Subject: New ideas for chemistry software

From: Ferenc Csizmadia <[email-masked]>
Date: Fri, 22 Jan 1999 09:57:06 +0100

A few weeks ago I asked your opinion about future trends in chemical
software development.

The first responses have already been published in CCL
(ftp://www.ccl.net/pub/chemistry/archived-messages/99/01/10)

The second batch follows:

11. ====

The summary you posted contained many interesting good ideas. I was
disappointed, however, in that most of the answers focused on the needs
of computational chemists rather than the needs of chemists in general.
Typical answers of the former type were "development of hot new method"
and "porting software to hot new machine".

Computational chemistry can impact chemistry in two ways: 1) by making
larger numbers of people into computational chemists, i.e., chemists who
enjoy spending lots of time with a computer and never go into the lab,
and 2) by providing "lab" chemists with useful information for their
work. I think the latter is more important in the long run.
Computational chemists and software developers certainly need to look at
ways of making their software more powerful, more friendly, more
portable, etc., but it won't count for much unless they also find ways
to make computations more relevant.

-Alan

-----------------
Alan Shusterman
Department of Chemistry
Reed College
www.reed.edu/~alan

12. ====

> It seems nearest future trends in chemistry are more or less visible. 
> To make it short: Biology, Biochemistry and related topics.
> 
   With regard to this discussion, I would like to add that the REASON
why
computational approaches and software are so enticing in biology,
biochemistry, etc. is because of the difficulty in obtaining
high-quality
experimental data -- quickly and at low cost.  The suggestion was made
later in this discussion that if one wanted to start a new software
project that one should look at structural biochemistry.

   I don't think that someone starting a new software project should
necessarily limit themselves to this one area.  There are many pressing
needs in biology, biochemistry and molecular medicine OTHER than in
structural modeling.  There are many pressing needs in other areas of
chemistry and engineering.  Certainly, a software developer should also
NOT neglect to examine the development of low-cost "user-friendly" 
software for data acquistion and control of analytical and chemical
instrumentation.

   If profit and funding are the sole criteria for determining what
software/computational project to start, then our accomplishments as
scientists are doomed.  I don't think that someone starting a new
project
should fall victim to the "bandwagon effect".  From a business
standpoint, it is difficult for a new software developer to break into a
saturated market.  It seems that profit and funding are the result of
how
we PROMOTE the results or application of the work to a potential grant
agency, industrial user, etc.  Our prime consideration in the work done
should be how IMPORTANT is the problem solved or the application.

Respectfully,
Anita I. Zvaigzne
<[email-masked]>

13. ====

Please keep in mind that PC does not mean Microsoft !
There have been several statements that want to get programs ported to
Windows to be able to run them on "cheap" PC-hardware.
Since there are many OSs that run these programs on exactly that cheap
hardware, I would not see this urgent need for porting but would like
the
programs to be enhanced in functionality !

PS: I know at least 10 OSs of very different flavour running on exactly
this PC
hardware, of which MS_DOS(+Win3.1+Win9x) and Windows NT are only two,
and will
be only one really soon, since the DOS branch is declared death already
by
Microsoft.
Moreover basically all of this can be installed in parallel on the same
machine.

So I would strongly suggest to work on the science part of the programs,
not
the operating system topics.

Greetings,
Jochen
-----------------------------------------------------------------------
  Jochen K"upper

  Heinrich-Heine-Universit"at D"usseldorf   [email-masked]
  Institut f"ur Physikalische Chemie I
  http://www-public.rz.uni-duesseldorf.de/~jochen

14. ====

Of particular interest to me, at any rate, would be developments 
in ab initio codes for handling "condensed phase" effects such as
solvation in liquids and lattice effects in solids. For example,
how is the potential energy surface for internal motion of a 
molecule/ion/radical affected by 1) H-bonding in solution, 
2) trapping in e.g. a zeolite, 3) lattice constraints in a 
molecular solid? In principle, of course, all these systems can
be handled completely at whatever level of calculation is appropriate,
but it would be nice to have ab initio software with a selection
of schemes which allow emphasis on the detailed electronic structure
at the "focal point" of the calculation and on a lower level of detail
(i.e. forces and dynamics) elsewhere. 

Regards,

Rod Macrae

-------------------------------------------------
Dr. R. M. Macrae
Muon Science Laboratory
Institute of Physical and Chemical Research (RIKEN)
<[email-masked]>

=============

Thank you for the contributions.

Ferenc

~~~~~~
Ferenc Csizmadia, Ph.D.
ChemAxon Ltd.
Valyog u. 7, H-1032 Budapest, Hungary
http://www.chemaxon.com
T:+3620 9570988
mailto:[email-masked]