From chemistry-request@ccl.net Wed Jun 4 05:32:22 2003 Received: from patronimo.umh.ac.be (patronimo.umh.ac.be [193.190.193.113]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h549WLgC028961 for ; Wed, 4 Jun 2003 05:32:21 -0400 Received: from patronimo (patronimo [193.190.193.113]) by patronimo.umh.ac.be (8.12.9/8.12.9) with ESMTP id h549VpBJ422386 for ; Wed, 4 Jun 2003 11:31:51 +0200 Date: Wed, 4 Jun 2003 11:31:51 +0200 (DFT) From: Victor Geskin X-X-Sender: Victor@patronimo To: chemistry..at..ccl.net Subject: CCL: Orbitals: a practical approach of a theoretical chemist Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Scanned-By: MIMEDefang 2.1 (www dot roaringpenguin dot com slash mimedefang) Dear CCLers, I was absent from office, only by now I have read all the discussion - a very stimulating one, and I would like to dwell on several points that have not received due attention, unless I overlooked something. A practical approach of a theoretical chemist. An almost trivial introduction. Scientific papers contain words, not only tables with numbers and graphs. And these words not only describe which number in a table is greater than another one, but tend to explain why. That is, as natural scientists and human beings we need images and qualitative models. We strive at discussing our results, not just cutting-pasting the numbers provided by our computers. If the computers were able to provide any number with necessary precision at reasonable computational cost, it would be of great importance for industry and the death of natural science; of theoretical chemistry in particular, as far as chemical research is concerned. Hopefully, this is not expected soon. The words in theoretical chemistry papers are supposed to be not just anything plausible we invent to make our numbers look less dull. (It could be like that before QM.) We have got an underlying physical theory, which is extremely well cast and of unquestionable applicability in our domain: QM, of course. Our words are rooted in its formalism and can be used only provided they do not contradict this formalism; the latter is taken for granted. Now closer to orbitals to illustrate this approach. A simple-minded question (one of those I used to ask myself as a high-school student, before getting acquainted with QM): are electrons just immobile clouds shaped as orbitals or do electrons move within the orbitals? Now I think that the correct answer is: no matter what electrons are, they do move, that is their velocity is non-zero, because the expectation value of the kinetic energy operator is non-zero. Are orbitals something like flats in which electron pairs (or poor lonely electrons) live? That could be an acceptable image for a Hartree product wave function, but not for a Slater determinant: in the latter it is blurred which electron is where. Therefore, MOs should not be viewed as flats in a molecule-hostel. It is widely accepted (in DFT, though not strictly proven, as far as I know) that any electron density in our 3D space can be obtained from one Slater determinant, squared (assuming all the numbers real), by integrating over the coordinates af all the electrons but one. Since the orbitals (the one-electron functions of which the determinant is built) are orthogonal by construction, the total electron density is the sum of orbitals squared (multiplied by the normalization factor, of course) - no cross terms. Therefore, MOs are good for decomposing the total electron density; I do not see a real problem in the fact that in this sense they are defined up to a phase factor. A corollary: the necessity of multideterminant CI wavefunctions is but an illusion; having obtained a precise electron density, one can reconstruct it from one determinant - built of Kohn-Sham, not Hartree-Fock orbitals. I suppose, they do it in the group of Baerends. However, these orbitals are not unique, even supposing that the detrminant is unique: one more reason why they are not flats for electrons. I would say that the electrons do not "live in" orbitals, but in many cases they "leave from" them. I mean the following. For ionization, as long as Koopmans works, it is reasonable to suppose that the electron density decreases in the spatial region of a given orbital. For excitation, when a CI or TD-DFT calculation shows which excited determinants constitute the excited state, it means in the region of which orbitals the electron density decreases and where it increases. In this sense, ionization and excitation take place between (among) canonincal orbitals. I would like also to mention experimental spin-density determinations in organic radicals performed some ten years ago in Grenoble, in the laboratory of Jacques Schweitzer, by neutron scattering (neutron has spin but no charge: most useful for spin density probing). If some MO based calculations (I suppose these have been done) show that the total spin density can be traced back to one MO predominantly - then we can even admit that, in a sense, the unpaired electron even lives in a given orbital. This bearing in mind that we cannot say which electron is unpaired: they are all antisymmetrized in a determinant. In particular for Kohn-Sham orbitals, there was a tradition to justify their meaning by Janak's theorem, stating that the partial derivative of the total energy wrt a given orbital's occupation number is equal to the eigenenergy of this orbital. A most confusing theorem based on an assumption that an electron can be ionized in infinitesimal parts! (Not the same as fractional occupation numbers of e.g. natural orbitals!) I think, better to forget about this theorem (it must already be forgotten since noone has mentioned it in this discussion). In conclusion, I consciously avoided any direct reply to whether the orbitals are real or not. I tried to exemplify that in many situations they can be used in a quantum-mechanically well-defined sense and help us building models that do not contradict QM. If you are not yet too tired of this discussion, I would be most grateful for any remarks and criticism. ___________________________________________________________________ Dr Victor GESKIN e-mail: Victor..at..averell.umh.ac.be Service de Chimie http://morris.umh.ac.be des Materiaux Nouveaux Universite de Mons-Hainaut phone: +32-(0)65.37.38.67 Place du Parc, 20 fax: +32-(0)65.37.38.61 B-7000 MONS, BELGIQUE GSM: +32-(0)486.779.799 ___________________________________________________________________ From chemistry-request@ccl.net Wed Jun 4 03:52:58 2003 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h547qvgC025397 for ; Wed, 4 Jun 2003 03:52:57 -0400 Received: from moka.ccr.jussieu.fr (moka.ccr.jussieu.fr [134.157.1.23]) by shiva.jussieu.fr (8.12.9/jtpda-5.4) with ESMTP id h547qm5Q096951 for ; Wed, 4 Jun 2003 09:52:48 +0200 (CEST) Received: from ccr.jussieu.fr (verdi.div.jussieu.fr [134.157.75.160]) by moka.ccr.jussieu.fr (8.10.0/jtpda-5.3.3) with ESMTP id h547qlE1839218 for ; Wed, 4 Jun 2003 09:52:47 +0200 Sender: seb..at..ccr.jussieu.fr Message-ID: <3EDE234B.9320792A..at..ccr.jussieu.fr> Date: Wed, 04 Jun 2003 09:50:20 -0700 From: Sebatien Laugaro Organization: Pharmacochime Moleculaire X-Mailer: Mozilla 4.79C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY..at..ccl.net Subject: Gaussian problem Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Antivirus: scanned by sophie at shiva.jussieu.fr Hy, I work on Gaussian98 and I have a problem. I have an error message : "increase integral accuracy, restarting incremental FockFormation". I use B3LYP/6-31G* OPT SCF(MAXCYCLE=256). Can you help me . Thank you Sebastien laugaro..at..ccr.jussieu.fr From chemistry-request@ccl.net Wed Jun 4 04:45:28 2003 Received: from smtp02.sohu.com ([61.135.132.105]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h548jQgC027407 for >ccl.net>; Wed, 4 Jun 2003 04:45:27 -0400 Received: from njuitccwx (jproxy.nju.edu.cn [202.119.32.27]) by smtp02.sohu.com (Postfix) with ESMTP id 3C5B46ABF5 for >ccl.net>; Wed, 4 Jun 2003 16:44:08 +0800 (CST) Date: Wed, 4 Jun 2003 16:45:13 +0800 From: wxin >sohu.com> To: "chemistry<>ccl.net" >ccl.net> Subject: About the lanczos diagnolization in G98 X-mailer: FoxMail 3.11 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <20030604084408.3C5B46ABF5<>smtp02.sohu.com> Dear CCL-lister, Does anyone knows how to change the maximum number of lanczos iterations in Gaussian98 (the default is 64) when doing casscf calculation? Xin Wang Dept Chem, Nanjing Univ P.R.China From chemistry-request@ccl.net Wed Jun 4 05:59:18 2003 Received: from hal.netbox.cz (hal.netbox.cz [212.96.166.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h549xIgC029768 for ; Wed, 4 Jun 2003 05:59:18 -0400 Received: from chemi.muni.cz (r10s01p08.home.nbox.cz [212.96.184.72]) by hal.netbox.cz (Postfix) with ESMTP id E1984171D44 for ; Wed, 4 Jun 2003 11:59:13 +0200 (CEST) Message-ID: <3EDDC287.2070609..at..chemi.muni.cz> Date: Wed, 04 Jun 2003 11:57:27 +0200 From: Lubos Vrbka Reply-To: shnek..at..chemi.muni.cz Organization: NCBR User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030529 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry..at..ccl.net Subject: chemical formula editors for windows Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit dear ccl'ers, i've used chemdraw for some time but now i have to switch to something else, preferably a FREE software. i'm trying mdl isis draw 2.5 now (it's free for academic and home use), but it has serious problems exporting .eps and other file types that are essential for me. anyone has seen the same behaviour? do you have any advices concerning this? or could you please suggest some other program for free that i could use? unix reccomendations are also welcome. i tried to search the archives, but with no results... i'll summarize the postings at the end... regards, lubos -- - ################################################# Lubos Vrbka National Centre for Biomolecular Research Masaryk university, Brno, Czech Republic shnek..at..chemi.muni.cz http://www.chemi.muni.cz/~shnek tel. +420 541 129 508 ################################################# From chemistry-request@ccl.net Wed Jun 4 12:13:49 2003 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h54GDmLB001202 for ; Wed, 4 Jun 2003 12:13:49 -0400 Received: from dedalus.lcc.ufmg.br (loopback [127.0.0.1]) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8) with ESMTP id h54G78eu053846; Wed, 4 Jun 2003 13:07:08 -0300 Received: from localhost (amolive@localhost) by dedalus.lcc.ufmg.br (8.12.8p1/8.12.8/Submit) with ESMTP id h54G778g038432; Wed, 4 Jun 2003 13:07:07 -0300 Date: Wed, 4 Jun 2003 13:07:07 -0300 (BSC) From: andre mauricio de oliveira X-X-Sender: amolive@dedalus To: Lubos Vrbka cc: chemistry=at=ccl.net Subject: Re: CCL:chemical formula editors for windows In-Reply-To: <3EDDC287.2070609=at=chemi.muni.cz> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have used ChemSketch 5.0 (www.acdlabs.com)that has many functionalities. On Wed, 4 Jun 2003, Lubos Vrbka wrote: > dear ccl'ers, > > i've used chemdraw for some time but now i have to switch to something > else, preferably a FREE software. i'm trying mdl isis draw 2.5 now (it's > free for academic and home use), but it has serious problems exporting > >.eps and other file types that are essential for me. anyone has seen the > same behaviour? do you have any advices concerning this? > > or could you please suggest some other program for free that i could > use? unix reccomendations are also welcome. > > i tried to search the archives, but with no results... i'll summarize > the postings at the end... > > regards, > lubos > > -- > - > ################################################# > Lubos Vrbka > National Centre for Biomolecular Research > Masaryk university, Brno, Czech Republic > > shnek=at=chemi.muni.cz > http://www.chemi.muni.cz/~shnek > tel. +420 541 129 508 > ################################################# > > > > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY=at=ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST=at=ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl=at=ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > Andre Mauricio de Oliveira VOICE +55-031-374-1325 +55-031-499-5765 FAX +55-031-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal (NEQUIM) NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim Departamento de Quimica ICEx Federal University of Minas Gerais Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901 Belo Horizonte MG Brazil From chemistry-request@ccl.net Wed Jun 4 09:26:15 2003 Received: from mail.ngdc.net (mail.ngdc.net [195.190.153.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h54DQF6B002025 for ; Wed, 4 Jun 2003 09:26:15 -0400 Received: from [10.20.30.120] (unknown [62.242.210.146]) by herodot (Postfix) with ESMTP id 82C4B17A94; Wed, 4 Jun 2003 16:25:18 +0200 (CEST) Date: Wed, 4 Jun 2003 15:25:33 +0200 (CEST) From: Kenneth Geisshirt Sender: kneth~at~hydrogen.ngdc.net Reply-To: kenneth~at~geisshirt.dk To: Lubos Vrbka Cc: "chemistry~at~ccl.net" Subject: Re: CCL:chemical formula editors for windows In-Reply-To: <3EDDC287.2070609~at~chemi.muni.cz> Message-ID: References: <3EDDC287.2070609~at~chemi.muni.cz> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=iso-8859-1 Content-Transfer-Encoding: 8BIT On Wed, 4 Jun 2003, Lubos Vrbka wrote: > or could you please suggest some other program for free that i could > use? unix reccomendations are also welcome. Take a look at xdrawchem: http://www.prism.gatech.edu/~gte067k/xdrawchem/ - there is also a Windows version. Kneth -- Kenneth Geisshirt, M.Sc., Ph.D. http://kenneth.geisshirt.dk Grxndals Parkvej 2A, 3. sal kenneth~at~geisshirt.dk DK-2720 Vanlxse +45 38 87 78 38 From chemistry-request@ccl.net Wed Jun 4 10:07:53 2003 Received: from mail1.rrz.Uni-Koeln.DE (mail1.rrz.Uni-Koeln.DE [134.95.100.208]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h54E7q6B003410 for ; Wed, 4 Jun 2003 10:07:53 -0400 Received: from uni-koeln.de ([134.95.151.118]) by mail1.rrz.Uni-Koeln.DE (8.12.9/8.12.7) with ESMTP id h54E7WjR018566; Wed, 4 Jun 2003 16:07:32 +0200 (MEST) Message-ID: <3EDDFD26.9050406~at~uni-koeln.de> Date: Wed, 04 Jun 2003 16:07:34 +0200 From: Christoph Steinbeck Reply-To: c.steinbeck~at~uni-koeln.de User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.3) Gecko/20030312 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Lubos Vrbka CC: chemistry~at~ccl.net Subject: Re: CCL:chemical formula editors for windows References: <3EDDC287.2070609~at~chemi.muni.cz> In-Reply-To: <3EDDC287.2070609~at~chemi.muni.cz> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new X-Spam-Report: EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA Completely free (as in "free software") is WinDrawChem, which is also available as a Linux version XDrawChem ( see http://www.prism.gatech.edu/~gte067k/windrawchem/ and links therein). Don't know about the export features, though. But because it is open source you could add them yourself :-) If you feel very adventurous, you could try our free structure editor JChemPaint (http://jchempaint.sf.net), but if your focus is nice output, that might not be an option (yet). Cheers, Chris -- Dr. Christoph Steinbeck (e-mail: c.steinbeck~at~uni-koeln.de) Groupleader Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z|lpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-5092 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. Lubos Vrbka wrote: > dear ccl'ers, > > i've used chemdraw for some time but now i have to switch to something > else, preferably a FREE software. i'm trying mdl isis draw 2.5 now (it's > free for academic and home use), but it has serious problems exporting > >> .eps and other file types that are essential for me. anyone has seen the > > same behaviour? do you have any advices concerning this? > > or could you please suggest some other program for free that i could > use? unix reccomendations are also welcome. > > i tried to search the archives, but with no results... i'll summarize > the postings at the end... > > regards, > lubos > From chemistry-request@ccl.net Wed Jun 4 10:01:16 2003 Received: from atom.ecn.purdue.edu (atom.ecn.purdue.edu [128.46.108.94]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h54E1G6B003170 for ; Wed, 4 Jun 2003 10:01:16 -0400 Received: from ecn.purdue.edu (chme117bpc3.ecn.purdue.edu [128.46.108.125]) (authenticated bits=0) by atom.ecn.purdue.edu (8.12.8p1/8.12.8) with ESMTP id h54E0ofL022355 for ; Wed, 4 Jun 2003 09:00:50 -0500 (EST) Message-ID: <3EDDFB92.4090008~at~ecn.purdue.edu> Date: Wed, 04 Jun 2003 09:00:50 -0500 From: Aaron Deskins Organization: Purdue University User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry~at~ccl.net Subject: Freezing atoms-modredundant Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned-ECN: by AMaVIS version 11 (perl 5.8) (http://amavis.org/) Hello all, I have (hopefully) a relatively simple question. I'm trying some simple test calculations using Gaussian 98, but am running into a little problem freezing atom positions. Essentially I want to freeze a few atoms, and allow others to relax. Below is a test file. The problem I see is that the geometry optimization algorithm moves all atoms to the same location on first pass and subsequently causes the program to crash. I've tried different atoms and arrangements with no luck. Any suggestions? Thank you # opt(maxcycle=200,modredundant) hf/lanl2dz scf(diis,maxcycle=300) Title Card Required 0 3 c 0.0000000000 0.0000000000 0.0000000000 c 2.7718585823 0.0000000000 0.0000000000 c 0.0000000000 2.7718585823 0.0000000000 c 2.7718585823 2.7718585823 0.0000000000 1 f 2 f 3 f -- Aaron Deskins Graduate Student Chemical Engineering Purdue University From chemistry-request@ccl.net Wed Jun 4 09:48:39 2003 Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h54Dmc6B002827 for ; Wed, 4 Jun 2003 09:48:38 -0400 Received: by lgdx04.lg.ehu.es id PAA0000000556; Wed, 4 Jun 2003 15:48:15 +0200 (MET DST) Message-ID: <00eb01c32a9f$f55bb2e0$222fe39e~at~lc.ehu.es> From: "Pablo Vitoria" To: "Sebatien Laugaro" , "CCL" References: <3EDE234B.9320792A~at~ccr.jussieu.fr> Subject: Re: CCL:Gaussian problem Date: Wed, 4 Jun 2003 15:48:19 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Hi Sebastien, They are not error messages, it is the normal behavior of G98. When using direct SCF (which is the default), G98 calculates the integrals to a low accuracy (to speed up the initial cycles) until the wavefunction is converged to 10^-5, then it prints "Initial convergence to 1.0D-05 achieved. Increase integral accuracy", and starts calculating with higher accuracy. Thsi behaviour can be turned off with SCF=NoVarAcc. Also by default, G98 uses the "Pulay's Direct Inversion in the Iterative Subspace extrapolation method " (DIIS), which (usually) accelerates the convergence of SCF. You will see a message "Restarting incremental Fock formation" every 20 cycles of the SCF. Best regards Pablo -------------------------------------------------------- Pablo Vitoria Garcia Dpto. Qummica Inorganica, Facultad de Ciencias Universidad del Pams Vasco (UPV/EHU) Aptdo. 644 48080 Bilbao (Bizkaia) Tfno. 94 6015992 Fax. 94 4648500 ----- Original Message ----- From: "Sebatien Laugaro" To: Sent: Wednesday, June 04, 2003 6:50 PM Subject: CCL:Gaussian problem | Hy, | I work on Gaussian98 and I have a problem. | I have an error message : "increase integral accuracy, restarting | incremental FockFormation". I use B3LYP/6-31G* OPT SCF(MAXCYCLE=256). | Can you help me . | Thank you | Sebastien | laugaro~at~ccr.jussieu.fr | | | | -= This is automatically added to each message by mailing script =- | To send e-mail to subscribers of CCL put the string CCL: on your Subject: line | and send your message to: CHEMISTRY~at~ccl.net | | Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST~at~ccl.net | HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs | | If your mail is bouncing from CCL.NET domain send it to the maintainer: | Jan Labanowski, jkl~at~ccl.net (read about it on CCL Home Page) | -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ | | | | | | From chemistry-request@ccl.net Wed Jun 4 10:10:28 2003 Received: from pump2.york.ac.uk (pump2.york.ac.uk [144.32.128.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h54EAR6B003484 for ; Wed, 4 Jun 2003 10:10:27 -0400 Received: from thallium.york.ac.uk (thallium.york.ac.uk [144.32.52.130]) by pump2.york.ac.uk (8.12.9/8.12.9) with ESMTP id h54EA6gX010575 for ; Wed, 4 Jun 2003 15:10:07 +0100 (BST) Content-Type: text/plain; charset="us-ascii" From: Grant Hill To: chemistry~at~ccl.net Subject: CCL:Extremely large basis sets Date: Wed, 4 Jun 2003 15:10:11 +0100 User-Agent: KMail/1.4.3 MIME-Version: 1.0 Message-Id: <200306041510.11973.jgh105~at~york.ac.uk> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h54EAS6B003488 Hi all, One of my current research interests requires a very large basis set, which would ideally support the elements of the first two periods (or at the very least hydrogen and oxygen). The basis set would need to be larger than (for example) aug-cc-pV6Z, and in principle be as close to the basis set limit as possible. Does anyone on the list know of any basis sets which may fulfil these requirements? Either a reference to a journal article, or a url for a website would be hugely appreciated. Please note that I'll also consider larger slater basis sets. Thanks in advance, Grant Hill From chemistry-request@ccl.net Wed Jun 4 11:23:04 2003 Received: from sccrmhc11.attbi.com (sccrmhc11.attbi.com [204.127.202.55]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h54FN46B005405 for ; Wed, 4 Jun 2003 11:23:04 -0400 Received: from C1353359A (12-207-205-144.client.attbi.com[12.207.205.144](untrusted sender)) by attbi.com (sccrmhc11) with SMTP id <20030604152244011006qgh3e>; Wed, 4 Jun 2003 15:22:44 +0000 Reply-To: From: "Mark Thompson" To: "Lubos Vrbka" , Subject: CCL: chemical formula editors for windows Date: Wed, 4 Jun 2003 08:18:20 -0700 Message-ID: <000301c32aac$88212180$0300a8c0|at|attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) In-Reply-To: <3EDDC287.2070609|at|chemi.muni.cz> X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal Dear Lubos, Try WinDrawChem (its free) http://www.prism.gatech.edu/~gte067k/windrawchem/ Mark ================================= Mark Thompson, Ph.D. Planaria Software PO Box 55207 Seattle, WA 98155 FAX: 206-440-3305 ArgusLab is available at: http://www.arguslab.com ================================= > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request|at|ccl.net]On > Behalf Of Lubos Vrbka > Sent: Wednesday, June 04, 2003 2:57 AM > To: chemistry|at|ccl.net > Subject: CCL:chemical formula editors for windows > > > dear ccl'ers, > > i've used chemdraw for some time but now i have to switch to something > else, preferably a FREE software. i'm trying mdl isis draw 2.5 now (it's > free for academic and home use), but it has serious problems exporting > >.eps and other file types that are essential for me. anyone has seen the > same behaviour? do you have any advices concerning this? > > or could you please suggest some other program for free that i could > use? unix reccomendations are also welcome. > > i tried to search the archives, but with no results... i'll summarize > the postings at the end... > > regards, > lubos > > -- > - > ################################################# > Lubos Vrbka > National Centre for Biomolecular Research > Masaryk university, Brno, Czech Republic > > shnek|at|chemi.muni.cz > http://www.chemi.muni.cz/~shnek > tel. +420 541 129 508 > ################################################# > > > > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY|at|ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST|at|ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl|at|ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Wed Jun 4 16:06:29 2003 Received: from atom.ecn.purdue.edu (atom.ecn.purdue.edu [128.46.108.94]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h54K6TLB006183 for ; Wed, 4 Jun 2003 16:06:29 -0400 Received: from ecn.purdue.edu (chme117bpc3.ecn.purdue.edu [128.46.108.125]) (authenticated bits=0) by atom.ecn.purdue.edu (8.12.9/8.12.9) with ESMTP id h54K6Pme028768; Wed, 4 Jun 2003 15:06:26 -0500 (EST) Message-ID: <3EDE5141.6050400_at_ecn.purdue.edu> Date: Wed, 04 Jun 2003 15:06:25 -0500 From: Aaron Deskins Organization: Purdue University User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Aaron Deskins CC: chemistry_at_ccl.net Subject: Re: CCL:Freezing atoms-modredundant References: <3EDDFB92.4090008_at_ecn.purdue.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned-ECN: by AMaVIS version 11 (perl 5.8) (http://amavis.org/) Thanks for the replies. I think I found the problem. I needed the Nosymm keyword for the optimization to work properly. Thanks again! Aaron Deskins wrote: > Hello all, > I have (hopefully) a relatively simple question. I'm trying some > simple test calculations using Gaussian 98, but am running into a little > problem freezing atom positions. Essentially I want to freeze a few > atoms, and allow others to relax. Below is a test file. The problem I > see is that the geometry optimization algorithm moves all atoms to the > same location on first pass and subsequently causes the program to > crash. I've tried different atoms and arrangements with no luck. Any > suggestions? Thank you > > > # opt(maxcycle=200,modredundant) hf/lanl2dz scf(diis,maxcycle=300) > > Title Card Required > > 0 3 > c 0.0000000000 0.0000000000 0.0000000000 > c 2.7718585823 0.0000000000 0.0000000000 > c 0.0000000000 2.7718585823 0.0000000000 > c 2.7718585823 2.7718585823 0.0000000000 > > 1 f > 2 f > 3 f > > > -- Aaron Deskins Graduate Student Chemical Engineering Purdue University From chemistry-request@ccl.net Wed Jun 4 15:07:03 2003 Received: from mail.uvigo.es (mail.uvigo.es [193.146.32.91]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h54J72LB005363 for ; Wed, 4 Jun 2003 15:07:02 -0400 Received: from mail.uvigo.es (localhost [127.0.0.1]) by mail.uvigo.es (8.12.9/8.12.1) with ESMTP id h54J6v8o006370 for ; Wed, 4 Jun 2003 21:06:57 +0200 Received: from correo.uvigo.es (correo.uvigo.es [193.146.32.68]) by mail.uvigo.es (8.12.9/8.12.1) with ESMTP id h54J6vTA006365 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Wed, 4 Jun 2003 21:06:57 +0200 Received: from correo (correo [193.146.32.68]) by correo.uvigo.es (8.12.9/8.12.5) with ESMTP id h54J6vIF030992; Wed, 4 Jun 2003 21:06:57 +0200 Date: Wed, 4 Jun 2003 21:06:57 +0200 (CEST) From: Carlos Silva Lopez X-X-Sender: To: Lubos Vrbka cc: Subject: Re: CCL:chemical formula editors for windows In-Reply-To: <3EDDC287.2070609)at(chemi.muni.cz> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id h54J73LB005364 I would suggest the use of xdrawchem (for linux/unix) and/or windrawchem (for windows). Both are completely compatible, so you can share your files between the two plattforms. Regards _-_-_-_-_-_-_-_-_-_-_-_- Carlos Silva Lspez Dept. Qummica Organica Universidade de Vigo Phone:0034 986812226 -_-_-_-_-_-_-_-_-_-_-_-_ From chemistry-request@ccl.net Wed Jun 4 14:17:39 2003 Received: from kelly.bath.ac.uk (kelly.bath.ac.uk [138.38.32.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h54IHdLB004412 for ; Wed, 4 Jun 2003 14:17:39 -0400 Received: from mary.bath.ac.uk ([138.38.32.14] ident=mmdf) by kelly.bath.ac.uk with smtp id 19Ncp5-0004fE-3K; Wed, 04 Jun 2003 19:17:19 +0100 Received: from prpcn144 ( prpc-n144.bath.ac.uk [138.38.128.144] ) by bath.ac.uk id aa03238 ; 4 Jun 2003 19:17 +0100 From: James Robinson To: Aaron Deskins , chemistry)at(ccl.net Subject: RE: Freezing atoms-modredundant Date: Wed, 4 Jun 2003 19:17:34 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 In-Reply-To: <3EDDFB92.4090008)at(ecn.purdue.edu> X-Scanner: *19Ncp5-0004fE-3K*d8QNaXq/1Yg* Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h54IHdLB004413 You could use Molden to freeze atoms in the zmatrix. I have found writing a cartesian file with Mopac, then put zero for optimisation flags that you want to freeze. Then use Mopac to do a single point calculation, and include AIGOUT keyword and you get an equivalent zmatrix usable in Gaussian. Its not perfect but I have found it useful. I wonder also if you need some zeros after immediately after the atom labels, should it be ? C 0 0.000 0.000 0.000 C 0 0.000 1.500 0.000 James, Bath. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request)at(ccl.net]On Behalf Of Aaron Deskins Sent: 04 June 2003 15:01 To: chemistry)at(ccl.net Subject: CCL:Freezing atoms-modredundant Hello all, I have (hopefully) a relatively simple question. I'm trying some simple test calculations using Gaussian 98, but am running into a little problem freezing atom positions. Essentially I want to freeze a few atoms, and allow others to relax. Below is a test file. The problem I see is that the geometry optimization algorithm moves all atoms to the same location on first pass and subsequently causes the program to crash. I've tried different atoms and arrangements with no luck. Any suggestions? Thank you # opt(maxcycle=200,modredundant) hf/lanl2dz scf(diis,maxcycle=300) Title Card Required 0 3 c 0.0000000000 0.0000000000 0.0000000000 c 2.7718585823 0.0000000000 0.0000000000 c 0.0000000000 2.7718585823 0.0000000000 c 2.7718585823 2.7718585823 0.0000000000 1 f 2 f 3 f -- Aaron Deskins Graduate Student Chemical Engineering Purdue University -= This is automatically added to each message by mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY)at(ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jkl)at(ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+