Subject: experience with semi-empirical MD

From: Martijn Zwijnenburg <[email-masked]>
Date: Thu, 28 Feb 2002 15:12:44 +0100

Hi,

Several people told me, in a reply to my question, that it's possible 
to do semi-empirical molecular dynamics (AM1, PM3) with 
Hyperchem, Mopac and Spartan. Now I wonder if somebody can 
give me some practical information on systems one can treat on a 
state of the art linux or windows 2000 machine. I know this is not 
something fixed and depends on how long one is willing to wait for 
the simulation to finish but I just want to get some feeling. Any 
experience, especially with solution systems, is more then welcome.

Cheers

Martijn 
-------------------------------------------------------------------------
Martijn Zwijnenburg
Lab. of Applied Organic Chemistry and Catalysis
Delft University of Technology
Julianalaan 136
2628 BL Delft
The Netherlands
Tel: 0031-(0)152782691
Fax: 0031-(0)152784700
e-mail: [email-masked]
web page: http://come.to/tock

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From: George Vacek <[email-masked]>
Date: Thu, 28 Feb 2002 15:28:30 -0800

Martijn Zwijnenburg wrote:

> state of the art linux or windows 2000 machine.

Martijn,

Mopac 2002 uses the linear scaling MOZYME algorithm, so it can tackle fairly
large systems (up to 20000 atom limit) in a reasonable amount of time.  For
practical purposes, in a dynamics run, after the first time step, additional
time steps can be calculated in only a fraction of the time (probably about
1/10th).  So for a couple hundred atoms and a time period of, say, 500
femtoseconds, you are probably looking at only a few hours on a decent linux
box.  I hope that helps.

For more information on Mopac 2002, please see http://www.schrodinger.com
Schrodinger distributes Mopac 2002 only in North and South America, but the page
also lists distributor information for Europe and other regionds if you decide
you are interested.

Regards,
George Vacek
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