From tank@pixie.udw.ac.za Tue Jan 28 02:19:18 1997 Received: from pixie.udw.ac.za for tank@pixie.udw.ac.za by www.ccl.net (8.8.3/950822.1) id CAA18824; Tue, 28 Jan 1997 02:09:53 -0500 (EST) Received: by pixie.udw.ac.za (Smail3.1.28.1 #1) id m0vp7ao-0003JYC; Tue, 28 Jan 97 09:04 SST Date: Tue, 28 Jan 1997 09:04:30 +0200 (SST) From: Tankiso Tshehla X-Sender: tank@pixie.udw.ac.za. To: chemistry@www.ccl.net Subject: disconnect In-Reply-To: <199701271452.PAA37020@crisv3.univ-pau.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello; please disconnect me from the ccl list. I will re-apply once I have got a new email address Thanks T.M. Tshehla From tank@pixie.udw.ac.za Tue Jan 28 02:30:08 1997 Received: from pixie.udw.ac.za for tank@pixie.udw.ac.za by www.ccl.net (8.8.3/950822.1) id CAA18816; Tue, 28 Jan 1997 02:07:45 -0500 (EST) Received: by pixie.udw.ac.za (Smail3.1.28.1 #1) id m0vp7Ys-0003JfC; Tue, 28 Jan 97 09:02 SST Date: Tue, 28 Jan 1997 09:02:29 +0200 (SST) From: Tankiso Tshehla X-Sender: tank@pixie.udw.ac.za. To: chemistry@www.ccl.net Subject: disconnect Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi; please disconnect me from the chemistry list for a while. I will re-apply once I have a new email address. Thanks Dr Tshehla T.M. From Francois.Baert@univ-lille1.fr Tue Jan 28 03:22:46 1997 Received: from lilserv.univ-lille1.fr for Francois.Baert@univ-lille1.fr by www.ccl.net (8.8.3/950822.1) id DAA19745; Tue, 28 Jan 1997 03:06:36 -0500 (EST) From: Received: from lip5rx.univ-lille1.fr (lip5rx.univ-lille1.fr [134.206.58.11]) by lilserv.univ-lille1.fr (8.7.6/jtpda-5.1) with SMTP id JAA00773 ; Tue, 28 Jan 1997 09:10:15 +0100 (MET) Received: by lip5rx.univ-lille1.fr; id AA08607; Tue, 28 Jan 1997 09:06:07 +0100 Message-Id: <9701280806.AA08607@lip5rx.univ-lille1.fr> To: chemistry@www.ccl.net Cc: Francois.Baert@univ-lille1.fr Subject: Mopac6 transition dipole moments Date: Tue, 28 Jan 97 09:06:07 +0100 X-Mts: smtp Dear CCL members, My problems concern the calculation of Transition Dipole Moments with MOPAC6. (received in May 1993 from QCPE) 1- Are Transition dipole moments calculated in this version ?. 2- If yes, is there a keyword to get directly the outputs ?. 3- If there are calculated in some modules I would be very glad to know them in order to do the necessary modifications. All my thanks. ############################################################################### Dr.Francois BAERT Physique Fondamentale, Bat. P5 Universite de Lille I 59655 VILLENEUVE D'ASCQ CEDEX FRANCE e-mail: Francois.Baert@univ-Lille1.fr ############################################################################### From Jeffrey.Gosper@brunel.ac.uk Tue Jan 28 03:36:23 1997 Received: from ceres.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id DAA19651; Tue, 28 Jan 1997 03:03:39 -0500 (EST) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by ceres.brunel.ac.uk with SMTP (PP); Tue, 28 Jan 1997 08:03:35 +0000 Date: Tue, 28 Jan 1997 08:03:34 GMT From: Jeffrey J Gosper Subject: PES and structure software To: CHEMISTRY@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear all, I am interested in locating software pacakges (both free and commerical) that provide a facility for displaying potential energy surfaces (probably as contour maps) and link these to chemical structures. That is, the software must included the ability to pick/locate points on the potential energy surface and display the structures associated with these points. I am aware that GridView and CAChe are able to this but what about SPARTAN or other programs. Any information would be greatly appreciated. /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://www.brunel.ac.uk/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://www.brunel.ac.uk/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From rozas@pinar1.csic.es Tue Jan 28 04:19:22 1997 Received: from pinar.csic.es for rozas@pinar1.csic.es by www.ccl.net (8.8.3/950822.1) id DAA20059; Tue, 28 Jan 1997 03:56:35 -0500 (EST) Received: from pinar.csic.es by pinarvms.csic.es (PMDF V5.1-4 #13290) id <01IEQQKNA2VK009AO7@pinarvms.csic.es> for chemistry@www.ccl.net; Tue, 28 Jan 1997 09:58:51 CE X400-Received: by /PRMD=iris/ADMD=mensatex/C=es/; Relayed; Tue, 28 Jan 1997 09:55:09 +0000 Date: Tue, 28 Jan 1997 09:55:09 +0000 From: Isabel Rozas Subject: thanks To: chemistry@www.ccl.net Message-id: <613*rozas@pinar1.csic.es> Content-identifier: 613 MIME-version: 1.0 (Generated by Ean X.400 to MIME gateway) X400-Content-type: P2-1984 (2) X400-MTS-identifier: [/PRMD=iris/ADMD=mensatex/C=es/;970128095509] X400-Originator: rozas@pinar1.csic.es X400-Recipients: non-disclosure:; Hello, Thanks a lot to everybody who sent an answer to my request about x-windows and nmr software, it has been a lot of help, thanks. Isabel Rozas From peon@medchem.dfh.dk Tue Jan 28 05:19:22 1997 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.8.3/950822.1) id EAA20227; Tue, 28 Jan 1997 04:38:22 -0500 (EST) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.7.5/8.6) with SMTP id KAA29633 for <@danpost.uni-c.dk:CHEMISTRY@www.ccl.net>; Tue, 28 Jan 1997 10:38:22 +0100 (MET) Received: from [130.225.177.59] (compmac2 [130.225.177.59]) by medchem.dfh.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id KAA05878 for ; Tue, 28 Jan 1997 10:51:40 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 28 Jan 1997 10:38:24 +0100 To: CHEMISTRY@www.ccl.net From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:PES and structure software Jeff Gosper wrote: >I am interested in locating software pacakges (both free and >commerical) that provide a facility for displaying potential energy >surfaces (probably as contour maps) and link these to chemical structures. >That is, the software must included the ability to pick/locate points on >the potential energy surface and display the structures associated with >these points. > >I am aware that GridView and CAChe are able to this but what about SPARTAN >or other programs. Any information would be greatly appreciated. Jeff, MacroModel can do something like this for 1D and 2D dihedral drivers. It's not perfect though, the structure displayed when you click at the map is not the actual calculated structure, but is just rotated to the corresponding dihedral angles. Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From Patrick.Bultinck@rug.ac.be Tue Jan 28 05:24:07 1997 Received: from infoserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.8.3/950822.1) id EAA20287; Tue, 28 Jan 1997 04:50:10 -0500 (EST) Received: from hartree1.rug.ac.be by infoserv.rug.ac.be with SMTP id AA02928 (5.67b/IDA-1.5 for ); Tue, 28 Jan 1997 10:48:50 +0100 Received: by hartree1.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA08096; Tue, 28 Jan 1997 17:47:27 +0100 Date: Tue, 28 Jan 1997 17:47:27 +0100 (NFT) From: Patrick Bultinck To: CCL Subject: Failing optimization (1 imag. freq) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, Could somebody inform me on their tips and tricks to optimize a structure towards a minimum. I have optimized a system containing two NH3 ligands and an alkaline metal ion center, but when calculating the hessian I found that there still is one imaginary freq. in the vibrational analysis. I turned of the C2v or Cs symmetries (I have two initial geometries) and re-optimized to again reach the saddle point. I used my bag of tricks but had no luck. In previous articles in JPC these structures were used for bonding analysis stating that ' these are probably transition states with respect to M-NH3 rotation, but barriers are expected to be negligible'. Can anybody tell me how they go about finding a minimum when they started >from something they optimized but has 1 or more neg. eigenfunctions of the hessian. I have the displacement coordinates of the freqs. Thanks a lot, ***************************************************************************** Patrick Bultinck Macrocycles Quantum Chemical Ph. D. Student Calculations Dept. Inorganic & Physical Chemistry University of Ghent Tel. Int'l code/32/9/264.44.44 Krijgslaan 281 (S-3) Fax. Int'l code/32/9/264.49.83 9000 Gent E-mail : Patrick.Bultinck@rug.ac.be Belgium http://allserv.rug.ac.be/~pbultink/ ***************************************************************************** From peon@medchem.dfh.dk Tue Jan 28 05:27:33 1997 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.8.3/950822.1) id EAA20215; Tue, 28 Jan 1997 04:35:44 -0500 (EST) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.7.5/8.6) with SMTP id KAA29357 for <@danpost.uni-c.dk:CHEMISTRY@www.ccl.net>; Tue, 28 Jan 1997 10:35:44 +0100 (MET) Received: from [130.225.177.59] (compmac2 [130.225.177.59]) by medchem.dfh.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id KAA05866 for ; Tue, 28 Jan 1997 10:49:02 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 28 Jan 1997 10:35:46 +0100 To: CHEMISTRY@www.ccl.net From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:(2) basis set balance continued Douglas A. Smith wrote: >OK, so the real issue is BSSE and basis set flexibility for describing the >space available to all electrons. For the latter, would the use of CI or >multi-reference-CI help alleviate the problem? Would that be a more >expensive cure than using a balanced basis? Don't! Two reasons: first, adding correlation is usually more expensive than adding basis, and second, it doesn't alleviate the problem! Correlation tends to "spread the electrons" more efficiently among the existing basis functions, but it cannot do anything about basis set deficiencies. In fact, correlated methods are MORE susceptible than HF to deficiencies in the basis (see, for example, the article by Scheiner in Rev. Comp. Chem., Vol 2, Chapter 5). That's part of why you should have H-polarization when doing MP2. A caveat though: I don't know the situation for DFT methods, I've got a feeling from my own work that, for example, B3LYP results aren't very much improved when going from 6-31G* to 6-311G**. >What, then, happens when one is performing calculations on systems >containing both very heavy atoms and very light atoms, let's say, a >lanthanide and hydrogen? If one uses an all electron basis for both atoms, >isn't the basis set unbalanced? You don't have to go that far. Even LiF is supposed to be pretty unbalanced with small basis sets. On the other hand, I assume you don't really need the absolute energy of LaH to several decimal places? With some experimentation, you should be able to find a combination of basis sets that reproduces some significant experimental fact you're interested in, then you can go on from there. Since we are living in a virtual world of finite basis sets, experimental verification is VERY important as soon as you go into a new field. >Is this at least part of the reason for >effective core potentials (ECPs) -- in addition to the problem of just >handling all the electrons in a reasonable time at reasonable cost? No, not really. The ECP replaces the core, which doesn't contribute significantly to BSSE. There are other very good reasons for using ECPs though, the savings and the cheap way to get SOME relativistic effects for the core electrons (especially important in the 2nd and 3rd transition metal row). Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From Patrick.Bultinck@rug.ac.be Tue Jan 28 09:19:24 1997 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.8.3/950822.1) id JAA21694; Tue, 28 Jan 1997 09:01:42 -0500 (EST) Received: from hartree1.rug.ac.be by mserv.rug.ac.be with SMTP id AA09319 (5.67b/IDA-1.5 for ); Tue, 28 Jan 1997 15:01:20 +0100 Received: by hartree1.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA08546; Tue, 28 Jan 1997 22:00:10 +0100 Date: Tue, 28 Jan 1997 22:00:09 +0100 (NFT) From: Patrick Bultinck To: CCL Subject: More details on Failing optimization (1 imag. freq) In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: QUOTED-PRINTABLE A suprisingly high number of people have already mailed me back, some=20 wanting more details on the calculations. Here they are : 1/ Software : I have access to G94, GAMESS(US) and CADPAC 6 2/ I have used GAMESS (my main platform) thusfar. 3/ I first optimized with initial guess hessian, using BFGS updating. I als= o tried the optimizations with calculated initial hessians, with no luck. 4/ Hessians are calculated numerically (I use ECP's which means numer.=20 hessians). 5/ I tried the tricks with DXMAX etc. in GAMESS. 6/ The magnitude of the imaginary freq. is about 55 cm-1. Hope this is enough, and thanks to all for helping me out. The problems have to do with alkaline and alkaline-earth metal ions in=20 complexes with e.g. two NH3 ligands. These form 'strange' geometries=20 where the NMN angle (M=3Dmetal ion) is not 180 but something like 125=B0. ***************************************************************************= ** Patrick Bultinck=09=09=09Macrocycles Quantum Chemical Ph. D. Student=09=09=09=09Calculations Dept. Inorganic & Physical Chemistry=20 University of Ghent=09=09=09Tel. Int'l code/32/9/264.44.44 Krijgslaan 281 (S-3)=09=09=09Fax. Int'l code/32/9/264.49.83 9000 Gent=09=09=09=09E-mail : Patrick.Bultinck@rug.ac.be Belgium=09=09=09=09=09http://allserv.rug.ac.be/~pbultink/ ***************************************************************************= ** From kessi@psizi1.psi.ch Tue Jan 28 10:19:37 1997 Received: from psizi1.psi.ch for kessi@psizi1.psi.ch by www.ccl.net (8.8.3/950822.1) id KAA22211; Tue, 28 Jan 1997 10:06:36 -0500 (EST) Received: by psizi1.psi.ch (AIX 3.2/UCB 5.64/4.03) id AA21392; Tue, 28 Jan 1997 16:06:36 +0100 Date: Tue, 28 Jan 1997 16:06:36 +0100 From: kessi@psizi1.psi.ch (Alain Kessi) Message-Id: <9701281506.AA21392@psizi1.psi.ch> To: Patrick.Bultinck@rug.ac.be, chemistry@www.ccl.net Subject: Re: CCL:Failing optimization (1 imag. freq) Cc: kessi@psizi1.psi.ch Maybe the following suggestion is too obvious, and you've probably already done this, but since I cannot imagine how it could fail, I'll mention it anyway: take a step into the direction corresponding to your negative curvature (imaginary frequency) and start your optimization again there. The point is that you need to break your symmetry explicitely, not only switch the symmetry off, since at a point of symmetry you'll never have a gradient to break the symmetry, except by numerical imprecision. If the more sophisticated algorithms using internal coordinates don't work, just do a simple Cartesian optimization. This cannot fail, basically, except if you take too large steps, which might happen depending on the curvature. The energy should be lower when you take the first step (by hand), and the optimizer should have no problems further lowering it. A slow method which really cannot fail, given small enough steps, is following the gradient (steepest descent). Hope this helps, Alain From ccl@www.ccl.net Sun Jan 26 13:19:02 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id NAA02313; Sun, 26 Jan 1997 13:05:44 -0500 (EST) Received: from mailhub1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by bedrock.ccl.net (8.8.3/950822.1) id NAA00660; Sun, 26 Jan 1997 13:05:42 -0500 (EST) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailhub1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id NAA02991; Sun, 26 Jan 1997 13:05:36 -0500 (EST) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id NAA27144; Sun, 26 Jan 1997 13:05:42 -0500 Date: Sun, 26 Jan 1997 13:05:42 -0500 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <199701261805.NAA27144@still3.chem.columbia.edu> To: chemistry@ccl.net, Walter Polkosnik Subject: Re: CCL:Quanta and X terminals > From chemistry-request@www.ccl.net Sun Jan 26 04:05:06 1997 > Yes, I forgot to add that whatever X terminals you use have to support DGL. > I haven't found a PC X server that supports it yet either. > Walter Polkosnik walt@panix.com Slight correction: DGL is a concept that is associated with the old IrisGL; there is no such thing as DGL with OpenGL. Instead, in the X world, what is needed to remotely display OpenGL is the "GLX extensions" on the server (display machine). And there are PC X emulators that have at least announced the intent to support these, though I don't remember which they are; I think Hummingbird is one. Some may be available already. -P. *** "Why worry about tomorrow when today is so far off?" ('60s graffito) ** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** MacroModel WWW page: http://www.cc.columbia.edu/cu/chemistry/mmod/mmod.html From ccl@www.ccl.net Mon Jan 27 09:28:43 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id IAA11736; Mon, 27 Jan 1997 08:36:47 -0500 (EST) Received: from faui45.informatik.uni-erlangen.de for model97@organik.uni-erlangen.de by bedrock.ccl.net (8.8.3/950822.1) id IAA09328; Mon, 27 Jan 1997 08:36:45 -0500 (EST) Received: from derioc1.organik.uni-erlangen.de (derioc1.organik.uni-erlangen.de [131.188.128.1]) by uni-erlangen.de with SMTP id OAA08691 (8.7.6/7.5c-FAU); Mon, 27 Jan 1997 14:34:24 +0100 (MET) Received: from indigo11.organik.uni-erlangen.de (indigo11.organik.uni-erlangen.de [131.188.128.69]) by organik.uni-erlangen.de with SMTP id OAA10616 (8.6.12/7.4f-FAU);; Mon, 27 Jan 1997 14:33:54 +0100 Date: Mon, 27 Jan 1997 14:33:53 +0100 (MET) From: "Modelling '97" To: chem-com@mailbase.ac.uk, chem-mod@mailbase.ac.uk, chemistry@ccl.net, ipmdg-l@venus.co.uk, watoc@ic.ac.uk cc: "Modelling '97" Subject: Modelling '97 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Model(l)ing '97 Model(l)ing '97 is the annual international meeting of the MGMS, which is being organised in cooperation with WATOC for the first time. The meeting will take place from Tuesday, September 2nd to Friday September 5th 1997 at the Institut fuer Organische Chemie and the Computer-Chemie-Centrum of the Universitaet Erlangen-Nuernberg in Erlangen, Germany. All lectures except for those on Wednesday, September 3rd are by invitation. Wednesday's sessions have been reserved for submitted lectures by young scientists (postdocs or non-tenured academic staff), who are invited to submit their contributions as outlined below. Two parallel sessions will emphasise biological/ pharmaceutical methods and applications (Session A) and calculational methodology and non-biological applications (Session B). Conference fees are as follows: MGMS or WATOC members non-members Normal particpant: before 1.6.97 DM 400.- DM 500.- after 1.6.97 DM 550.- DM 650.- Student participants: before 1.6.97 DM 200.- DM 250.- after 1.6.97 DM 275.- DM 325.- Program and registration details are available from: Dr. T. Clark Model(l)ing '97 Computer-Chemie-Centrum Naegelsbachstraae 25 D-91052 Erlangen Germany Email: model97@organik.uni-erlangen.de FAX: +49-(0)9131-856565 URL: http://www.organik.uni-erlangen.de/model97/ From ccl@www.ccl.net Mon Jan 27 10:24:05 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id JAA12101; Mon, 27 Jan 1997 09:21:05 -0500 (EST) Received: from shiva.jussieu.fr for picard@ext.jussieu.fr by bedrock.ccl.net (8.8.3/950822.1) id JAA10642; Mon, 27 Jan 1997 09:21:01 -0500 (EST) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.8.5/jtpda-5.2) with ESMTP id PAA14465 for ; Mon, 27 Jan 1997 15:20:40 +0100 (MET) Received: from [134.157.11.19] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Mon, 27 Jan 1997 15:20:37 +0100 Date: Mon, 27 Jan 1997 15:20:37 +0100 X-Sender: picard@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: picard@ext.jussieu.fr (G.S. PICARD) Subject: MolDraw The MolDraw from the University of Paris: Molecular Graphics for the Macintosh by Jean-Michel CENSE Tetrahedron Computer Methodology, 2, 65-71, 1989 has a web page : http://www.enscp.jussieu.fr/labos/MAC/cense/mld.html Gerard S. PICARD , Directeur de Recherche au C.N.R.S., LABORATOIRE D'ELECTROCHIMIE ET DE CHIMIE ANALYTIQUE, Unite de Recherche associee au C.N.R.S. no 216, Equipe : "REACTIVITE EN MILIEUX IONIQUES LIQUIDES" 11 rue Pierre et Marie Curie - 75231 Paris cedex 05 - FRANCE. Tel : (33) 1.43.54.53.84. Fax : (33) 1.44.27.67.50. WWW Home Page : http://alcyone.enscp.jussieu.fr/Pages/LECA/GP/ (serveur W3 experimental). >From euresco@esf.org Mon Jan 27 11:51 EST 1997 Received: from esf2.esf.org for euresco@esf.org by www.ccl.net (8.8.3/950822.1) id LAA13568; Mon, 27 Jan 1997 11:51:45 -0500 (EST) Received: from esf2.esf.org by esf2.esf.org (NTMail 3.02.10) with ESMTP id ja105491 for ; Mon, 27 Jan 1997 17:49:35 +0100 Received: by Val.esf.org with Microsoft Mail id <01BC0C7A.736259A0@Val.esf.org>; Mon, 27 Jan 1997 17:49:32 +-100 Message-ID: <01BC0C7A.736259A0@Val.esf.org> From: "EURESCO (Valerie Allspach)" To: "'chemistry-request@www.ccl.net'" Subject: Euroconference on Fullerenes 97 Date: Mon, 27 Jan 1997 17:49:27 +-100 MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" This conference is part of the 1997 Programme of European Research Conferences. Further information on the programme - and on the conference below - can be obtained on our www server or by writing to our office (addresses at the bottom of the ad). Thank you very much for your co-operation Yours sincerely, Val=E9rie Allspach EURESCO Publicity Officer ************************************************************************* EUROPEAN RESEARCH CONFERENCE on CHEMISTRY AND PHYSICS OF MULTIFUNCTIONAL MATERIALS : FULLERENES IN CONTEXT Espinho, Portugal, 6-11 September 1997 Chairman: P.W. Fowler (Exeter) Vice-Chairman: F. Zerbetto ( Bologna) SPEAKERS WILL PROVISIONALLY INCLUDE: W. Andreoni (Zurich), F. Kajzar (Gif sur Yvette), K. Prassides (Sussex), P. Bernier (Montpellier), H. Kroto (Sussex), M. Prato (Trieste), E. Campbell (Berlin), H. Kuzmany (Vienna), P. Rudolf (Namur), T. Ebbesen (Strasbourg), D. Leigh (Manchester), J.F. Stoddart (Birmingham), J. Fischer (Pennsylvania), F. Negri (Bologna), R. Taylor (Sussex), A. Hirsch (Erlangen), G. Orlandi (Bologna), F. Wudl (Santa Barbara) SCOPE OF THE CONFERENCE The aim of this conference is to build a bridge between chemists and physicists working in the recently established field of fullerene research and interested scientists in the more traditional disciplines of organic chemistry, supramolecular chemistry, polymer science and materials science. Speakers from across the whole range of disciplines will survey chemical, physical, spectroscopic and theoretical aspects of their latest research and will assess the potential of fullerenes, tubes and related structures as building blocks for chemical functionalisation, supramolecular assembly, materials applications and devices. The conference is open to researchers world-wide, whether from industry or academia. Participation will be limited to 100. The emphasis will be on discussion about new developments. A poster session will also take place. The Registration Fee covers full board and lodging. Grants will be available for younger scientists, in particular those from less favoured regions in Europe. Deadline for applications: 30 April 1997 For information & application forms, contact the Head of the EURESCO Unit: Dr. Josip Hendekovic, European Science Foundation, 1 quai Lezay-Marn=E9sia, 67080 Strasbourg Cedex, France. Tel.+33 3 88 76 71 35 Fax.+33 3 88 36 69 87 E-mail: euresco@esf.org on-line information and application on WWW at: http://www.esf.org/euresco *************************************************************************= From ccl@www.ccl.net Mon Jan 27 23:19:16 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id WAA18234; Mon, 27 Jan 1997 22:24:55 -0500 (EST) Received: from uniwa.uwa.edu.au for mw@crystal.uwa.edu.au by bedrock.ccl.net (8.8.3/950822.1) id WAA02517; Mon, 27 Jan 1997 22:24:53 -0500 (EST) Received: from graf.crystal.uwa.edu.au (graf.crystal.uwa.edu.au [130.95.232.1]) by uniwa.uwa.edu.au (8.8.3/8.8.0) with SMTP id LAA09030 for ; Tue, 28 Jan 1997 11:24:51 +0800 Received: from pack.crystal.uwa.edu.au by graf.crystal.uwa.edu.au with SMTP (5.61+IDA+MU) id AA23677; Tue, 28 Jan 1997 13:55:30 +0800 From: mw@crystal.uwa.edu.au (Magda Wajrak) Message-Id: <9701280323.AA02723@pack.crystal.uwa.edu.au> Subject: Mulliken Populations? To: CHEMISTRY@ccl.net Date: Tue, 28 Jan 97 11:23:29 WST Mailer: Elm [revision: 70.85] Dear Computer Chemists, I have a question regarding Mulliken Populations, I appologise if this is an obvious question, but I haven't got much experience with mulliken populations, so I am not sure what is going on. How reliable are Mulliken Populations? The reason I ask is because, recently I ran two exactly the same jobs one using G94 and another using Cadpac and when I checked the charge distribution it was completely different. The final geometry and energies were the same, so I am confused. Also sometimes when I ran a job (water+metal) using G94 I get very strange charge distribution and other times it is as expected. Thank you for your time. Magda Wajrak (email: mw@crystal.uwa.edu.au) From ccl@www.ccl.net Tue Jan 28 10:19:26 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id JAA22041; Tue, 28 Jan 1997 09:45:16 -0500 (EST) Received: from myriad.cis.pitt.edu for SATYAM@vms.cis.pitt.edu by bedrock.ccl.net (8.8.3/950822.1) id JAA09144; Tue, 28 Jan 1997 09:45:15 -0500 (EST) From: Received: from vms.cis.pitt.edu by vms.cis.pitt.edu (PMDF V4.3-10 #16365) id <01IEQPWVEW7K90MZEW@vms.cis.pitt.edu>; Tue, 28 Jan 1997 09:45:11 -0400 (EDT) Date: Tue, 28 Jan 1997 09:45:11 -0400 (EDT) Subject: Which Softwares exists to help Chiral Synthesis ? To: chemistry@ccl.net Message-id: <01IEQPWVGHNM90MZEW@vms.cis.pitt.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters We are interested in finding which softwares exists for help in (1) Research and (2) Teaching about Chiral Synthesis. We know one "CHIRON" from Professor Hanessian. Has anybody used this package either for research or teaching ? Any help will be useful. Please send response (satyam+@pitt.edu) Satyam From David.Decorte@unifr.ch Tue Jan 28 12:19:48 1997 Received: from swifr9 for David.Decorte@unifr.ch by www.ccl.net (8.8.3/950822.1) id MAA23654; Tue, 28 Jan 1997 12:01:24 -0500 (EST) Received: from UFPER6.UNIFR.CH by swifr9 with SMTP (PP); Tue, 28 Jan 1997 18:01:02 +0100 Received: from ichpc00 by UFPER6.UNIFR.CH via Pony Express SMTP with TCP (v8.1.1-dmr001); Tue, 28 Jan 97 18:00:56 MET Message-ID: <32EE304A.7263@unifr.ch> Date: Tue, 28 Jan 1997 17:58:50 +0100 From: david de corte X-Mailer: Mozilla 2.0 (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: GROMOS87-problem Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I'm a Phd-student staring a work on MD using the GROMOS87 program. I've tried the program out and have had some problems in the minimization part. How did y proceed: 1) I created a molecular topology file (no problems) 2) I created a waterbox + a solute-ion (no problems) 3) Then I wanted to do a minimization but the following error-message appeared: COORDINATE RESETTING CANNOT BE ACCOMPLISHED, DEVIATION IS TOO LARGE NITER, NIT, NN, LL, L, I AND J ARE : 0 1 1 2***** 1 3 I don't now where the problems come from and therefor I would find it very kind if someone could help me with this problem. Kind regards, David -- David De Corte Institute of Inorganic Chemistry Tel: 0041-26-300.87.52(49) University Fribourg e-mail: David.Decorte@unifr.ch CH-1700 Switzerland From chpajt@bath.ac.uk Tue Jan 28 13:19:29 1997 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.8.3/950822.1) id MAA24088; Tue, 28 Jan 1997 12:39:48 -0500 (EST) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Tue, 28 Jan 1997 17:35:37 +0000 Date: Tue, 28 Jan 1997 17:35:15 +0000 (GMT) From: A J Turner To: Alain Kessi cc: Patrick.Bultinck@rug.ac.be, chemistry@www.ccl.net Subject: Re: CCL:Failing optimization (1 imag. freq) In-Reply-To: <9701281506.AA21392@psizi1.psi.ch> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! Why not take a IRC down the negative eign value? Best 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 d3g359@fido.pnl.gov Tue Jan 28 20:19:31 1997 Received: from pnl.gov for d3g359@fido.pnl.gov by www.ccl.net (8.8.3/950822.1) id UAA07665; Tue, 28 Jan 1997 20:05:42 -0500 (EST) Received: from fido.pnl.gov by pnl.gov (PMDF V4.3-13 #6012) id <01IER5FVFBXS934V29@pnl.gov>; Tue, 28 Jan 1997 17:04:54 -0800 (PST) Received: by fido.pnl.gov (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) for CHEMISTRY@www.ccl.net id RAA28906; Tue, 28 Jan 1997 17:02:41 -0800 Date: Tue, 28 Jan 1997 17:02:41 -0800 From: d3g359@fido.pnl.gov (John Nicholas) Subject: g94opt/basis set opt To: CHEMISTRY@www.ccl.net Message-id: <199701290102.RAA28906@fido.pnl.gov> Content-transfer-encoding: 7BIT In response to a recent posting, several people suggested using g94opt (also called gauopt) as a tool for optimizing basis sets. G94opt does look like exactly what I want, but often gives unusual results. In particular the initial energies calculated in g94opt do not match those obtained with a single point in g94, often by as much as a hartree. Anyone out there with experience in g94opt/basis set opts? Thanks, john ------------------------------------------------------------------------------ John Nicholas Office: (509) 375-6559 Senior Research Scientist FAX: (509) 375-6631 Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Mailstop K1-96 Richland, WA 99352 ------------------------------------------------------------------------------ From ross@cgl.ucsf.EDU Tue Jan 28 21:19:30 1997 Received: from socrates.ucsf.EDU for ross@cgl.ucsf.EDU by www.ccl.net (8.8.3/950822.1) id VAA07862; Tue, 28 Jan 1997 21:08:31 -0500 (EST) From: Received: (from ross@localhost) by socrates.ucsf.EDU (8.8.5/GSC4.25) id SAA09682 for CHEMISTRY@www.ccl.net; Tue, 28 Jan 1997 18:08:31 -0800 (PST) Date: Tue, 28 Jan 1997 18:08:31 -0800 (PST) Message-Id: <199701290208.SAA09682@socrates.ucsf.EDU> To: CHEMISTRY@www.ccl.net Subject: PPro investigations I have been benchmarking & collecting info on Pentium Pro 200MHz machines. So far I have not come across anything comparing cache size (256K vs. 512K). Does anyone have such results? Here is what I have so far, beginning with some benchmark results comparing linux + Absoft compiler to other machines on molecular dynamics. The numbers are times in seconds. '-OZ', '-N69' etc. are various Absoft optimization flags. Some 'standard' machines are given first for comparison; '-' indicates that the vendor ran the benchmark. Bill Ross dnawat*: 6 base pairs of DNA in water box (7682 atoms: 274 DNA, 10 ions, 2466 waters) dnavac*: 68 base pairs of DNA in vacuum (4282 atoms) prowat: plastocyanin in water box (11585 atoms: 1460 solute, 3375 waters) Benchmark: dnawat1 dnawat2 dnawat3 dnawat4 dnavac dnavacG prowat Cutoff: 8A 9/12A 12A Ewald 10A 10A 12A date -- cpu non-setup %%%%%%%%SGI -O2000.1 43 67 137 103 31 65 210 1/97 -O200.1 48 74 153 123 34 73 230 1/97 R8000_75 81 120 209 326 115 111 331 3/95 %%%%%%%%HP 735_125 102 163 352 385 85 521 3/95 %%%%%%%%DEC axp_275 120 182 361 358 85 138 565 10/96 %%%%%%%%PPro_200 --128M g77* 152 228 452 549 98 154 652 1/97 g77* 156 238 465 510 164 183 737 1/97 --32M absoft 150 471 778 abs.OZ 162 248 469 547 144 - 833 1/97 abs.OZ.N69 209 513 abs.OZ.U 164 534 abs.OZ.U.N69 155 517 767 abs.U.N69 167 493 709 -- cpu total DEC axp_275 115 180 371 358 87 139 573 1/97 --PPro 128M absoft 169 480 789 abs.OZ 175 263 489 529 144 - 868 1/97 abs.OZ.N69 158 396 abs.OZ.U 166 401 abs.OZ.U.N69 156 394 735 abs.U.N69 173 475 791 Note: cpu total is used for a 128M, 2-cpu symmetric processor PPro, since most time reported by 'time' and the internal timing calls was system time, not user. The 'cpu non-setup' times are internal timings of the main dynamics loop. * - different 128M PPros than the other 128M numbers. -- Gaussian 94 Benchmarks - http://mephisto.ca.sandia.gov/benchmarks.html times in seconds ------------test #------------- machine processor 1 28 94 155 194 296 302 relative speed 1. PDOF PPro200.2(a) 7 23 66 390 225 1129 103 1.0 1. PDOF PPro200.2(b) 6 18 61 336 177 1067 84 1.2 2. PPro200.1 7 21 70 495 334 1429 121 0.9 3. Endeavor P5/133 10 36 144 1364 667 6747 340 0.4 4. Indigo2 r8000 8 23 85 303 91 1111 139 1.2 a-Pentium Pro jobs run with two G94 jobs on the machine; b-Pentium Pro jobs run with the second CPU idling Machine Details: 1.Pentium Pro/200 MHz; PDOF dual processor motherboard; running Linux; 128 MB Ram, 4 way interleaved memory; G94 run with 4MW 2.Pentium Pro 200 MHz: single processor motherboard; running Linux; 128MB Ram; f2c compiler w/ -O2 optimization; gcc 2.7.0 and libc 5.2.18; G94 run with 4MW 3.Pentium 133 MHz; Endeavor motherboard; running Linux; 64 MB Ram, compiled w/o optimization; G94 w/ 2 MW 4.Indigo-2; R8000; running IRIX 6.1; 192 MB Ram; G94 run with 5 MW Test Details: 1 - STO-3G single point energy on O2 28 - RHF/3-21G H2O frequencies 94 - MP2/STO-3G H2O geometry optimization 155 - HF/6-31+G* Ethene, frequencies 194 - QCISD(tq) generic basis H2O 296 - G1, G2, G2MP2, H2O 302 - HF/3-21G transition state for SiH2 + H2 -> SiH4 Benchmark by Joe Durant. He commented in Jul '96: > The dual P6 boards offer 4 way interleaving on the memory, which > I believe explains the speedup of the dual board over the single > processor board. The loss in performance for things like QCISD is > due, I am told, to the gcc compilers not yet being as good at optimizing > matrix calculations. These same people expect the differences to disappear > as the gnu compilers for the P6 mature. -- relating this to a bigger molecule, C6H6N6O6 (TATB), rhf/6-31g**//hf/6-31g** http://www.chem.joensuu.fi/people/juha_muilu/Misc/benchmarks.html GAUSSIAN94 Computer Proc MHz time versions /MB(* elapsed cpu+sys(* G94 OS F77 ------------------------------------------------------------------------ DEC 3900/192MB Alpha 275 16:31 13:52 RevD.1 3.2 3.8 SGI Power Onyx/2GB 8*R8000 75 8:42 RevB.1 5.3(** SGI Power Indigo/128MB R8000 75 8:02 Job is single point HF calculation with NPA population analysis. Number of basis functions is 300 and number of (direct) SCF iterations is 8. -- http://www.cpma.u-psud.fr/ccl/405 Date: Wed, 31 Jul 1996 15:58:28 -0600 To: chemistry@www.ccl.net Subject: CCL:G:Summary: Performance of PPro Pedro A M Vazquez wrote: > Subject: [COMP-CHEM] CCL:G:performance of PPro (fwd) > Hello > We just started to benchmark a PPro200MHz for quantum chemistry > calculations. > While I've not completed all sets of tests I've results for the > Stream benchmark (Memory bandwidth), Bonnie (I/O) and the 4 Gamess > benchmarks. > These results are for an Asustek Motherboard with 64M of RAM, > an Adaptec 2940 SCSI2 adaptor and a NEC 2.1G SCSI2 hard disk running > under FreeBSD2.1.0: > > Stream:(a g94 job running during the benchmark) > > Function Rate (MB/s) RMS time Min time Max time > Assignment: 97.5238 0.1965 0.1641 0.2109 > Scaling : 85.3333 0.1969 0.1875 0.2031 > Summing : 87.7714 0.2813 0.2734 0.2969 > SAXPYing : 90.3529 0.2797 0.2656 0.2891 > > Just for comparision, these are the results for an Alpha Server 1000 4/266 > DEC Unix3.2C: (idle machine) > > Function Rate (MB/s) RMS time Min time Max time > Assignment: 96.0000 0.1801 0.1667 0.1833 > Scaling : 96.0000 0.1836 0.1667 0.2000 > Summing : 96.0000 0.2586 0.2500 0.2833 > SAXPYing : 96.0000 0.2618 0.2500 0.2667 > > Bonnie: > -------Sequential Output-------- ---Sequential Input-- --Random-- > -Per Char- --Block--- -Rewrite-- -Per Char- --Block--- --Seeks--- > Machine MB K/sec %CPU K/sec %CPU K/sec %CPU K/sec %CPU K/sec %CPU /sec %CPU > > 2940/PP200 > 100 3275 56.5 3194 12.8 1424 11.2 4978 80.4 4926 17.8 103.8 4.1 > > Alpha 1000 4/266 DEC RZ28 > 100 4906 95.4 5439 17.4 2550 10.4 4746 82.6 5322 12.6 428.0 10.8 > > GAMESS: > Bench 10 04 13 07 > ============================================= > IBM370 64 74 366 391 > P166 61 78 281 335 > IBM580 59 69 322 381 > > PPro200 43.6 69.3 163.7 254.6 <<<<<< > > IBM590 33 33 147 202 > Alpha1000 4/266 23.3 30.5 126.9 147.0 > > The results for the Pentium166 (64M/RAM,FreeBSD2.1.0,2940/NEC2.1HD) and > for the PPro200 were obtained with GAMESS (22/nov/95) compiled with > GNU Fortran 0.5.18 (slightly faster than f2c/gcc). > > I need to benchmark gaussian yet to have a more representative sampling > but as you can see these are very good results for a cheap computer. > If you opt to buy 2 PPro to run GAMESS in parallel you'll got near > two times the above reported performance. > > Pedro >-- End of excerpt from Pedro A M Vazquez