Summary: Quntom Chem. MD



Dear Netter
 Enclosed I collect the responses to my question about quantom chemical
 molecular dynamics. Thanx all for their answers.
 The question:
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 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
 rvenable -8 at 8- deimos.cber.nih.gov       \/    |=|    position of the FDA;
 for that,
 http://nmr1.cber.nih.gov/venable.html    |=|    see   http://www.fda.gov  )
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 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         |A.J.Turner -8 at 8- bath.ac.uk                  |
 |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
 pabash -8 at 8- anl.gov
 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
 echamot -8 at 8- xnet.com
 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:       Krys.Radacki -8 at 8-
 ac.RWTH-Aachen.DE  ---
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 Try HyperChem (available for both IBM-compatible PC and for SGI).
 The URL is http://www.hyper.com
 Dan Berger
 bergerd -8 at 8- bluffton.edu
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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: schrecke -8 at 8-
 zinc.chem.ucalgary.ca
 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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 WWW: http://www.hyper.com/
 ***************************************************************************
 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
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 *  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: cap -8 at 8- zurich.ibm.com
 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: E.Tajkhorshid -8 at 8- DKFZ-Heidelberg.DE
 69009 Heidelberg, FRG
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