively. Anybody only 
used to point-and-click GUI "computing" needs to seriously rework their 
assumptions before using much of it.


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