From: walter@hyper.hyper.com (Walter R. Steinemann)
Subject: Re: IBM PC Clone in Vis. Labs.
Followup-To: comp.graphics.visualization
Organization: HyperCube Inc., Waterloo, Ontario, Canada.
Date: 16 Apr 92 18:11:22

Hello Fellow Visualizers,

In article <2009@ra.nrl.navy.mil> buck@ra.nrl.navy.mil (Loren Buchanan) writes:
>  I manage a Visualization Lab, and currently we have systems from SGI, Sun,
>  IBM, Apple, HP, and Stardent (well it used to be Stardent).  We are now
>  shopping for a PC clone to round out the equipment list.  I have not paid
>  much attention to the PC side of the world and could use some help in
>  specifying what should be on the PC in terms of software and hardware.
>  
>  We support a wide variety of scientist from those who work on the very
>  small (atoms) and those who look at the very large (quasars).  I would
>  be interested in both general purpose software and more specialized 
>  software to support molecular dynamics, chemistry (in various flavors),
>  remote sensing, fluid dynamics, acoustics, optics, radar, and meteorology
>  to name the biggies.
>  

[BLATANT PLUG ALERT]

I work for Hypercube, and we are the developers of a package
which may be what you are looking for to do molecular modeling.

   *******  AUTODESK has recently announced HyperChem  *******

I won't be able to give you an outsider's view of HyperChem, of course,
but in brief what it does is the following:

(1)	It runs under Microsoft Windows, and has capability to exchange
information with other applications (spreadsheets, wordprocessors, etc.), 
via DDE and through the WIndows clipboard.  
(A Silicon Graphics version is due for release later this year.)

(2)	It contains a graphical front end that enables molecules to be
drawn easily (there is a model-building capability that produces 3D
structures from rough sketches).  It has an extensive range of
facilities for manipulation and display of molecules.  Proteins and DNA
fragments can be built residue-by-residue in a particularly easy manner.

(3)	It contains four molecular mechanics force fields: MM+ (our
implementation of MM2, with a default scheme to fill in the gaps in
parameters), OPLS, AMBER and BIO+ (our implementation of the CHARMM
force field, including the published parameters).

(4)	Using these force fields, geometry optimizations on all or part
of a system can be carried out, using constraints where needed.

(5)	Using these force fields, molecular dynamics calculations can be
carried out, again on all or part of a system and with or without
constraints.  There are playback tools for analysis of molecular
dynamics runs, and geometrical features as well as energies can be
monitored during a run.

(6)	It contains our implementation of six semi-empirical methods.
Extended Huckel, CNDO, INDO, MINDO/3, MNDO and AM1.  PM3 parameters are
available for the latter option.  Geometry optimizations can be carried
out using these methods (except for Extended Huckel), and also molecular
dynamics (if you have the time to wait!).  CNDO and INDO calculations
can also be carried out on part of a system, with the remainder serving 
as an electrostatic background.

(7)	All the molecular mechanics and semi-empirical parameters are
available in files, and can be added to and changed by the user.

(8)	There is an extensive set of scripting (macro) commands, that
can be run as scripts from within the program or built into macros from 
other Windows applications via DDE.

	Should you require any other technical information, please 
do feel free to contact me.  Autodesk has a product information line at
1-800-424-9737, or you can FAX them at 1-415-491-8311.

-- WalteR --
Walter R. Steinemann                    HYPERCUBE, INC.
email:  walter@hyper.com                Phone:  (519) 725-4040 



--
Walter R. Steinemann                    HYPERCUBE, INC.
email:  walter@hyper.com                Phone:  (519) 725-4040 



-- 
Walter R. Steinemann                    HYPERCUBE, INC.
email:  walter@hyper.com                Phone:  (519) 725-4040