From chemistry-request@ccl.net Thu Jul 15 21:14:52 2004 Received: from smtp.prodigy.net.mx (nlpproxy07.prodigy.net.mx [148.235.52.27]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6G2EoF0005208 for ; Thu, 15 Jul 2004 21:14:51 -0500 Message-Id: <200407160214.i6G2EoF0005208)at(server.ccl.net> Disposition-notification-to: dglossman)at(prodigy.net.mx Received: from smtp.prodigy.net.mx (nlpproxy07 [148.235.52.27]) by smtp.prodigy.net.mx (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTP id <0I0X002FSAIYFJ)at(smtp.prodigy.net.mx>; Thu, 15 Jul 2004 21:20:59 -0500 (CDT) Received: from laquicom (dsl-201-135-55-41.prod-infinitum.com.mx [201.135.55.41]) by smtp.prodigy.net.mx (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTP id <0I0X004X8AISFO)at(smtp.prodigy.net.mx>; Thu, 15 Jul 2004 21:20:58 -0500 (CDT) Date: Thu, 15 Jul 2004 20:20:58 -0600 From: Daniel Glossman Mitnik Subject: problem with Gaussian Freq calculation To: CHEMISTRY)at(ccl.net MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-Mailer: Microsoft Outlook, Build 10.0.6626 Content-type: multipart/related; boundary="----=_NextPart_000_0006_01C46AA9.3DA446D0" Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal X-imss-version: 2.5 X-imss-result: Passed X-imss-scores: Clean:19.83075 C:21 M:1 S:5 R:5 X-imss-settings: Baseline:3 C:2 M:2 S:2 R:2 (0.5000 1.0000) X-Spam-Status: No, hits=3.1 required=7.5 tests=HTML_60_70,HTML_FONTCOLOR_BLUE, HTML_FONTCOLOR_UNKNOWN,HTML_FONT_BIG,HTML_MESSAGE,MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0006_01C46AA9.3DA446D0 Content-Type: multipart/alternative; boundary="----=_NextPart_001_0007_01C46AA9.3DA928D0" ------=_NextPart_001_0007_01C46AA9.3DA928D0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear netters: =20 I have a problem with a Gaussian Freq calculation. I have performed the optimization of a rather large molecule (155 atoms) using G03W and DFT with a LANL2MB basis set. The optimization runs fine, but then I tried a frequency calculation and the calculation aborted with the following message: =20 Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. FoFCou: FMM=3DT IPFlag=3D 0 FMFlag=3D 100000 FMFlg1=3D = 8193 NFxFlg=3D 0 DoJE=3DF BraDBF=3DF KetDBF=3DF FulRan=3DT. Symmetry not used in FoFCou. FMM levels: 10 Number of levels for PrismC: 9 PrismC: NFx=3D 2048 NFxT=3D 12 NFxU=3D 11. PrismC: NFx=3D 2048 NFxT=3D 12 NFxU=3D 11. PrismC: NFx=3D 2048 NFxT=3D 12 NFxU=3D 11. There are 468 degrees of freedom in the 1st order CPHF. File extend in NtrExt1 failed; probably out of disk space. =20 I cannot understand the meaning of the failure because I think that disk space is enough. =20 Anyhow, I will be grateful if someone can help me to avoid this problem. =20 Thanks in advance =20 Daniel =20 *************************************************************************= *** ************************ Dr. Daniel Glossman-Mitnik CIMAV - Centro de Investigaci=F3n en Materiales Avanzados, SC QCOSMO - Grupo de Qu=EDmica Computacional, Simulaci=F3n y Modelado = Molecular Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - M=C9XICO Tel.: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: = daniel.glossman)at(cimav.edu.mx dglossman)at(prodigy.net.mx P=E1gina WEB: http://www.cimav.edu.mx http://www.qcosmo.org *************************************************************************= *** ************************=20 =20 ------=_NextPart_001_0007_01C46AA9.3DA928D0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear netters:

 

I have a problem = with a Gaussian Freq calculation. I have performed the = optimization

of a rather large = molecule (155 atoms) using G03W and DFT with a LANL2MB

basis set. The = optimization runs fine, but then I tried a frequency calculation and = the

calculation aborted = with the following message:

 

=A0=A0=A0=A0=A0=A0=A0=A0=A0 Differentiating once with respect to electric field.

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 with respect to dipole field.

=A0=A0=A0=A0=A0=A0=A0=A0=A0 Differentiating once with respect to nuclear coordinates.

=A0FoFCou: FMM=3DT IPFlag=3D=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0 FMFlag=3D=A0=A0=A0=A0=A0 100000 FMFlg1=3D=A0=A0=A0=A0=A0=A0=A0 = 8193

=A0NFxFlg=3D=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 0 DoJE=3DF BraDBF=3DF KetDBF=3DF FulRan=3DT.

=A0Symmetry not used in FoFCou.

=A0FMM = levels:=A0 10=A0 Number of levels for PrismC:=A0=A0 9

=A0PrismC:=A0 NFx=3D=A0=A0=A0=A0=A0 2048 NFxT=3D=A0=A0=A0=A0=A0=A0=A0 12 NFxU=3D=A0=A0=A0=A0=A0=A0=A0 = 11.

=A0PrismC:=A0 NFx=3D=A0=A0=A0=A0=A0 2048 NFxT=3D=A0=A0=A0=A0=A0=A0=A0 12 NFxU=3D=A0=A0=A0=A0=A0=A0=A0 = 11.

=A0PrismC:=A0 NFx=3D=A0=A0=A0=A0=A0 2048 NFxT=3D=A0=A0=A0=A0=A0=A0=A0 12 NFxU=3D=A0=A0=A0=A0=A0=A0=A0 = 11.

=A0=A0=A0=A0=A0=A0=A0=A0=A0 There are 468 degrees of freedom in the 1st order CPHF.

=A0File extend in NtrExt1 failed; probably out of disk space.

 

I cannot understand = the meaning of the failure because I think that disk space is = enough.

 

Anyhow, I will be = grateful if someone can help me to avoid this problem.

 

Thanks in = advance

 

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Daniel

=A0

***********************************= *****************************************************************<= /font>

    Dr. Daniel = Glossman-Mitnik

CIMAV - Centro de Investigaci=F3n en Materiales Avanzados, = SC

QCOSMO - Grupo de Qu=EDmica Computacional, Simulaci=F3n y Modelado = Molecular

Miguel de Cervantes 120 - Complejo Industrial Chihuahua

Chihuahua, Chih. 31109 - = M=C9XICO

Tel.: (52) 614 4391151           FAX: = (52) 614 4391112

E-mail:  = daniel.glossman)at(cimav.edu.mx       = dglossman)at(prodigy.net.mx

P=E1gina = WEB:  http://www.cimav.edu.mx       = http://www.qcosmo.org

***********************************= *****************************************************************<= /font> 

 

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id <0I0X00GYSOBUNW!at!smtp.unimi.it> for chemistry!at!ccl.net; Fri, 16 Jul 2004 09:19:07 +0200 (MEST) Date: Fri, 16 Jul 2004 09:31:36 +0200 From: Alessandro Contini Subject: Re: CCL:PCM calculations - transition state structure In-reply-to: <20040715153459.26891.qmail!at!web41502.mail.yahoo.com> To: "ManojKumar T. K." Cc: chemistry!at!ccl.net Reply-to: alessandro.contini!at!unimi.it Message-id: <200407160931.36830.alessandro.contini!at!unimi.it> Organization: =?iso-8859-1?q?Universit=E0=20di?= Milano MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-disposition: inline User-Agent: KMail/1.5.4 References: <20040715153459.26891.qmail!at!web41502.mail.yahoo.com> X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i6G7CskR015810 Hi Manojkumar, in locating a TS wich involved an hydrogen shift with PCM I had some good resuts by using the pauling radii (scrf=(pcm, read) and radii=pauling at the end of molecule specifications) instead that the default united atom UA0 model. In this way every hydrogen is explicit and things went fine. Hope this help, Alessandro Alle 17:34, giovedl 15 luglio 2004, ManojKumar T. K. ha scritto: > Hi all, > > > > I have problem with PCM calculations (optimization) > > of a transition state structure. (b3lyp/6-311++G** solvent=water) > > > > When optimizing using Gaussian-03, I am getting following error > > UA0: Hydrogen 9 is unbound. Keep it explicit at all point on the > > UA0: potential energy surface to get meaningful results > > > > The error is coming with the sphereonH=9 also. > > > > It would be a great help for me, if some one can > > suggest me a solution for this. > > > > Sincerely > > > > Manojkumar > > > > --------------------------------- > Do you Yahoo!? > New and Improved Yahoo! Mail - Send 10MB messages! -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini!at!unimi.it From chemistry-request@ccl.net Fri Jul 16 15:31:29 2004 Received: from exmails1.chem.ucla.edu (exmails1.chem.ucla.edu [169.232.134.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6GKVQkR020415 for ; Fri, 16 Jul 2004 15:31:26 -0500 Received: from chem.ucla.edu (d-128-97-138-138.chem.ucla.edu [128.97.138.138]) by exmails1.chem.ucla.edu (8.12.8/8.12.8) with ESMTP id i6GKbYEa013861; Fri, 16 Jul 2004 13:37:34 -0700 Date: Fri, 16 Jul 2004 13:42:43 -0700 Subject: International Conference on Philosophy of Chemistry Content-Type: multipart/alternative; boundary=Apple-Mail-4-34214313 Mime-Version: 1.0 (Apple Message framework v553) Cc: chemed~at~exmails1.chem.ucla.edu, HOPOS~at~exmails1.chem.ucla.edu, hist~at~exmails1.chem.ucla.edu, CCL To: philchem philchem From: Eric Scerri In-Reply-To: <38F4279E-D765-11D8-BD28-000A95945A0E~at~chem.ucla.edu> Message-Id: X-Mailer: Apple Mail (2.553) X-Spam-Status: No, hits=2.6 required=7.5 tests=HTML_30_40,HTML_MESSAGE, IMPRONONCABLE_1,MK_BAD_HTML_04,MY_HTML_OBFU autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --Apple-Mail-4-34214313 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed 8th International Conference on Philosophy of Chemistry, University of Durham, August 15-19th. > http://www.georgetown.edu/faculty/earleyj/ISPC.html > Monday 16th August > > 9am Michael Akeroyd > Bradford College > Mechanistic Explanation versus Deductive-Nomological Explanation > Melville Room > Leo N=E4pinen > Tallinn University > The need for historical understanding of nature in physics and=20 > chemistry > Senior Common Room > 10am R.J. Snooks > University of Toronto > Another scientific practice separating chemistry from physics: thought=20= > experiments > Melville Room > Guillermo Restrepo > Universidad de Pamplona > Are chemical and physical concepts appropriate to matter=20 > classification? > Senior Common Room > 11am Tea and coffee > 11.30am David Knight > University of Durham > Baconian Induction or Deductive Logic: Chemistry in the early 19th=20 > century > Melville Room > 12.30pmLunch > 1.30pm > Fernanda Madalena, Elisa Maia and Sara Carvalho > Lisbon University Museum of Science > The origin of research schools of chemistry in the 19th Century and=20 > the rising of the different areas of chemistry > Melville Room > Grant Fisher > University of Leeds > Developmental Models in the Early History of 'Pericyclic' Reaction:=20 > The Cope and Claisen Rearrangements > Senior Common Room > 2.30pm Nikodem Miranowicz > Adam Mickiewicz University, Poznan > How do we see science? Categories of illustrations in science = textbooks > Melville Room > Michael Weisberg > University of Pennsylvania > Modeling in Chemistry > Senior Common Room > 3.30pm Tea and coffee > 4pm Anne Chapman > University of Lancaster > Natural and non-natural chemicals > Melville Room > Robin Findlay Hendry > University of Durham > Elements and other chemical kinds > Senior Common Room > 5pm Wybo Houkes and Pieter Vermaas > Delft University of Technology > A functional puzzle in chemistry > Melville Room > Valentin N. Ostrovsky > V. Fock Institute of Physics, St Petersburg State University > Towards philosophy of approximations in =91exact=92 sciences > Senior Common Room > > Tuesday 17th August > 9am Paul Needham > University of Stockholm > Processes > Melville Room > Ko Hojo > Process and Place: Structure of Experience and Structure of=20 > Consciousness > Senior Common Room > 10am G.K. Vemulapalli > University of Arizona > Fugacity: A Uniquely Chemical Concept > Melville Room > Slawomir Michalak > University of Medical Sciences, Poznan > Ice =96 9: two faces of the same metaphor > Senior Common Room > 11amTea and coffee11.30am > Alan Chalmers > Flinders University > The status of Daltonian atomism > Melville Room > 12.30pmLunch > 1.30pm Eric Scerri, UCLA > Some questions concerning the theoretical foundations > of the periodic system and the nature of the elements. > Melville Room > Hans Grelland > Agder University College > The Philosophy of pH. A deconstructive approach > Senior Common Room > 2.30pm Eugen Schwarz > University of Siegen > Explanations of the periodic table of chemical elements using concepts=20= > of quantum physics: the view of a chemical scientist and quantum=20 > theoretician. > Melville Room > Magdalen Self and Claus Jacob > University of Exeter > The impact factor in chemical research > Senior Common Room > 3.30pmTea and coffee > 4pm Mark R. Leach > Meta-Synthesis > Quantum patterns, classical linearities and chemical chaos > Melville Room > Paul Bogaard > Mount Allison University > =93After Substance:=94 > How Aristotle's argument still bears on the Philosophy of Chemistry > Senior Common Room > 5pm Hrvoj Vancik > University of Zagreb > Behind the Limits of Complexity > Melville Room > Joseph Earley, Sr. > Georgetown University > =91La Nouvelle Alliance=92 =97 and its Opponents > Senior Common Room. > Wednesday 18th August > 9am Werner Brandt > University of Wisconsin - Milwaukee > Nonreductive physicalism and emergentism in chemistry > Melville Room > Christina McLeish > University of Cambridge > How not to talk about phlogiston: truth in the mouths of past chemists > Senior Common Room > 10am Rein Vihalemm > University of Tartu > Understanding the Theory of Chemical Structure and its History > Melville Room > Ioannis Votsis > London School of Economics > Caloric: Centre or Offstage? > Senior Common Room11amTea and coffee > 11.30am Rom Harr=E9 > University of Oxford > Activity Concepts in Chemistry: A Philosophico-Historical Examination > Melville Room > 12.30pmLunch > 1.30pm Jaap van Brakel > KU Leuven > Modelling in chemical engineering > Melville Room3-5pm > Rare books session, Palace Green Library > 7pmConference dinner, Hatfield College > > > Dr. Eric Scerri, Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA 90095- 1569 E-mail scerri~at~chem.ucla.edu Tel: 310 206 7443 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.kluweronline.com/issn/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html --Apple-Mail-4-34214313 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 8th International Conference on Philosophy of Chemistry, University of Durham, August 15-19th. = Timeshttp://www.georget= own.edu/faculty/earleyj/ISPC.html TimesMonday 16th August = Times9am=20 Michael Akeroyd Bradford College Mechanistic Explanation versus Deductive-Nomological Explanation Melville Room TimesLeo N=E4pinen Tallinn University The need for historical understanding of nature in physics and chemistry Senior Common Room Times10am R.J. Snooks University of Toronto Another scientific practice separating chemistry from physics: thought experiments Melville Room TimesGuillermo Restrepo Universidad de Pamplona Are chemical and physical concepts appropriate to matter classification? Senior Common Room Times11am Tea and coffee Times11.30am=20 David Knight University of Durham Baconian Induction or Deductive Logic: Chemistry in the early 19th century Melville Room Times12.30pmLunch = Times1.30pm TimesFernanda Madalena, Elisa Maia and Sara Carvalho Lisbon University Museum of Science The origin of research schools of chemistry in the 19th Century and the rising of the different areas of chemistry Melville Room TimesGrant Fisher University of Leeds Developmental Models in the Early History of 'Pericyclic' Reaction: The Cope and Claisen Rearrangements Senior Common Room Times2.30pm=20 Nikodem Miranowicz Adam Mickiewicz University, Poznan How do we see science? Categories of illustrations in science textbooks Melville Room TimesMichael Weisberg University of Pennsylvania Modeling in Chemistry Senior Common Room Times3.30pm =20 Tea and coffee Times4pm Anne Chapman University of Lancaster Natural and non-natural chemicals Melville Room TimesRobin Findlay Hendry University of Durham Elements and other chemical kinds Senior Common Room Times5pm Wybo Houkes and Pieter Vermaas Delft University of Technology A functional puzzle in chemistry Melville Room TimesValentin N. Ostrovsky V. Fock Institute of Physics, St Petersburg State University Towards philosophy of approximations in =91exact=92 sciences Senior Common Room TimesTuesday 17th August = Times9am=20 Paul Needham University of Stockholm Processes Melville Room TimesKo Hojo Process and Place: Structure of Experience and Structure of Consciousness Senior Common Room Times10am G.K. Vemulapalli University of Arizona Fugacity: A Uniquely Chemical Concept Melville Room TimesSlawomir Michalak University of Medical Sciences, Poznan Ice =96 9: two faces of the same metaphor Senior Common Room Times11amTea and coffee11.30am TimesAlan Chalmers Flinders University The status of Daltonian atomism Melville Room Times12.30pmLunch Times1.30pm=20 Eric Scerri, UCLA TimesSome questions concerning the theoretical foundations=20 of the periodic system and the nature of the elements. = Times= Melville Room TimesHans Grelland Agder University College The Philosophy of pH. A deconstructive approach Senior Common Room Times2.30pm Eugen Schwarz University of Siegen Explanations of the periodic table of chemical elements using concepts of quantum physics: the view of a chemical scientist and quantum theoretician. Melville Room TimesMagdalen Self and Claus Jacob University of Exeter The impact factor in chemical research Senior Common Room Times3.30pmTea and coffee Times4pm Mark R. Leach Meta-Synthesis Quantum patterns, classical linearities and chemical chaos Melville Room TimesPaul Bogaard Mount Allison University =93After Substance:=94 How Aristotle's argument still bears on the Philosophy of Chemistry Senior Common Room Times5pm Hrvoj Vancik University of Zagreb Behind the Limits of Complexity Melville Room TimesJoseph Earley, Sr. Georgetown University =91La Nouvelle Alliance=92 =97 and its Opponents Senior Common Room. TimesWednesday 18th August = Times9am=20 Werner Brandt University of Wisconsin - Milwaukee Nonreductive physicalism and emergentism in chemistry Melville Room TimesChristina McLeish University of Cambridge How not to talk about phlogiston: truth in the mouths of past chemists Senior Common Room Times10am Rein Vihalemm University of Tartu Understanding the Theory of Chemical Structure and its = History Melville Room TimesIoannis Votsis London School of Economics Caloric: Centre or Offstage? Senior Common Room11amTea and coffee Times11.30am=20 Rom Harr=E9 University of Oxford Activity Concepts in Chemistry: A Philosophico-Historical Examination Melville Room Times12.30pmLunch Times1.30pm=20 Jaap van Brakel KU Leuven Modelling in chemical engineering Melville Room3-5pm TimesRare books session, Palace Green Library Times7pmConference dinner, Hatfield College Dr. Eric Scerri, Department of Chemistry & Biochemistry, UCLA, Los Angeles, CA 90095- 1569 E-mail scerri~at~chem.ucla.edu Tel: 310 206 7443 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.kluweronline.com/issn/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html =20 --Apple-Mail-4-34214313-- From chemistry-request@ccl.net Fri Jul 16 10:41:00 2004 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6GFexkR004058 for ; Fri, 16 Jul 2004 10:40:59 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0I0Y00ERPBUTPF_at_mailserver.unimi.it> for CHEMISTRY_at_ccl.net; Fri, 16 Jul 2004 17:47:17 +0200 (MEST) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0I0Y00HI6BUPN3_at_smtp.unimi.it> for CHEMISTRY_at_ccl.net; Fri, 16 Jul 2004 17:47:13 +0200 (MEST) Date: Fri, 16 Jul 2004 17:59:48 +0200 From: Alessandro Contini Subject: Re: CCL:problem with Gaussian Freq calculation In-reply-to: <200407160214.i6G2EoF0005208_at_server.ccl.net> To: Daniel Glossman Mitnik Cc: CHEMISTRY_at_ccl.net Reply-to: alessandro.contini_at_unimi.it Message-id: <200407161759.49087.alessandro.contini_at_unimi.it> Organization: =?iso-8859-1?q?Universit=E0=20di?= Milano MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-disposition: inline User-Agent: KMail/1.5.4 References: <200407160214.i6G2EoF0005208_at_server.ccl.net> X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i6GFf0kR004062 Hi Daniel, probably the problem you are facing depends to the inability of your version gaussian to treat .rwf files greater than 2GB, as are often produced by large freq calculations. All 32-bit operating systems (e.g. Windows) are limited to 16 GB of scratch space for each calculation and this space must be divided into 2 GB pieces. This can be solved by specifying the keyword "MaxDisk=1960MW" (that somehow works better than "MaxDisk=16GB") and by adding a line to your root section with: %rwf=a,245mw,b,245mw,c,245mw,d,245mw,e,245mw,f,245mw,g,245mw,h,245mw where a, b, c etc. are arbitrary names. Hope this help, Alessandro Alle 04:20, venerdl 16 luglio 2004, Daniel Glossman Mitnik ha scritto: > Dear netters: > > > > I have a problem with a Gaussian Freq calculation. I have performed the > optimization > > of a rather large molecule (155 atoms) using G03W and DFT with a LANL2MB > > basis set. The optimization runs fine, but then I tried a frequency > calculation and the > > calculation aborted with the following message: > > > > Differentiating once with respect to electric field. > > with respect to dipole field. > > Differentiating once with respect to nuclear coordinates. > > FoFCou: FMM=T IPFlag= 0 FMFlag= 100000 FMFlg1= 8193 > > NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T. > > Symmetry not used in FoFCou. > > FMM levels: 10 Number of levels for PrismC: 9 > > PrismC: NFx= 2048 NFxT= 12 NFxU= 11. > > PrismC: NFx= 2048 NFxT= 12 NFxU= 11. > > PrismC: NFx= 2048 NFxT= 12 NFxU= 11. > > There are 468 degrees of freedom in the 1st order CPHF. > > File extend in NtrExt1 failed; probably out of disk space. > > > > I cannot understand the meaning of the failure because I think that disk > space is enough. > > > > Anyhow, I will be grateful if someone can help me to avoid this problem. > > > > Thanks in advance > > > > Daniel > > > > *************************************************************************** >* ************************ > > Dr. Daniel Glossman-Mitnik > > CIMAV - Centro de Investigacisn en Materiales Avanzados, SC > > QCOSMO - Grupo de Qummica Computacional, Simulacisn y Modelado Molecular > > Miguel de Cervantes 120 - Complejo Industrial Chihuahua > > Chihuahua, Chih. 31109 - MIXICO > > Tel.: (52) 614 4391151 FAX: (52) 614 4391112 > > E-mail: > daniel.glossman_at_cimav.edu.mx > dglossman_at_prodigy.net.mx > > Pagina WEB: http://www.cimav.edu.mx > http://www.qcosmo.org > > *************************************************************************** >* ************************ -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini_at_unimi.it From chemistry-request@ccl.net Fri Jul 16 13:58:23 2004 Received: from web51301.mail.yahoo.com (web51301.mail.yahoo.com [206.190.38.167]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i6GIwLkR010277 for ; Fri, 16 Jul 2004 13:58:22 -0500 Message-ID: <20040716190435.17436.qmail/at/web51301.mail.yahoo.com> Received: from [206.111.112.115] by web51301.mail.yahoo.com via HTTP; Fri, 16 Jul 2004 12:04:35 PDT Date: Fri, 16 Jul 2004 12:04:35 -0700 (PDT) From: Sengen Sun Subject: CCL: Re: Question on molecular structure and QM To: chemistry/at/ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.3 required=7.5 tests=FVGT_s_OBFU_Q1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net molecular structure cannot be strictly deduced from QM. I certainly have a problem with such a claim. I got some hints from the earlier posts on this subject. The question in mind is what the strict or pure QM really means. Scientific theories can only be used to treat some defined or roughly defined physical events. For example, we can describe an apple falling down > from a tree to the ground. It is totally a separate issue that the apple is blown up into sky by a tornado. That is, we cannot solve a universal equation for the apple floating in the whole universe without knowing where it is and what it does and why it does what. The same thing is true in QM. A Hamiltonian for a set of nuclei and electrons remains meaningless without boundary conditions that define a particular physical event. The nuclei and electrons could be anywhere in the whole universe at anytime for any reason! It would be crazy to dream of a strict WF in this situation or to dream of extracting something physically meaningful from it. It is meaningless and useless. Further in terms of molecular structures, I don t think that QM under B-O approximation is less strict than time-dependant QM. At any given time point, the nuclear positions are defined. In this sense, the BO approximation is not simply an approximation but an approach that defines and extracts the issue of concern, as Konrad Hinsen pointed out earlier. I probably have philosophical difficulties. But I hardly see that chemists molecular structures are just an approximation of strict QM. Each molecular structure represents a set of nuclei and electrons in a defined physical setting. When you apply a time-dependent QM, you at least have to define whether you are studying chemical reactions or a stable substance. It is not a realistic science to include everything with all the nuclei indistinguishable. If strict QM exists, we can deduce molecular structures strictly from the strict QM by applying boundary conditions unless we choose not to. It is totally different thing if we don t think the strict QM really exists at all. Finally, should human pursue a more strict science so that the whole universe is mixed up that no one distinguishes anything in it? Less strict science would be much better?. What is the purpose of that more strict science? I certainly have to learn and think more on this in order to understand better. Thanks for attention. Sengen __________________________________ Do you Yahoo!? New and Improved Yahoo! Mail - 100MB free storage! http://promotions.yahoo.com/new_mail From chemistry-request@ccl.net Fri Jul 16 09:50:25 2004 Received: from mx3.trentu.ca (mx3.trentu.ca [192.75.12.4]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i6GEoOkR001309 for ; Fri, 16 Jul 2004 09:50:24 -0500 Received: (qmail 23936 invoked by uid 510); 16 Jul 2004 14:56:38 -0000 Received: from elewars$at$trentu.cA by mx3.trentu.ca by uid 501 with qmail-scanner-1.20rc3 (f-prot: 4.4.1/3.14.11. spamassassin: 2.62. Clear:RC:1:. Processed in 0.019303 secs); 16 Jul 2004 14:56:38 -0000 X-Qmail-Scanner-Mail-From: elewars$at$trentu.cA via mx3.trentu.ca X-Qmail-Scanner: 1.20rc3 (Clear:RC:1:. Processed in 0.019303 secs) Received: from unknown (HELO trentu.cA) (209.42.102.47) by mx3.trentu.ca with SMTP; 16 Jul 2004 14:56:38 -0000 Message-ID: <40F7EDB9.3020007$at$trentu.cA> Date: Fri, 16 Jul 2004 11:01:14 -0400 From: Errol Lewars User-Agent: Mozilla/5.0 (Windows; U; WinNT4.0; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry$at$ccl.net Subject: Re: CCL:Gaussian output treatment, answer References: <1089839083.40f59feb5cd64$at$webmail.nd.edu> In-Reply-To: <1089839083.40f59feb5cd64$at$webmail.nd.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=2.2 required=7.5 tests=MK_YAHOO_REDIR_01, WLS_URI_OPT_150 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net 2004 July 16 re contributions to MOs: I suspect the kind of information you want will come from an NBO analysis. Look in the Gaussian manual, and consult the literature references given there; also, a detailed manual devoted to NBO analysis can be bought from Gaussian Inc. EL === Jan K Labanowski wrote: >----- Forwarded message from Godefroid Gahungu ----- > Date: Wed, 14 Jul 2004 07:51:45 +0200 (CEST) > From: Godefroid Gahungu >Reply-To: ggahungu$at$yahoo.fr > Subject: Gaussian output treatment! > To: jlabanow$at$nd.edu > >My greetings first, > > > > I am a new user of Gaussian program. I was navigating when I saw your site something >very interesting for from your site. In fact, I was looking for a help with Guassian 98 >calculation, but haven`t been able to ask my questions to the Users. The following was my >question: > > From a Single Point calculation or let`s say an structural optimization out file, >how can I extract or calculate the Percent Compositions (% atomic contribution) of >Molecular orbitals (e.g for the HOMO and LUMO)? Can any one suggests another way to >solve this problem? > > Thanks alot for your coming help. > > >--------------------------------- >Criez gratuitement votre Yahoo! Mail avec 100 Mo de stockage ! >Criez votre Yahoo! Mail > >Dialoguez en direct avec vos amis grbce ` Yahoo! Messenger ! >----- End forwarded message ----- > > > > > > ------------------------------------------------------------------------ > > My greetings first, > > > > I am a new user of Gaussian program. I was navigating when I saw > your site something very interesting for from your site. In fact, I > was looking for a help with Guassian 98 calculation, but haven`t been > able to ask my questions to the Users. The following was my question: > > From a Single Point calculation or let`s say an structural > optimization out file, how can I extract or calculate the Percent > Compositions (% atomic contribution) of Molecular orbitals (e.g for > the HOMO and LUMO)? Can any one suggests another way to solve this > problem? > > Thanks alot for your coming help. > > ------------------------------------------------------------------------ > Criez gratuitement votre Yahoo! Mail avec *100 Mo de stockage !* > Criez votre Yahoo! Mail > > > > Dialoguez en direct avec vos amis grbce ` Yahoo! Messenger ! > From chemistry-request@ccl.net Fri Jul 16 15:05:20 2004 Received: from smtp4.es.uci.edu (smtp4.es.uci.edu [128.200.80.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6GK5IkR012341 for ; Fri, 16 Jul 2004 15:05:19 -0500 Received: from 128.200.204.164 (dhcp-204164.bio.uci.edu [128.200.204.164]) by smtp4.es.uci.edu (8.12.8/8.12.8) with ESMTP id i6GKBMRs015701 for ; Fri, 16 Jul 2004 13:11:27 -0700 Date: Fri, 16 Jul 2004 13:11:17 -0700 From: Qiang Lu X-Mailer: The Bat! (v1.62r) Reply-To: Qiang Lu Organization: UCI MBB X-Priority: 3 (Normal) Message-ID: <1419415672.20040716131117$at$uci.edu> To: chemistry$at$ccl.net Subject: Question about binding energy and deprotonation energy MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-NACS_ES-MailScanner: No viruses found X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi CCLERs, Think about the following two reaction: A + B-H = AB-H A + B = AB The total energy of AB-H is lower than AB, but the binding energy between A and B of AB is higher than that of AB-H. Then which state is prefer between AB-H and AB? In another words, is it prefer a deprotonated state of AB-H or not in the nature? -- Best regards, Qiang Lu mailto:qiangl$at$uci.edu From chemistry-request@ccl.net Fri Jul 16 10:26:08 2004 Received: from mx3.trentu.ca (mx3.trentu.ca [192.75.12.4]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i6GFQ7kR003475 for ; Fri, 16 Jul 2004 10:26:07 -0500 Received: (qmail 3156 invoked by uid 510); 16 Jul 2004 15:32:23 -0000 Received: from elewars^at^trentu.cA by mx3.trentu.ca by uid 501 with qmail-scanner-1.20rc3 (f-prot: 4.4.1/3.14.11. spamassassin: 2.62. Clear:RC:1:. Processed in 0.049382 secs); 16 Jul 2004 15:32:23 -0000 X-Qmail-Scanner-Mail-From: elewars^at^trentu.cA via mx3.trentu.ca X-Qmail-Scanner: 1.20rc3 (Clear:RC:1:. Processed in 0.049382 secs) Received: from unknown (HELO trentu.cA) (209.42.102.47) by mx3.trentu.ca with SMTP; 16 Jul 2004 15:32:23 -0000 Message-ID: <40F7F61A.2080201^at^trentu.cA> Date: Fri, 16 Jul 2004 11:36:58 -0400 From: Errol Lewars User-Agent: Mozilla/5.0 (Windows; U; WinNT4.0; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry^at^ccl.net Subject: CCL: conformers and rate, MORE Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net 2004 July 16 Two more contributions to the question below. Thanks very much. ---- QUESTION 2004 July 8 The rate of formation of products Pa and Pb from quickly interconverting conformers Ca and Cb is treated with the the Curtin/Hammett and Winstein-Holness equations (the Curtin-Hammett principle, in particular, is well-known): J. I Seeman, Chem Rev, 1983, 83, 83; E. L. Eliel, "From Cologne to Chapel Hill", ACS, 1990, pp. 31-33. Question: has anyone a reference to a discussion of the case of rapidly interconverting conformers Ca and Cb, where Ca, although the minor conformer, is the only one that can react with X to form a product CaX, through transition state Ta; intuition aside, has someone explicitly addressed whether the _experimental_ activation E is measuring the Ta-Ca energy difference, or the Ta-Cb difference? Thanks. EL === 1 A _very_ detailed kinetic treatment of various situations: "It looks to me that some part of our paper A computational study-of the hydroxy-group directivity in the peroxyformic acid epoxidation of the chiral allylic alcohol (Z)-3-methyl-3-penten-2-ol: Control of threo diastereoselectivity through allylic strain and hydrogen bonding" JOURNAL OF ORGANIC CHEMISTRY 65 (20): 6715-6728 OCT 6 2000 could be of some use for you. We discuss there multi-transition state reaction using an extended Curtin-Hammet principle." Best regards, Olga Dmitrenko ------- 2 An addendum: Dear Per-Ola, regarding the discussion in CCL on the rates, where both of us replied, I now fully agree with you. In my comment I forgot the fact that the population of Ca increases with exp(-(Ca-Cb)/kT) and hence this adds to the apparent activation energy. On the other hand in a rigorous definition of the activation energy we would have extracted the population of the start species out of the rate constant and then the temperature dependence of the rate constant obviously would depend on exp(-(Ta-Ca)/kT). But I guess your andwer is more what is requested here. Andreas Dr Andreas Klamt COSMOlogic GmbH&CoKG ======================================