From schiffer@h1tw0036.hoechst.com Tue Apr 8 03:34:45 1997 Received: from backup.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id DAA07642; Tue, 8 Apr 1997 03:26:54 -0400 (EDT) Received: by backup.hoechst.com (SMI-8.6/SMI-SVR4) id JAA01000; Tue, 8 Apr 1997 09:24:27 +0200 Received: from unknown(134.81.79.248) by backup via smap (V1.3) id sma000986; Tue Apr 8 09:24:09 1997 Received: from 134.81.76.36 by fra28.hiserv.de with SMTP (Microsoft Exchange Internet Mail Connector Version 4.0.994.63) id 2ASZCCT1; Tue, 8 Apr 1997 09:30:42 +0200 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id JAA06765; Tue, 8 Apr 1997 09:25:23 +0200 Message-ID: <3349F2E3.794B@h1tw0036.hoechst.com> Date: Tue, 08 Apr 1997 09:25:23 +0200 From: "Dr. Heinz Schiffer" Organization: Hoechst Corporate Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Dale Andrew Braden , Computational Chemistry List Subject: Re: CCL:G:geometry optimization methods References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dale Andrew Braden wrote: > > Dear CCL, > > A brief question: Are there any circumstances in which a geometry > optimization in Cartesian coordinates would be *faster* than in redundant > internal coordinates? > > The reason I am asking is because I am trying to optimize the geometry of > a hydrogen-bonded dimer in a solvent medium using Gaussian 94, and the > change in the two intermolecular Z-matrix coordinates (distance and angle) > remains large for many, many iterations. The geometry isn't exactly > oscillating between two structures, but it isn't settling down, either, > and I thought that perhaps by changing the optimization method from > redundant internal coordinates (the default method in G94) to cartesians, > the optimization might proceed more smoothly to a converged minimum. I > don't want to try this unless it can work, because the calculation is > expensive. Hi Dale, Optimization with Z-matrix coordinates is always the worst that you can do, next come cartesian coordinates, and the best are the natural internal coordinates of Pulay. Cartesian coordinates are o.k. if you have a good initial guess of the Hessian matrix (e.g. computed by a less expensive method). See : Jon Baker, Techniques for Geometry Optimization : A Comparison of Cartesian and Natural Internal Coordinates, J. Comput. Chem. 14(9) (1993) 1085-1100. Ciao, Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main schiffer@msmwia.hoechst.com From chersil@farm.unipi.it Tue Apr 8 05:34:44 1997 Received: from mixer.unipi.it for chersil@farm.unipi.it by www.ccl.net (8.8.3/950822.1) id EAA08011; Tue, 8 Apr 1997 04:36:00 -0400 (EDT) Received: from alceo.farm.unipi.it (slip08.unipi.it [131.114.21.29]) by mixer.unipi.it (8.8.0/8.8.0) with SMTP id KAA19374 for ; Tue, 8 Apr 1997 10:36:54 -0100 (GMT) Sender: silvio@mixer.unipi.it Message-ID: <2F86C995.2781@farm.unipi.it> Date: Sat, 08 Apr 1995 10:36:21 -0700 From: Silvio Chericoni Organization: Dipartimento di Scienze Farmaceutiche X-Mailer: Mozilla 3.0SC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: CCL Subject: Thanks Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I'm Silvio Chericoni and I just want to thank all that answered me and helped me to solve my problem. Thanks Silvio From famava@usc.es Tue Apr 8 06:34:52 1997 Received: from uscmail.usc.es for famava@usc.es by www.ccl.net (8.8.3/950822.1) id FAA08234; Tue, 8 Apr 1997 05:37:21 -0400 (EDT) Received: by uscmail.usc.es (5.67b/1.34) id AA19792; Tue, 8 Apr 1997 11:38:03 +0200 Date: Tue, 8 Apr 1997 11:38:03 +0200 (MET DST) From: Xose Manuel Valladares Pernas To: chemistry@www.ccl.net Subject: Complex diagonalization Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello to everybody We are looking for a efficient algorithm to make the diagonalization of a complex matrix. We would prefer forttran language. If you know any internet address please let we know. We will sumarize all the responses if there is interest on it. Thank you very much ###################################################################### ############### Manuel Pereiro-Lopez ################## ############### Manuel Valladares-Pernas ################## ############### David Suarez-de-Lis ################## ############### Moises Iglesias-Gonzalez ################## ## ## ## Applied Physics Department ## ## Physics faculty ## ## University of Santiago de Compostela ## ## Santiago de Compostela- A Corunha- Spain ## ## Tln. 563100- Ext. 4020 ## ###################################################################### From smelchor@goliat.ugr.es Tue Apr 8 07:34:47 1997 Received: from goliat.ugr.es for smelchor@goliat.ugr.es by www.ccl.net (8.8.3/950822.1) id GAA08540; Tue, 8 Apr 1997 06:50:18 -0400 (EDT) Received: (from smelchor@localhost) by goliat.ugr.es (8.8.5/8.7.3) id MAA22069; Tue, 8 Apr 1997 12:47:58 +0200 (MET DST) Date: Tue, 8 Apr 1997 12:47:55 +0200 (MET DST) From: Santiago Melchor Ferrer To: Foro de Quimica computacional Subject: Gaussian: Helical symmetry and nanotubes Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: QUOTED-PRINTABLE =09Dear CCL-maniacs: =09A very simple question: Does Gaussian 94 recognizes helical symmetry? =09We are working with Carbon nanotubes that are easily described using helical symmetry operators (rotation and translation along the rotation axis), but these operators implies that the structure has an=20 infinite number of atoms, so I think that Gaussian doesn't support this,=20 but I suppose that ab-initio computational programs may use this symmetry t= o reduce the computing time. Any suggestions? =09I'm also wondering if there is anyone in the CCL list who works=20 in the field of Carbon nanotubes. If so, please tell me about your recent= =20 works and publications. I'll summarize. =09Thanks in advance. =09Santiago Melchor smelchor@goliat.ugr.es =09GRUPO DE MODELIZACION Y DISE=D1O MOLECULAR =20 =09Facultad de Ciencias. Universidad de Granada GRANADA SPAIN From vkitzing@sunny.mpimf-heidelberg.mpg.de Tue Apr 8 08:34:48 1997 Received: from otto.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-heidelberg.mpg.de by www.ccl.net (8.8.3/950822.1) id IAA09084; Tue, 8 Apr 1997 08:31:48 -0400 (EDT) Received: from sunny.mpimf-Heidelberg.mpg.de by otto.mpimf-heidelberg.mpg.de (4.1/SMI-4.1) id AA16569; Tue, 8 Apr 97 14:31:44 +0200 Received: from [149.217.50.47] (mac20) by sunny.mpimf-Heidelberg.mpg.de (4.1/SMI-4.1) id AA24272; Tue, 8 Apr 97 14:29:27 +0200 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 8 Apr 1997 13:28:31 +0100 To: Xose Manuel Valladares Pernas , chemistry@www.ccl.net From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) Subject: Re: CCL:Complex diagonalization At 11:38 Uhr 08.04.1997, Xose Manuel Valladares Pernas wrote: >Hello to everybody >We are looking for a efficient algorithm to make the diagonalization of a >complex matrix. We would prefer forttran language. If you know any >internet address please let we know. We will sumarize all the responses >if there is interest on it. >Thank you very much Have a look at: William H. Press, Saul A. Teukolsky, William T. Vetterling and Brian P. Fannery (1992). Numerical recipes in C. Cambridge, Cambridge University Press. There is also a FORTRAN version of this book. ====================================================================== Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29 D 69115 Heidelberg Germanny email: vkitzing@sunny.mpimf-heidelberg.mpg.de WWW: http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/Eberhard.html From ROBMARJ@msn.com Tue Apr 8 09:34:48 1997 Received: from upsmot03.msn.com for ROBMARJ@msn.com by www.ccl.net (8.8.3/950822.1) id IAA09665; Tue, 8 Apr 1997 08:56:21 -0400 (EDT) Received: from upmajb02.msn.com (upmajb02.msn.com [204.95.110.74]) by upsmot03.msn.com (8.6.8.1/Configuration 4) with SMTP id FAA10023 for ; Tue, 8 Apr 1997 05:50:37 -0700 Date: Tue, 8 Apr 97 12:57:03 UT From: "ROBERT NICHOLSON" Message-Id: To: chemistry@www.ccl.net Subject: dreiding models ANYBODY OUT THERE KNOW OF UK OR USA SUPPLIERS OR EUROPEAN SUPPLIERS OF DREIDING MODELS REGARDS DR ROBERT NICHOLSON From chpajt@bath.ac.uk Tue Apr 8 09:38:08 1997 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.8.3/950822.1) id IAA09607; Tue, 8 Apr 1997 08:50:00 -0400 (EDT) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Tue, 8 Apr 1997 13:39:38 +0100 Date: Tue, 8 Apr 1997 13:39:32 +0100 (BST) From: A J Turner To: Xose Manuel Valladares Pernas cc: chemistry@www.ccl.net Subject: Re: CCL:Complex diagonalization In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! Have a look at http://netlib.org Cheers Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@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 | ------------------------------------------------------------------- From kessi@psizi1.psi.ch Tue Apr 8 09:41:17 1997 Received: from psizi1.psi.ch for kessi@psizi1.psi.ch by www.ccl.net (8.8.3/950822.1) id IAA09624; Tue, 8 Apr 1997 08:51:09 -0400 (EDT) Received: by psizi1.psi.ch (AIX 4.1/UCB 5.64/4.03) id AA31410; Tue, 8 Apr 1997 14:50:24 +0200 Date: Tue, 8 Apr 1997 14:50:24 +0200 From: kessi@psizi1.psi.ch (Alain Kessi) Message-Id: <9704081250.AA31410@psizi1.psi.ch> To: genghis@darkwing.uoregon.edu, chemistry@www.ccl.net, schiffer@h1tw0036.hoechst.com Subject: Re: CCL:G:geometry optimization methods Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Md5: x+pChR0tWwHEQ31sp4SpuQ== Heinz Schiffer wrote: > Optimization with Z-matrix coordinates is always the worst that you > can do, next come cartesian coordinates, and the best are the natural > internal coordinates of Pulay. Cartesian coordinates are o.k. if you > have a good initial guess of the Hessian matrix (e.g. computed by > a less expensive method). See : Jon Baker, Techniques for Geometry > Optimization : A Comparison of Cartesian and Natural Internal > Coordinates, J. Comput. Chem. 14(9) (1993) 1085-1100. You may also want to have a look at our more recent paper Jon Baker, Alain Kessi and Bernard Delley, The generation and use of delocalized internal coordinates in geometry optimization, J. Chem. Phys. 105(1) (1996) 192-212. which shows some trends for much larger systems. Alain From berriz@chasma.harvard.edu Tue Apr 8 11:35:05 1997 Received: from chasma.harvard.edu for berriz@chasma.harvard.edu by www.ccl.net (8.8.3/950822.1) id LAA10740; Tue, 8 Apr 1997 11:17:36 -0400 (EDT) Received: by chasma.harvard.edu (AIX 3.2/UCB 5.64/4.03) id AA05837; Tue, 8 Apr 1997 11:15:58 -0400 Date: Tue, 8 Apr 1997 11:15:58 -0400 From: berriz@chasma.harvard.edu (Gabriel Berriz) Message-Id: <9704081515.AA05837@chasma.harvard.edu> To: chemistry@www.ccl.net In-Reply-To: (ROBMARJ@msn.com) Subject: Re: CCL:dreiding models Date: Tue, 8 Apr 97 12:57:03 UT From: "ROBERT NICHOLSON" ANYBODY OUT THERE KNOW OF UK OR USA SUPPLIERS OR EUROPEAN SUPPLIERS OF DREIDING MODELS What *are* Dreiding models? Gabriel Berriz berriz@chasma.harvard.edu Dept. of Chemistry and Chemical Biology Harvard University 12 Oxford St., Cambridge, MA 02138 USA From ramon@ce.ifisicam.unam.mx Tue Apr 8 11:52:34 1997 Received: from ce.ifisicam.unam.mx.ifisicam.unam.mx for ramon@ce.ifisicam.unam.mx by www.ccl.net (8.8.3/950822.1) id LAA10693; Tue, 8 Apr 1997 11:09:06 -0400 (EDT) Message-Id: <199704081509.LAA10693@www.ccl.net> Received: by ce.ifisicam.unam.mx (1.38.193.3/16.2) id AA29658; Tue, 8 Apr 97 10:09:05 -0500 From: Ramon Garduno Subject: Is SGI ORIGIN a parallel machine?. To: CHEMISTRY@www.ccl.net (CCL POST MSG) Date: Tue, 8 Apr 97 10:09:04 CDT Mailer: Elm [revision: 70.85] Dear CCLers: Our university computer center has just purchase a SGI ORIGIN with 40 array processors. Since we want to write our own parallel version of a program we have been using for years, we have been confronted with the question of whether this machine has its own Multiple Data/Multiple Instruction library routines. We have asked this to our computer gurus in the campus and nobody gives us a consistent answer. Some say we have to paste it a public domain library (no warranty of course), and some say that the SG Web site does not clearly say that these libraries are to be sold or provided by the company. We would like to use a well known and stablished set of MD/MI library instructions that will work under SG operating systems. Does any one outhere have more to say?. Any comments should be sent DIRECTLY to me in order to keep noise low. All help will be appreciated. Much obliged, -- ____________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA | EMAIL: ramon@ce.ifisicam.unam.mx UNIVERSIDAD NAL. AUTONOMA DE MEXICO | rgard@redvax1.dgsca.unam.mx Laboratorio de Cuernavaca | VOICE: (5)6227749 ; (73)291749 Apdo. Postal 48-3 | (73)111611 & 175388 62251 Cuernavaca, Morelos | FAX: (5)6227775 MEXICO | (73)173077 ___________________________________ EOF _____________________________________ From ps@ocisgi7.unizh.ch Tue Apr 8 12:28:50 1997 Received: from rzusuntk.unizh.ch for ps@ocisgi7.unizh.ch by www.ccl.net (8.8.3/950822.1) id KAA10363; Tue, 8 Apr 1997 10:36:47 -0400 (EDT) Received: from ocisgi7.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.14) id AA26269; Tue, 8 Apr 97 16:36:46 +0200 Received: by ocisgi7.unizh.ch (950215.SGI.8.6.10/920502.SGI) for CHEMISTRY@www.ccl.net id QAA07266; Tue, 8 Apr 1997 16:36:46 +0200 From: ps@ocisgi7.unizh.ch (Serge Pachkovsky) Message-Id: <199704081436.QAA07266@ocisgi7.unizh.ch> Subject: Re: CCL:Complex diagonalization To: CHEMISTRY@www.ccl.net Date: Tue, 8 Apr 1997 16:36:45 +0200 (MDT) In-Reply-To: from "Eberhard von Kitzing" at Apr 8, 97 01:28:31 pm X-Mailer: ELM [version 2.4 PL25] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit > Have a look at: > William H. Press, Saul A. Teukolsky, > William T. Vetterling and Brian P. Fannery (1992). > Numerical recipes in C. Cambridge, Cambridge University Press. > > There is also a FORTRAN version of this book. Numerical Recipes is undoubtedly a nice book, which serves as very nice introduction into the field. However, *programs* supplied with this book are not always as robust and hands-off as one would hope. Moreover, attaining best performance on widest possible range of architectures and input sizes is very far from trivial, and certainly goes beyond the scope of the book. Additionally, programs supplied with NR are bound by a rather nasty (IMHO) restrictions on their use and redistribution, which make them essentially useless unless your code is intended strictly for internal consumption (IMHO again - I am not a layer). In this particular case (complex diagonalization), LAPACK is a much better (again IMHO) alternative, which is public domain, highly efficient (and least for larger inputs), well tested (and comes with an extensive validation set) and extremely well documented. It may be a little awkward to install if you'd never done it before, but the chances are that a binary distribution for your particular platform would be already available. LAPACK is available at http://www.netlib.org/lapack GAMS (NIST Guide to Available Mathematical Software), which may be able to suggest other alternatives for you is available at http://gams.nist.gov/ Regards, /Serge.P P.S. Please do not consider this as an attack on Numerical Recipes - I had enjoyed reading the book very much indeed! From stephen_andruski@fmc.com Tue Apr 8 12:34:51 1997 Received: from igw.fmc.com for stephen_andruski@fmc.com by www.ccl.net (8.8.3/950822.1) id LAA10963; Tue, 8 Apr 1997 11:45:35 -0400 (EDT) Received: by igw.fmc.com id AA17390 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Tue, 8 Apr 1997 10:45:31 -0500 Message-Id: <199704081545.AA17390@igw.fmc.com> Received: by igw.fmc.com (Internal Mail Agent-1); Tue, 8 Apr 1997 10:45:31 -0500 Mime-Version: 1.0 Date: Tue, 8 Apr 1997 11:27:11 -0500 From: stephen_andruski@fmc.com (STEPHEN ANDRUSKI) Subject: Re:dreiding models To: chemistry@www.ccl.net Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part Aldrich sells Dreiding model sets of various sizes. Customer Service can be reached through Internet e-mail at: aldrich@sial.com. I also remember having a brochure from Brinkman about Dreiding models, but I can't seem to find it right now. Brinkman sells through a number of distributors such as VWR in the US so I would be surprised if you can't find a local source in the UK and other parts of Europe. Dr. Stephen W. Andruski FMC Corporation Princeton, NJ USA stephen_andruski@fmc.com From mckelvey@kodakr.kodak.com Tue Apr 8 12:49:05 1997 Received: from kodakr.kodak.com for mckelvey@kodakr.kodak.com by www.ccl.net (8.8.3/950822.1) id LAA10854; Tue, 8 Apr 1997 11:32:18 -0400 (EDT) Received: from mail.rl.kodak.com by kodakr.kodak.com with SMTP id AA15798 (5.67b/IDA-1.5 for ); Tue, 8 Apr 1997 11:28:00 -0400 Received: from mozart.rl.kodak.com by mail.rl.kodak.com (8.8.3/1.1.10.5/17Jan97-0515PM) id LAA24788; Tue, 8 Apr 1997 11:22:21 -0400 (EDT) Received: from stomper (stomper.rl.kodak.com [150.220.76.39]) by mozart.rl.kodak.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id LAA15608; Tue, 8 Apr 1997 11:13:51 -0400 Message-Id: <334A1AE2.5D0A@kodak.com> Date: Tue, 08 Apr 1997 11:16:02 +0100 From: John McKelvey Reply-To: mckelvey@kodakr.kodak.com Organization: Eastman Kodak Company X-Mailer: Mozilla 3.0 (WinNT; I) Mime-Version: 1.0 To: "Dr. Heinz Schiffer" Cc: Dale Andrew Braden , Computational Chemistry List Subject: Re: CCL:G:geometry optimization methods References: <3349F2E3.794B@h1tw0036.hoechst.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dr. Heinz Schiffer wrote: > > Dale Andrew Braden wrote: > > > > Dear CCL, > > > > A brief question: Are there any circumstances in which a geometry > > optimization in Cartesian coordinates would be *faster* than in redundant > > internal coordinates? > > > > The reason I am asking is because I am trying to optimize the geometry of > > a hydrogen-bonded dimer in a solvent medium using Gaussian 94, and the > > change in the two intermolecular Z-matrix coordinates (distance and angle) > > remains large for many, many iterations. The geometry isn't exactly > > oscillating between two structures, but it isn't settling down, either, > > and I thought that perhaps by changing the optimization method from > > redundant internal coordinates (the default method in G94) to cartesians, > > the optimization might proceed more smoothly to a converged minimum. I > > don't want to try this unless it can work, because the calculation is > > expensive. > > Hi Dale, > > Optimization with Z-matrix coordinates is always the worst that you > can do, next come cartesian coordinates, and the best are the natural > internal coordinates of Pulay. Cartesian coordinates are o.k. if you > have a good initial guess of the Hessian matrix (e.g. computed by > a less expensive method). See : Jon Baker, Techniques for Geometry > Optimization : A Comparison of Cartesian and Natural Internal > Coordinates, J. Comput. Chem. 14(9) (1993) 1085-1100. > > Ciao, > Heinz > > -- > Dr. Heinz Schiffer Phone ++49-69-305-2330 > Hoechst CR&T Fax ++49-69-305-81162 > Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com > 65926 Frankfurt am Main schiffer@msmwia.hoechst.com > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: schiffer@h1tw0036.hoechst.com > -- Original Sender From: Address: schiffer@h1tw0036.hoechst.com > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html I think I do not agree entirely with this. Localised sub units, such as rings whose relative torsion angles are uncertain pose challenging problems. A bad initial guess at the angle will make cartesians a bad choice, and a good Hessian won't help much. Then, either Z-matrices or redundant internals are FAR superior. If the torsion has a low barrier then the Hessian becomes very important. Torsion angles and all their characteristics are rampant in dyes, and we have to worry more about then than any other single geometry factor. Regards, John From chpajt@bath.ac.uk Tue Apr 8 12:49:32 1997 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.8.3/950822.1) id LAA11047; Tue, 8 Apr 1997 11:55:25 -0400 (EDT) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Tue, 8 Apr 1997 16:55:09 +0100 Date: Tue, 8 Apr 1997 16:55:01 +0100 (BST) From: A J Turner To: chemistry@www.ccl.net cc: G D Ruggiero , C F Rodriquez Subject: h2o + ch3cl Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! Has anyone found a transition state for this reaction in the GAS phase? specifically h2o + ch3cl -> h2och3+ + cl- Thanks for any help. Bets wishes Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@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 | ------------------------------------------------------------------- From elewars@alchemy.chem.utoronto.ca Tue Apr 8 13:07:58 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id MAA11337; Tue, 8 Apr 1997 12:30:50 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id MAA12779 for chemistry@www.ccl.net; Tue, 8 Apr 1997 12:30:06 -0400 (EDT) Date: Tue, 8 Apr 1997 12:30:06 -0400 (EDT) From: "E. Lewars" Message-Id: <199704081630.MAA12779@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: PM3 AND AM1 FOR H BONDS 1997 April 8 There was a recent question about AM1 vs. PM3 for studying hydrogen bonds. Dr J. J. P. Stewart, the inventor of PM3, tells me that he can't find a specific ref to this, but Shields has published on the superiority of PM3 in the last 3 years or so. Some other refs to PM3 cf. AM1 (I don't know offhand if any of these are on H bonding): 1) Extensive comparison: J Computer-Aided Molecular Design, 4 (1990) Issue 1 (Special issue) ; discusses PM3, AM1 and MNDO 2) W. Thiel, Tetrahedron, 44 (1988) 7393 3) J. J. P. Stewart, J Comp Chem 11 (1990) 543 10 (1989) 209 10 (1989) 221 12 (1991) 320 4) Dewar et al J Comp Chem 11 (1990) 541 5) Smith et al J Comp Chem 13 (1992) 640 6) In a letter to the Net (1995), Andy Holder (SemiChem) said: PM3 is better than AM1 for NO2 compounds and usually a little better for geom's. It is not as good for MO's and is unreliable for charges. ------------- If you try to optimize the water dimer with PM3, you get the right geom.; if you use AM1 you get the wrong one. See too "Experiments in Computational Organic Chemistry", by Hehre, Burke, Shusterman and Pietro (Wavefunction, 1993), p. 43, where PM3 is recommended for H-bonded molecules because, it is said, it works better than AM1. E. Lewars Chem Dept Trent U, Peterborough Ontario Canada ===== From raman@indigo1.biomol.uci.edu Tue Apr 8 14:34:52 1997 Received: from indigo1.biomol.uci.edu for raman@indigo1.biomol.uci.edu by www.ccl.net (8.8.3/950822.1) id NAA12021; Tue, 8 Apr 1997 13:50:35 -0400 (EDT) Received: by indigo1.biomol.uci.edu (8.8.5) id RAA10519; Tue, 8 Apr 1997 17:50:27 GMT From: CS Raman Message-Id: <199704081750.RAA10519@indigo1.biomol.uci.edu> Subject: Re: CCL:dreiding models To: ROBMARJ@msn.com (ROBERT NICHOLSON) Date: Tue, 8 Apr 1997 10:50:27 -0700 (PDT) Cc: chemistry@www.ccl.net In-Reply-To: from "ROBERT NICHOLSON" at Apr 8, 97 12:57:03 pm X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Robert: > ANYBODY OUT THERE KNOW OF UK OR USA SUPPLIERS OR EUROPEAN SUPPLIERS OF > DREIDING MODELS SIGMA Chem. Co., Check out their Technical Bulletin AL-199. Cheers -raman ___________________________________________________________________ C.S.Raman Tel: (714) 824-4322 University of California Fax: (714) 824-8540 Dept. MB & B email: raman@indigo1.biomol.uci.edu 3205 Bio Sci II Irvine, CA 92697-3900 ------------------------------------------------------------------- If we really understand the problem, the answer will come out of it, because the answer is not separate from the problem. - J.Krishnamurti ___________________________________________________________________ From gadre@chem.unipune.ernet.in Fri Apr 4 06:33:54 1997 Received: from sangam.ncst.ernet.in for gadre@chem.unipune.ernet.in by www.ccl.net (8.8.3/950822.1) id GAA08482; Fri, 4 Apr 1997 06:17:41 -0500 (EST) Received: from iucaa (iucaa.ernet.in [144.16.31.4]) by sangam.ncst.ernet.in (8.7.5) with SMTP id QAA22208 for ; Fri, 4 Apr 1997 16:52:11 +0530 (GMT+05:30) Received: from unipune.ernet.in by iucaa (5.65v3.2/SMI-4.1) id AA32542; Fri, 4 Apr 1997 16:43:37 +0500 Received: from chem.unipune.ernet.in by unipune.ernet.in (8.8.5/UNIPUNE-HUB-2.4.97) id QAA04717; Fri, 4 Apr 1997 16:44:01 -0500 (GMT) Received: by chem.unipune.ernet.in (8.7.5/SMI-SVR4) id QAA07597; Fri, 4 Apr 1997 16:55:55 -0500 Date: Fri, 4 Apr 1997 16:55:55 -0500 From: gadre@chem.unipune.ernet.in (Prof. Shridhar R. Gadre) Message-Id: <199704042155.QAA07597@chem.unipune.ernet.in> To: CHEMISTRY@www.ccl.net Subject: XII ICCCRE XII International Conference on Computers in Chemical Research and Eduction First Annoucement The Twelfth International Conference on Computers in Chemical Research and Education (ICCCRE XII) will be held at the University of Pune in Pune, India, in the week of 5-10 January 1998. Pune is one of the premier centers of learning in India, located about 100 miles south of Mumbai (Bombay). The purpose of the ICCCRE is to present a sweeping and state-of-the-art description and critical examination of the applications of computers in chemistry presented by outstanding computational chemists. The program will be organized such that all interested parties can experience a broad range of topics. There will be ample opportunities for small group and one-on-one discussions. In particular, it is our endeavour that the program will especially cater to the needs of junior faculty, researchers, and students who are just starting out in the field. In addition, those based in other disciplines, whose work overlaps with computers applied in chemistry, will be exposed to authoritative treatments of computers in chemistry and related disciplines. Tentatively, the technical program will focus on the following topics : (1) Computers in Chemical Education (2) Electronic Journals, Publishing and Conferencing (3) Artificial Intelligence, Chemometrics, Neural Networks and their Chemical Application. (4) Molecular Modeling, Quantitative Structure-Activity Relationship (QSAR). (5) Semi-Empirical and Ab initio Quantum Chemistry, Density Functional Methods. (6) New Algorithms and Techniques in Computational Chemistry Under consideration is the possibility of pre-conference sharing of invited/contributed papers via electronic conferencing (a new feature of the ICCCRE). Given the rich and varied history and cultural attractions of India, the organizers hope to arrange pre-and/or post-conference excursions of varying duration. Programmatic suggestions and nominations for speakers are encouraged and are indeed very welcome. Please send your comments and/or let us know whether you would like to have your name and address added to the distribution list for further information via one of the following channels : (1) Official Mailing Address : ICCCRE XII c/o Professor Shridhar R. Gadre Department of Chemistry, University of Pune Pune - 411 007. INDIA e-mail : gadre@unipune.ernet.in Phone and Fax : 91-212-351728 (2) Facilitators working with Professor S.R. Gadre : Professor Peter Lykos Professor Rama Viswanathan Illinois Inst. of Technology Beloit College Chicago IL 60616. U.S.A. Beloit, WI 53511. U.S.A. 1-312-567-3430 1-608-363-2273 lykos@charlie.cns.iit.edu ramav@beloit.edu We will appreciate your comments/suggestions, please help us to publicize ICCCRE XII by forwarding and/or posting this announcement on bulletin boards, L-servs, WWW sites. newsletters, society publications and calendars and your own distribution lists. The details regarding this conference can be found at the web page : http://www.beloit.edu/~chem/ICCCCRE.html. Response Sheet XII ICCCRE Please mail to Professor Shridhar R. Gadre Department of Chemistry University of Pune Pune - 411 007 INDIA Fax : 91-212-351728 e-mail : gadre@chem.unipune.ernet.in 1. I will be interested in attending XII ICCCRE in Pune (January 5-10, 1998). 2. I plan to present A paper Yes/No A poster Yes/No 3. I/My Company would like to sponsor a Session/Satelite Meeting. Yes/No Details : ______________________________________________________ ________________________________________________________________ ________________________________________________________________ ________________________________________________________________ 4. Any Other Remarks/Suggestions _________________________________________________________________ _________________________________________________________________ _________________________________________________________________ _________________________________________________________________ Please write your complete name and institutional address _________________________________________________________________ _________________________________________________________________ _________________________________________________________________ _________________________________________________________________ Fax : e-mail Phone : From youngd2@mallard.duc.auburn.edu Fri Apr 4 09:37:04 1997 Received: from mallard.duc.auburn.edu for youngd2@mallard.duc.auburn.edu by www.ccl.net (8.8.3/950822.1) id IAA09465; Fri, 4 Apr 1997 08:51:46 -0500 (EST) Received: from wood.mail.auburn.edu by mallard.duc.auburn.edu (SMI-8.6/SMI-SVR4) id HAA16433; Fri, 4 Apr 1997 07:51:45 -0600 Received: by wood.mail.auburn.edu (SMI-8.6/SMI-SVR4) id HAA15120; Fri, 4 Apr 1997 07:51:43 -0600 Date: Fri, 4 Apr 1997 07:51:43 -0600 From: youngd2@mail.auburn.edu Message-Id: <199704041351.HAA15120@wood.mail.auburn.edu> To: CHEMISTRY@www.ccl.net Subject: Chem Topic: Spin Contamination Hello all, I have written the following short essay for my users and am posting it here for your enjoyment and comments. Please let me know if I missed any important points. My compilation of chemical topics can be accessed via the web at URL http://www.auburn.edu/~youngd2/topics/contents.html Dave Young youngd2@mail.auburn.edu --------------------------------------------------------------------------- Spin Contamination David Young Division of University Computing 144 Parker Hall Auburn University Auburn, AL 36849 WHAT IS SPIN CONTAMINATION Introductory descriptions of Hartree-Fock calculations (usually using Rootaan's SCF method) focus on singlet systems for which all electron spins are paired. By assuming that the calculations is restricted to having two electrons per occupied orbital, the computation can be done relatively easily. This is often referred to as a restricted calculation or RHF. For systems with a multiplicity other than one, it is not possible to use the RHF method as is. Often an unrestricted SCF calculation (UHF) is performed. In an unrestricted calculation, there are two complete sets of orbitals, one for the alpha electrons and one for the beta electrons. Usually these two sets of orbitals use the same set of basis functions but different molecular orbital coefficients. The advantage of unrestricted calculations is that they can be performed very efficiently. The disadvantage is that the wave function is no longer an eigenfunction of the total spin, , thus some error may be introduced into the calculation. This error is called spin contamination. HOW DOES SPIN CONTAMINATION AFFECT RESULTS Spin contamination results in having orbitals which appear to be the desired spin state, but have a bit of some other spin state mixed in. This results in slightly lowering the computed total energy. However, this lowering is an artifact of an incorrect wave function. Since this is not a systematic error, the difference in energy between states will be adversely affected. A high spin contamination can affect the geometry and population analysis and significantly affect the spin density. As a check for the presence of spin contamination, most ab initio programs will print out the expectation value of the total spin, . If there is no spin contamination this should equal s(s+1) where s equals 1/2 times the number of unpaired electrons. One rule of thumb which was derived from experience with organic molecule calculations is that the spin contamination is negligible if the value of differs from s(s+1) by less than 10%. Although this provides a quick test, it is always advisable to double check the results against experimental evidence or more rigorous calculations. Unrestricted calculations often incorporate a spin annihilation step which removes a large percentage of the spin contamination from the wave function at some point in the calculation. This helps minimize spin contamination but does not completely prevent it. The final value of is always the best check on the amount of spin contamination present. In Gaussian, the option "iop(6/15=2)" tells the program to use the annihilated wave function to produce the population analysis. I am not aware of any programs that use the annihilated wave function to perform the geometry optimization. RESTRICTED OPEN SHELL CALCULATIONS It is possible to run spin-restricted open shell calculations (ROHF). The advantage of this is that there is no spin contamination. The disadvantage is that there is an additional cost in the form of CPU time required in order to correctly handle both singly occupied and doubly occupied orbitals and the interaction between them. As a result of the mathematical method used, ROHF calculations give good total energies and wave functions but the singly occupied orbital energies don't rigorously obey Koopman's theorem. When it has been shown that the errors introduced by spin contamination are unacceptable, restricted open shell calculations are the best way to get a reliable wave function. Within the Gaussian program, restricted open shell calculations can be performed for Hartree-Fock, density functional theory, MP2 and some semiempirical wave functions. The ROMP2 method does not yet support analytic gradients, thus the fastest way to run the calculation is as a single point energy calculation with a geometry from another method. If a geometry optimization must be done at this level of theory, a non-gradient based method such as the Fletcher-Powell optimization must be used (note that the G94 manual implies that this may not still be functional for all cases). SPIN PROJECTION METHODS Another approach is to run an unrestricted calculation then project out the spin contamination after the wave function has been obtained (PUHF, PMP2). This gives a correction to the energy, but does not improve other properties. A spin projected result does not give the energy obtained by using a restricted open shell calculation. This is because the unrestricted orbitals were optimized to describe the contaminated state rather than being optimized to describe the spin projected state. HALF-ELECTRON APPROXIMATION Semiempirical programs often use the half electron approximation for radical calculations. The half electron method is a mathematical technique for treating a singly occupied orbital in an RHF calculation. This results in a consistent total energy at the expense of having an approximate wave function and orbital energies. Since a single determinant calculation is used, there is no spin contamination. The consistent total energy makes it possible to compute singlet-triplet gaps using RHF for the singlet and the half electron calculation for the triplet. Koopman's theorem is not obeyed for half electron calculations. Also, no spin densities can be obtained. The Mulliken population analysis is usually fairly reasonable. FURTHER INFORMATION Some discussion and results are in W. J. Hehre, L. Radom, P. v.R. Schleyer, J. A. Pople "Ab Initio Molecular Orbital Theory" Wiley (1986) An article that compares unrestricted, restricted and projected results is M. W. Wong, L. Radom J. Phys. Chem. 99, 8582 (1995) Some specific examples and a discussion of the half electron method are given in T. Clark "A Handbook of Computational Chemistry" Wiley (1985) A more mathematical treatment can be found in the paper J. S. Andrews, D. Jayatilake, R. G. A. Bone, N. C. Handy, R. D. Amos Chem. Phys. Lett. 183, 423 (1991) --------------------------------------------------------------------------- From ccl@www.ccl.net Fri Apr 4 11:34:03 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id LAA11233; Fri, 4 Apr 1997 11:31:29 -0500 (EST) Received: from theory.tc.cornell.edu for kshippos@tc.cornell.edu by bedrock.ccl.net (8.8.3/950822.1) id LAA10560; Fri, 4 Apr 1997 11:31:26 -0500 (EST) Received: from [128.84.51.45] (FIREFLY.TC.CORNELL.EDU [128.84.51.45]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with ESMTP id LAA04709; Fri, 4 Apr 1997 11:28:25 -0500 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 4 Apr 1997 11:28:24 -0500 To: Recipient List Suppressed:;@ccl.net From: kshippos@TC.Cornell.EDU (Kathy Shippos) Subject: Virtual Workshop --Using Scientific Visualization offered by CTC Cornell Theory Center CTC Virtual Workshop Using Scientific Visualization June 2-27, 1997 Registration deadline: May 1, 1997 Cornell Theory Center (CTC) has expanded its successful Virtual Workshop (VW) series to include visualization. This four week workshop introduces concepts of scientific visualization and shows how to visualize four general categories of data. Hands on examples use IBM's Data Explorer (DX). The VW allows you to learn new concepts in high performance computing and visualization at your own pace from your own machine. Details and registration can be found at: http://www.tc.cornell.edu/Edu/VW/Viz97 Kathy Shippos Conference Assistant Cornell Theory Center Cornell University Ithaca, NY 14853 kshippos@tc.cornell.edu (607) 254-8640 From harvey@www.chem.tu-berlin.de Mon Apr 7 13:34:37 1997 Received: from www.chem.TU-Berlin.DE for harvey@www.chem.tu-berlin.de by www.ccl.net (8.8.3/950822.1) id NAA03146; Mon, 7 Apr 1997 13:30:40 -0400 (EDT) Received: from ioc42 (unverified [130.149.42.3]) by www.chem.TU-Berlin.DE (EMWAC SMTPRS 0.83) with SMTP id ; Mon, 07 Apr 1997 19:30:40 +0200 Message-Id: <1.5.4.32.19970407172934.0090bcb4@www.chem.tu-berlin.de> X-Sender: harvey@www.chem.tu-berlin.de X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 07 Apr 1997 19:29:34 +0200 To: chemistry@www.ccl.net From: Jeremy Harvey Subject: drawings Dear CCL subscribers, I am looking for a free, simple, programme which generates 3D ball-and-stick pictures of small molecules (< 30 atoms), suitable for publication, starting from, e.g. Gaussian Output files or XMol xyz cartesian coordinate files. Possible corresponding OSs are Windows NT (much preferred) or XWindows/UNIX. The ouput should be in bitmap or (even better) vectorized form of some sort. I know the Raswin/Rasmol program, but somehow it doesn't seem to be possible to get the sort of picture I want. I also searched the web quite extensively for something suitable, again without success. In the literature, everyone seems to have nice pictures so they must come from somewhere !!?! Many thanks, especially to anyone who can suggest a good solution. Jeremy Dr. Jeremy N. Harvey Technische Universitaet Berlin Institut fur Organische Chemie Sekretariat C4 Strasse des 17. Juni, 135 D-10623 BERLIN Tel. (49) 030 314 26546 Fax. (49) 030 314 21102 harvey@www.chem.tu-berlin.de From daizadeh@indigo.ucdavis.edu Tue Apr 8 16:34:56 1997 Received: from indigo.ucdavis.edu for daizadeh@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id PAA12914; Tue, 8 Apr 1997 15:44:03 -0400 (EDT) Received: by indigo.ucdavis.edu (940816.SGI.8.6.9/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id MAA18271; Tue, 8 Apr 1997 12:50:40 -0700 From: "Iraj Daizadeh" Message-Id: <9704081250.ZM18269@indigo.ucdavis.edu> Date: Tue, 8 Apr 1997 12:50:28 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Dreiding Models Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. Distributers for Dreiding models are probably MSI. We are currently using a program called BIOGRAF written by Prof. Goddard at Cal. Tech. Therein, there exist many Dreiding Force Fields, etc... I think the rights for this program have been transferred to MSI (now BIOSYM/MSI). Iraj Daizadeh Department of Chemistry University of California, Davis, CA 95616 From rvenable@deimos.cber.nih.gov Tue Apr 8 16:51:54 1997 Received: from deimos.cber.nih.gov for rvenable@deimos.cber.nih.gov by www.ccl.net (8.8.3/950822.1) id QAA13160; Tue, 8 Apr 1997 16:04:02 -0400 (EDT) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA285449137; Tue, 8 Apr 1997 15:52:17 -0400 Date: Tue, 8 Apr 1997 15:52:17 -0400 (EDT) From: Rick Venable To: Eberhard von Kitzing Cc: Xose Manuel Valladares Pernas , chemistry@www.ccl.net Subject: Re: CCL:Complex diagonalization In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > At 11:38 Uhr 08.04.1997, Xose Manuel Valladares Pernas wrote: > >Hello to everybody > >We are looking for a efficient algorithm to make the diagonalization of a > >complex matrix. We would prefer forttran language. If you know any > >internet address please let we know. We will sumarize all the responses > >if there is interest on it. > >Thank you very much On Tue, 8 Apr 1997, Eberhard von Kitzing wrote: > Have a look at: > William H. Press, Saul A. Teukolsky, > William T. Vetterling and Brian P. Fannery (1992). > Numerical recipes in C. Cambridge, Cambridge University Press. > > There is also a FORTRAN version of this book. Have a look, but get your code from NETLIB (www.netlib.org) if performance or rights to the code are issues. Note that NR code is *copyrighted* (NETLIB is public domain) and you are obligated to buy the book if you use any of the code. Redistribution of NR code also requires royalty payments to the authors. I replaced Numerical Recipes routines with their NETLIB equivalents (matrix diag, matrix inv, etc.) and observed a ca. 50-fold performance increase. Part of this was due to the easy integration of the workstation vendor's BLAS library into the NETLIB code, of course. The NR book is good and provides many valuable explanations, but the code has "strings" attached, and isn't the best available. Also, be sure to get the second edition; there are a few bugs in the code published in the first edition. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov ) From jdurant@mephisto.ca.sandia.gov Tue Apr 8 18:34:54 1997 Received: from mephisto.ca.sandia.gov for jdurant@mephisto.ca.sandia.gov by www.ccl.net (8.8.3/950822.1) id RAA14382; Tue, 8 Apr 1997 17:47:22 -0400 (EDT) Received: by mephisto.ca.sandia.gov (950413.SGI.8.6.12/890607.SGI) (for chemistry@www.ccl.net) id VAA03209; Tue, 8 Apr 1997 21:46:43 GMT From: jdurant@mephisto.ca.sandia.gov (Joe Durant) Message-Id: <199704082146.VAA03209@mephisto.ca.sandia.gov> Subject: DGauss basis set To: chemistry@www.ccl.net Date: Tue, 8 Apr 1997 14:46:43 -0700 (PDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi! A while back the DGauss DFT-optimized basis sets were posted... are they still using Cartesian D functions, or pure D functions? Joe -- #################################################################### # Joe Durant voice: (510) 294-3343 # # Mail Stop 9057 FAX: (510) 294-2276 # # Sandia National Laboratories jdurant@ca.sandia.gov # # Livermore, CA 94551 http://mephisto.ca.sandia.gov # #################################################################### From renate_griffith@uow.edu.au Tue Apr 8 19:34:55 1997 Received: from wyrm.its.uow.edu.au for renate_griffith@uow.edu.au by www.ccl.net (8.8.3/950822.1) id TAA15289; Tue, 8 Apr 1997 19:10:55 -0400 (EDT) Received: from [130.130.56.113] (chem-pc13.sci.uow.edu.au [130.130.56.113]) by wyrm.its.uow.edu.au (8.8.5/8.8.5) with SMTP id JAA17598 for ; Wed, 9 Apr 1997 09:10:52 +1000 (EST) X-Sender: renate@pop.uow.edu.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 9 Apr 1997 10:12:06 +1000 To: CHEMISTRY@www.ccl.net From: renate_griffith@uow.edu.au (Renate Griffith) Subject: GRID ? Dear computational chemists, does anybody know what happened to GRID? We wanted to obtain the latest version of this nice and well-used little package and have been told that GRID is not supported in Australia any more????? What can we do (yes, I know, if we just reset the clock, we can keep using our old version, but that really isn't the done thing, is it...)? All else failing, does anybody know of any (preferably free) replacement? Regards Renate Dr. Renate Griffith Email: renate_griffith.uow.edu.au Department of Chemistry phone: +61 42 213516 University of Wollongong fax: +61 42 214287 Northfields Ave Wollongong NSW 2522 Australia From ahocquet@tamarugo.cec.uchile.cl Tue Apr 8 22:34:56 1997 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.3/950822.1) id WAA15742; Tue, 8 Apr 1997 22:15:17 -0400 (EDT) Received: from [146.83.10.18] by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA07244; Tue, 8 Apr 1997 22:15:11 +0400 Date: Tue, 8 Apr 1997 22:15:11 +0400 Message-Id: <9704090215.AA07244@tamarugo.cec.uchile.cl> X-Sender: ahocquet@tamarugo.cec.uchile.cl X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Alexandre Hocquet Subject: Re: CCL:Dreiding Models I guess we are talking about two different things, here. - DREIDING (capital letters ?) is an empirical force field, ie a set of equations and parameters designed to perform molecular mechanics calculations (Mayo et al. J.Phys.Chem., 1990, 94, 8897-8909). Its ambition is to provide reasonable results with a minimum of general parameters, within the entire periodic table. - Dreiding models are physical metallic molecular models. Compared to plastic models (like Cochranes) they provide no choice for L0 in the stretching term and the bending Ktheta are nearly infinite (the only way you can twist them is by a torsional term). On the other hand, the Vn terms for torsion are very low (rotation around bonds are free) while you can count on friction to fix the molecule into a conformation in Cochranes. For example, Dreiding models are very useful for the 1,4-cyclohexadiene trick, because they spectacularly fail to find a planar minimum, whereas Cochranes can be forced on a planar structure simply because plastic atoms allow a light bend deformation and metallic ones do not. Does the DREIDING force field corrrectly predict a boatlike conformation ? I suppose so. Alexandre Hocquet Laboratorio de Cristalografia Facultad de Ciencias Fisicas Universidad de Chile Blanco Encalada, 2008 Santiago Centro Chile fono : 56 2 678 45 19 fax : 56 2 696 73 59 email : ahocquet@cec.uchile.cl