Subject: Hyperchem and good science

From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" <[email-masked]>
Date: Fri, 03 Jun 1994 09:53:06 -0500 (EST)

Leif Laaksonen writes:

>This HyperChem discussion takes incredible stupid forms. I have always 
>been in the (stupid) believe that science is independent of the software
>or hardware which produced it. I can hardly believe that supercomputers
>produce better science than PC:s. But with supercomputers one can tackle
>more difficult problems. All computational chemistry software is based on
>some sort of approximations. Depending on the level of approximations
>and size of system it can be run on different levels of hardware. In fact
>it's good policy to run a particular problem on the lowest level of 
>hardware which can handle the problem. Quite many write the final 
>manuscript on a PC or on a Mac. Does this mean that a manuscript produced
>on a PC or Mac is worse than a manuscript produced using LaTex on a 
>workstation?

Here, here!  This is not the place to discuss Windows vs. System 7 vs. UNIX,
nor FORTRAN vs. C, nor anything else that silly.  Let's talk CHEMISTRY.

Neil Ostlund is an excellent scientist who has been involved in MO methods
for longer than some people on this exploder have been alive.  I have no
problems with his science, done years ago with Pople or independently, or
with his current science (which seems to be primarily implemented in 
HyperChem).  I know some of the others at Hypercube - they are not a gang
of fly-by-night computer jockeys either!

I have been involved with HyperChem as a beta tester and documentation 
editor/proofreader since version 2.0, first with Autodesk and most recently
with Hypercube. I have also worked with some of their other products. While
I am not the world's greatest theoretician (far from it!), I have not found
any reason to complain about the science in the products or the results
produced.  I use HyperChem when it is appropriate for my research; I use
MOPAC, AMPAC, Gaussian, GAMESS, MacroModel, SYBYL, and more the same way -
when the software/methods are appropriate and the available combination of
software and hardware is sufficient to solve the problem at hand.

>C'mon an paper is good or bad depending on its scientific value! 

Exactly!  And we use peer review to judge that value, although that system
is also far from perfect.

HyperChem is no more black box than Gaussian!  Many people do not have source
code access to Gaussian any more.  And even for those who do, how many of
you know the meaning of "iop(4/20=7)", which John McKelvey recently suggested
as a keyword when choosing initial Hessian force constants? (Please don't
waste bandwidth telling me you know the meaning -- many more people don't
than do.) The HyperChem manuals provide an excellent theoretical description
and background for the calculations the program performs, which is more than
many, more acceptible (or accepted?) academic codes provide.

Let's not be hardware or software snobs.  Instead, let us applaud the use of
the proper tool for a problem, and encourage our peers, students, colleagues
and chemists (and even physicists and biologists) to use computational
chemistry as much as possible.  Then, let us all help them to use it 
properly and effectively. Who knows, you may get your name in the author 
list.

Douglas A. Smith
Assistant Professor, Department of Chemistry
Center for Drug Design and Development
 and
Chairman-elect, ACS Division of Computers in Chemistry

The University of Toledo
Toledo, OH  43606-3390

voice    419-537-2116
fax      419-537-4033
email    [email-masked]