Subject: Anwsers on question on Md on a PC-486

From: <[email-masked]>
Date: Tue, 13 Sep 1994 16:04:01 GMT+0200

Hi Netters,
A month ago I ask a question on any software for doing MD on a PC-486.
Please find herein the anwsers I got.
Yours truly,
Carlos JAIME, Univ. Autonoma de Barcelona, Spain.
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From:	IN%"[email-masked]"  9-AUG-1994 21:08:07.01

Yes, I have AMBER going for a 486 using the Salford 486 compiler.  It runs
well giving about 10ps per day for a 2000 atom system with a cutoff of 10A.
You will have to get the permission of the University of California and
Peter Kollman before I can send it to you.

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From:	IN%"[email-masked]"  "Abby Parrill" 10-AUG-1994 00:11:31.79

Have you tried Hyperchem?

__________________________________________________________
                                              
                      Abby Parrill
                  Chemistry Department
      Artificial Intelligence in Chemistry Laboratory                         
                The University of Arizona                    
             [email-masked]              
                                           
__________________________________________________________

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From:	IN%"[email-masked]" 10-AUG-1994 11:04:11.89

Put Linux on your PC-486 and compile all freely available UNIX MD programs?
mail me back for more info :-)

Greetings,
Frits Daalmans

Frits Daalmans
OIO Conformational Analysis
Gorlaeus Laboratoria
Leiden, The Netherlands
E-mail: [email-masked]
Tel: [+31] (0)71-274505

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From:	IN%"[email-masked]" 10-AUG-1994 15:33:20.25

Hello,
The HyperCube's HyperChem ([email-masked]) performs MD
simulation using MM+,AMBER,OPLS and BIO+ force fields.
it uses cartesian model similar to that used in GROMOS and AMBER.
It is very well optimized with respect to speed, and has
very good visualizations. However for typical MD calculations
it is not easy to calculate some typical data: g(r), vacf etc.
I am working on extension which could automaticly calculate these !

We have also implemented GROMOS at our lab on a 486 PC. It works fine,
- if you acquire the licence for GROMOS - I could send you our implementation.
Now we acquired AMBER and we are working on a PC implementation of this sources!

Hope this helps,

Mirek

dr Miroslaw Sopek
Institute of Applied RAdiation Chemistry
Technical University
Lodz, Poland
and:
MAKO-lab - HyperCube's dealer in Poland

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From:	IN%"[email-masked]" 10-AUG-1994 18:31:02.87

I use Amber 4.0 on PC-486 - it does also Molecular Dynamics calculations.
I compile it with NDP Fortran without problems - DOS has no cpp preprocesor
and I had to do preprocessing manually but it can be done on Unix to 
have clear Fortran code and then compile it. With 8 or 16 Mb and 486/66 MHz
Amber 4.0 has quite good performance.

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From:	IN%"[email-masked]" 10-AUG-1994 19:29:20.12

HyperChem for Windows can do molecular dynamics using one of four force
fields or one of eight semi-empirical quantum mechanics methods to calculate
the forces on the atoms.  It requires at least a 386 with math coprocessor
(i.e. not 486SX), 4MB RAM, 20 MB free hard disk space and Windows 3.1.

For more information send email to [email-masked] or download the demo
from www.ccl.net in pub/chemistry/software/MS-WINDOWS/hcdemo.zip.

Cheers,

Graham
------------
Graham Hurst ([email-masked])
Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040
Info requests to: [email-masked]    Support questions to: [email-masked]
Email group: Send "subscribe hyperchem" to [email-masked]

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From:	IN%"[email-masked]" 10-AUG-1994 23:14:28.56

Dear Jaime,

I would certainly recommend the molecular modeling/computational chemistry
software package HyperChem (Hypercube, Inc.) as a possible answer to both 
of your questions.

HyperChem integrates molecular mechanics, molecular dynamics,
and semiempirical quantum mechanics together with a graphical
user interface and model builder.

The MD can be run at constant energy or constant temperature,
in vacuo or with solvent, as an isolated cluster or with periodic
boundary conditions using either AMBER, Bio+(CHARMM), OPLS, or MM+(MM2)
force fields.

For Andrew's work, HyperChem offers nine semiempirical Hamiltonians
(Extended Huckel, CNDO, INDO, MINDO/3, MNDO, AM1, PM3, ZINDO/1, ZINDO/S).
MOPAC and AMPAC also offer semimpirical QM on PC's, and your choice
should depend upon your specific problem. For what it's worth,
HyperChem was written specifically for PC's.

My knowledge of HyperChem is a bit dated, and I'm sure that Graham Hurst 
(of Hypercube) will respond to these inquiries as well.

Hope this helps,

Bill

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=============================================================================
From:	IN%"[email-masked]"  "Keith Refson" 11-AUG-1994 12:12:27.15

Depends on what you mean by "molecular dynamics".  This term covers
at least two fairly different fields.

If you want to model molecules using molecular-mechanics type force
fields I can't help.  But if you want to do MD simulations of solids or
liquids based on small molecules/ions using pair potentials then you
may find my MD code "Moldy" of use.  Check out the WWW page, URL=

http://www.earth.ox.ac.uk/~keith/moldy.html

for details.  You will need a decent C compiler plus a DOS extender
to compile it.

Keith Refson
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