Subject: Summary: Quntom Chem. MD

From: "Emadeddin Tajkhorshid" <[email-masked]>
Date: Mon, 4 Nov 1996 13:38:34 +0100

Dear Netter

Enclosed I collect the responses to my question about quantom chemical
molecular dynamics. Thanx all for their answers.

The question:
*************

I want to know if there is any program applying semiempirical and/or ab initio
quantom chemical calculation in molecular dynamics simulation. Any related
information and comments is highly appreciated.

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Recent academic versions of CHARMM have both AM1 (semi-empirical) and
GAMESS (ab-initio) interfaces and code; distribution is arranged through
Prof. Martin Karplus's group at Harvard for a modest fee to non-profit
research organizations.

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \  /   |=|  ( Not an official statement or
[email-masked]       \/    |=|    position of the FDA; for that,
http://nmr1.cber.nih.gov/venable.html    |=|    see   http://www.fda.gov  )
***************************************************************************

Hi!

Charmm will do just that.  Charmm 24b2 should do the ab-initio stuff - but
I found a bunch of routines missing when I tried to compile.  The am1
method is quite stable now.

There are numberous others - but that one is availible commercially (for
the am1 at least) and straight forward.

Good luck

Alex

 -------------------------------------------------------------------
|Alexander J Turner         [email-masked]                  |
|Post Graduate              |http://www.bath.ac.uk/~chpajt/home.html|
|School of Chemistry        |+144 1225 8262826 ext 5137             |
|University of Bath         |                                       |
|Bath, Avon, U.K.           |Field: QM/MM modeling                  |
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You might have a look at:

Bash P. A., Ho L. L., MacKerell A., Levine D., Halstrom P.,
“Progress Toward Chemical Accuracy in Computer  Simulations of Condensed Phase
Chemical Reactions”,
Proc. Nat. Acad. Sci., 93, 3698, 1996

Ho L. L., MacKerell, A., Bash P. A.
“Proton and Hydride Transfers in Solution: Hybrid QM/MM Free Energy
Perturbation Study”,
J. Phys. Chem., 100, 4466, 1996

Paul Bash

________________________________________
Paul A. Bash
Argonne National Laboratory
Bldg 202/A349
9700 S. Cass Avenue
Argonne, IL. 60439
[email-masked]
Work Phone: 708-252-8631
Home Phone: 312-642-3029
Fax: 708-252-3387
----------------------------------------
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There are probably more, but the two I am aware of off hand are
Carr-Parinello, which does dynamics with the local density functional
approximate ab initio code, and some work by Dave Dixon, while at Dupont,
which he as reported at ACS meetings.  It's been some time, but the Cornell
Theory Center had the Carr-Parinello code, and Dave Dixon is now at Pacific
Northwest Laboratories I believe.

I would be interested in hearing a summary, if there isn't already one in
the CCL archives.  Thanks.

EC
---
Chamot Laboratories, Inc.
530 E. Hillside Rd.
Naperville, Illinois 60540
Phone/Fax: (630) 637-1559
[email-masked]
http://www.xnet.com/~chamotlb
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HyperChem 4 (semiempirical level), 4.5-5 both ab initio and semiempirical -
but of cours it's comercial. If it's still interesting I can ad some comments.

regards,
           Krzys Radacki

 _________________________----------------------------------------------------
 -------------------------   e-mail:       [email-masked]  ---
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Try HyperChem (available for both IBM-compatible PC and for SGI).
The URL is http://www.hyper.com

Dan Berger
[email-masked]

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Hi Emad,

I am not entirely sure what you mean with your request...
However, I know that "combined QM/MM" (a method where the most interesting
part of the molecule is being treated by QM, e.g. DFT, the rest by
MM) is very actively under study these days. No references, though.

On the other hand, there is the "ab initio molecular dynamics",
as has been developed by Car and Parinello. References that I would
have on hand would be
  P.E. Blochl, Phys.Rev.B.50 (1994), 17953 and other papers
by Blochl (the name contains an "Umlaut o").
D.K.Remler, P.A.Madden, Mol. Phys. 70 (1990), 921 (review paper).
Look, of course, also for papers by M.Parinello and / or R.Car.

Hope this helps a bit....
Please summarize!

Yours, Georg

This is a P.S. to my message that I sent before:
one should call the Car-Parinello approach "first principle molecular
dynamics" since it is a DFT based method rather then an "ab initio"
method.
G.
--
==============================================================================
Georg Schreckenbach                      Tel: (Canada)-403-220 8204
Department of Chemistry                  FAX: (Canada)-403-289 9488
University of Calgary                    Email: [email-masked]
2500 University Drive N.W.,  Calgary,  Alberta,  Canada,  T2N 1N4
==============================================================================
***************************************************************************

HyperChem can do this; I can send you more information, or put you in
contact with a local dealer, if you wish.

Regards,
Joel

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Email to: [email-masked]

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Info requests to: [email-masked]    Support questions to: [email-masked]
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WWW: http://www.hyper.com/

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Contact or search for papers by Paul Bash at Argonne National Laboratory,
Argonne, IL, USA.  He has been doing work in that area for years.

--
						Jeff Nauss

***********************************************************************
*  UU    UU             Jeffrey L. Nauss, PhD                         *
*  UU    UU             Director, Molecular Modeling Services         *
*  UU    UU             Department of Chemistry                       *
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Dear Emad,
I read your note on Computational Chemistry List (CCL).
I am presently applying ab initio molecular dynamics on biological
systems. The method, who allow you to solve the time-dependent Sro
equation in  simulations a smart way, was devised 11 years ago by Car
and Parrinello,
If you're interested, I can send you some reprints.

Sincerely yours

Paolo

--
Paolo Carloni
IBM Zurich Research Laboratory
Saeumerstrasse 4
CH-8803 Rueschlikon/Switzerland
Internet: [email-masked]
Phone:             +41-1-724-8490
Fax:               +41 1-724 0809
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Thanx again.

-- 
Emad
*********************************************************************
E. Tajkhorshid				
German Cancer Research Center; DKFZ  Tel: +49 6221 42 2339
Dept. Molecular Biophysics (0810)    FAX: +49 6221 42 2333
P.O.Box 101949			   Email: [email-masked]
69009 Heidelberg, FRG
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