Subject: Summary: CCL:Need some reference about molecular geometry optimization.

From: "yubofan" <[email-masked]>
Date: Fri, 28 Nov 1997 09:14:38 +0800

Hi,

I am doing geometry optimization of a big molecule. I think it is
impossible for me to do these jobs for the whole molecule which contains
over 40 C atoms, so I want to split it into several parts and calculate
each of them respectively. Then I will put them together. Is this thought
possible? If possible, could you please give me some advice or reference
with the same kind of work.

With best regards

Y. Fan
=============================================================
Yubo Fan                         Email: [email-masked]
Organic Synthesis Lab                   [email-masked]
The Department of Chemistry
Fudan University                 Phone: 8621-65648139
No. 220 Handan Road              Fax:   8621-65641470
Shanghai, 200433
P. R. China
=============================================================

Hi Yubo,

There's a method called "Divide-and Conquer" ( See: "A density-matrix
divide-and-conquer approach for electronic structure of large molecules",
Weitao Yang and Tai-Suang Lee, J.Chem.Phys., 103(13),5674,1995) may solve
your
problem. I know the method is not easy to use if you don't have programs in
your hand, but at least the paper can supply some clues to help you
thinking.

Best wishes!

Jianguo Yu

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|Jianguo Yu, Ph.D.      |  ______________  | E-Mail: [email-masked]  |
|Computational Chemist  |  \  _________ /  | Phone:  (714)955-2120   |
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Since you say it is impossible to optimize the geometry for the whole
molecule, I assume you are using quantum mechanics (ab initio etc.) or
semi-
empirical methods. This would however be no problem with the use of
molecular
mechanics calculations which are supported by a lot of programs: AMBER, 
CHARMM, GROMOS, XPLOR, ChemX, Hyperchem etc. etc.

Best regards,
Eldbjoerg S. Heimstad

dear yubo

there is one dft program called the amsterdam density functional ADF 2.x
where you can put together your molecule from fragments. These fragments
itself are built with<italic> basic atoms</italic>, the smallest
fragments possible. For more information see 

http://tc.chem.vu.nl./SCM/welcome.html.

For organic molecules it is often absolute adequate to use semi-empirical
methods like PM3 or MNDO to get qualitatively sufficient results. With
these methods you can calculate even big molecules with more than 40
atoms.  There was a intersting discussion going on last month about
semi-empirical methods, look for the summary about extented hueckel
methods initiated by E. Lewars

CCL:EXTENDED HUECKEL--SUMMARY AND THANKS VERY MUCH

CCL:EXTENDED HUECKEL--MORE INFO AND A FINAL SUMMARY

I hope this information will help you

christoph

----

Christoph Widauer

Laboratorium f. Anorganische Chemie

ETH-Zentrum CAB C8

Universit漪sstrasse 6

CH-8092 Zuerich 

Phone (Zurich): +41 (1) 632 61 19

Fax (Zurich): +41 (1) 632 10 90

e-mail: [email-masked]

Dear Mr. Fan,

    Have you tried some Molecular Mechanics calculation? It can select
only the most promising structures, and then you could make your QM
calculation just on them.

Regards,
--

----------------------------------------------------------------------------
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                            Gustavo de Miranda Seabra
MSc Student in Chemistry                     E-Mail: [email-masked]
Universidade Federal de Pernambuco - Recife - Pernambuco - Brazil
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=============================================================
Yubo Fan                         Email: [email-masked]
Organic Synthesis Lab                   [email-masked]
The Department of Chemistry
Fudan University                 Phone: 8621-65648139
No. 220 Handan Road              Fax:   8621-65641470
Shanghai, 200433
P. R. China
=============================================================