From tajkhors: at :mbp-sgi7.inet.dkfz-heidelberg.de Mon Nov 4 07:18:40 1996 Received: from ns1.DKFZ-Heidelberg.de for tajkhors*- at -*mbp-sgi7.inet.dkfz-heidelberg.de by www.ccl.net (8.8.2/950822.1) id GAA19882; Mon, 4 Nov 1996 06:40:57 -0500 (EST) Received: from mbp-sgi7.inet.dkfz-heidelberg.de (mbp-sgi7.inet.dkfz-heidelberg.de [193.174.48.96]) by ns1.DKFZ-Heidelberg.de (8.7.3/DKFZ-8.6.4) with ESMTP id MAA03044 for ; Mon, 4 Nov 1996 12:36:05 +0100 (MET) Received: (tajkhors: at :localhost) by mbp-sgi7.inet.dkfz-heidelberg.de (940816.SGI.8.6.9/DKFZ-8.6.4) id NAA25004 for chemistry /at\www.ccl.net; Mon, 4 Nov 1996 13:38:35 +0100 From: "Emadeddin Tajkhorshid" Message-Id: <9611041338.ZM25000 ":at:" mbp-sgi7.inet.dkfz-heidelberg.de> Date: Mon, 4 Nov 1996 13:38:34 +0100 Reply-To: E.Tajkhorshid[ AT ]DKFZ-Heidelberg.de To: chemistry # - at - # www.ccl.net (Computational Chemistry List) Subject: Summary: Quntom Chem. MD Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="PART-BOUNDARY=.19611041338.ZM25000.inet.dkfz-heidelberg.de" --PART-BOUNDARY=.19611041338.ZM25000.inet.dkfz-heidelberg.de Content-Description: Text Content-Type: text/plain ; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Zm-Decoding-Hint: mimencode -q -u 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 i= nitio quantom chemical calculation in molecular dynamics simulation. Any relate= d information and comments is highly appreciated. *************************************************************************= *** 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 =3D=3D=3D=3D=3D\ |=3D| "Eschew Obfus= cation" FDA/CBER Biophysics Lab |____/ |=3D| Bethesda, MD U.S.A. | \ / |=3D| ( Not an official stateme= nt or rvenable[ AT ]deimos.cber.nih.gov \/ |=3D| position of the FDA; fo= r that, http://nmr1.cber.nih.gov/venable.html |=3D| see http://www.fda.go= v ) *************************************************************************= ** Hi! Charmm will do just that. Charmm 24b2 should do the ab-initio stuff - bu= t 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 "-at-" 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 | ------------------------------------------------------------------- *************************************************************************= ** You might have a look at: Bash P. A., Ho L. L., MacKerell A., Levine D., Halstrom P., =93Progress Toward Chemical Accuracy in Computer Simulations of Condense= d Phase Chemical Reactions=94, Proc. Nat. Acad. Sci., 93, 3698, 1996 Ho L. L., MacKerell, A., Bash P. A. =93Proton and Hydride Transfers in Solution: Hybrid QM/MM Free Energy Perturbation Study=94, 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 ^%at%^ anl.gov Work Phone: 708-252-8631 Home Phone: 312-642-3029 Fax: 708-252-3387 ---------------------------------------- *************************************************************************= ** 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 Corne= ll Theory Center had the Carr-Parinello code, and Dave Dixon is now at Pacif= ic 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 $#at#$ xnet.com http://www.xnet.com/~chamotlb *************************************************************************= ** 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 comm= ents. regards, Krzys Radacki _________________________-----------------------------------------------= ----- ------------------------- e-mail: Krys.Radacki \\at// ac.RWTH-Aachen.DE= --- ------------------------------------------------------------------------= ----- *************************************************************************= ** Try HyperChem (available for both IBM-compatible PC and for SGI). The URL is http://www.hyper.com Dan Berger bergerd;at;bluffton.edu *************************************************************************= ** 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 interestin= g 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. -- =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D Georg Schreckenbach Tel: (Canada)-403-220 8204 Department of Chemistry FAX: (Canada)-403-289 9488 University of Calgary Email: schrecke.,at,.zinc.chem.ucalga= ry.ca 2500 University Drive N.W., Calgary, Alberta, Canada, T2N 1N4 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D *************************************************************************= ** HyperChem can do this; I can send you more information, or put you in contact with a local dealer, if you wish. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin&$at$&hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-404= 0 Info requests to: info-!at!-hyper.com Support questions to: support-!at!-hyper.c= om Email group: Send "subscribe hyperchem" to hyperchem-request $#at#$ hyper.com 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 *********************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: Jeffrey.Nauss /at\UC.Edu * * CCCCCCC URL http://www.che.uc.edu/~nauss * *********************************************************************** *************************************************************************= ** 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 -A_T- zurich.ibm.com Phone: +41-1-724-8490 Fax: +41 1-724 0809 *************************************************************************= ** 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 ^at^ DKFZ-Heidelberg.DE 69009 Heidelberg, FRG *********************************************************************** * A friend may well be reckoned a masterpiece of the nature (Emerson) * *********************************************************************** --PART-BOUNDARY=.19611041338.ZM25000.inet.dkfz-heidelberg.de--