From chemistry-request@ccl.net Wed Oct 15 01:51:41 2003 Received: from kdmail2.netcologne.de (kdmail2.netcologne.de [194.8.194.86]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9F5pAdH015640 for ; Wed, 15 Oct 2003 01:51:10 -0400 Received: from cosmologic.de (xdsl-213-168-109-204.netcologne.de [213.168.109.204]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 3.3.6-GR) with ESMTP id ABB22475 (AUTH klamt-.at.-cosmologic.de); Wed, 15 Oct 2003 07:51:08 +0200 (CEST) Message-ID: <3F8CE049.1080402-.at.-cosmologic.de> Date: Wed, 15 Oct 2003 07:51:05 +0200 From: Andreas Klamt User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; 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: Re: CCL:2nd Industrial Fluids Properties Simulation Challenge References: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-1.1 required=7.0 tests=EMAIL_ATTRIBUTION,REFERENCES,USER_AGENT_MOZILLA_UA, X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear Colleagues, I just like to point out a small drawback of the 2nd challenge: For what reason ever the organization committee decided to exclude all methods > from the competition (or at least from the candidates to be winners) which do not obey their definition of molecular simulation given on their web page. This definition is constructed exactly in a way, that it excludes my COSMO-RS method, which happened to be winner of the VLE part of the first competition. Since all 3 problem sets given this time are VLE problems, there would have been a good chance for us to do a good job this time again. It would take us about a day to solve the given problems with our COSMO-RS method. But we do not want to participate as second class contributors. Therefore we will publish our results for the problem sets exactly on the day of the submission deadline on our homepage. So everybody who is interested to see our performance for the contest will be able to see them and compare them with the final submissions. If the goal of the contest really would be to "to obtain an in-depth and objective assessment of our current abilities and inabilities in the prediction of physical properties for industrially challenging fluids", then I do not see a good reason to exclude one proven powerful approach > from the contest. COSMO-RS is a combination of good quality quantum chemistry with good quality statistical thermodynamics, and we are just making our approximations at different points than the MD/MC force field methods. Regards Andreas Dr. Jan K Labanowski wrote: >---------- Forwarded message ---------- >Date: Wed, 24 Sep 2003 15:07:08 -0500 >From: rbross-.at.-mmm.com >To: jkl-.at.-ccl.net > >Topic: 2nd Industrial Fluids Properties Simulation Challenge > >It is with great pleasure we announce the Second Industrial Fluid >Properties Simulation Challenge. The second challenge follows the >successful conclusion of the first challenge which led to significant >assessment and advancements of simulation methodology via the application >to research challenge problems for prediction of vapor-liquid equilibria, >density, and viscosity. The Second Simulation Challenge will focus on >prediction of vapor pressures and heats of vaporization, gas solubility, >and enthalpies of mixing for materials. For details on Second Simulation >Challenge as well as on the results of the first competition and could you >please see the attached announcement and/or >http://www.cstl.nist.gov/FluidSimulationChallenge. > >The goal of the Industrial Fluid Properties Simulation Challenge (IFPSC) >is to obtain an in-depth and objective assessment of our current abilities >and inabilities in the prediction of physical properties for industrially >challenging fluids. > >The accuracy of property prediction is based on the choice of forcefield >and modeling technique. As a result, it is anticipated that the awardees >of each problem in this competition will develop or apply an accurate and >general forcefield that can model a range of different chemistries and >develop or apply a modeling technique that can handle materials in different >states (liquid/vapor), is precise and accurate, and computationally swift. > >Industrial and NIST Organizing Committee > > >-= This is automatically added to each message by the 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) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt-.at.-cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@ccl.net Wed Oct 15 02:49:42 2003 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 h9F6nAdH016631 for ; Wed, 15 Oct 2003 02:49:10 -0400 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 <0HMS00AV6DLYLG~at~mailserver.unimi.it> for chemistry~at~ccl.net; Wed, 15 Oct 2003 08:49:11 +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 <0HMS00HQLDLXRG~at~smtp.unimi.it> for chemistry~at~ccl.net; Wed, 15 Oct 2003 08:49:09 +0200 (MEST) Received: by heisenberg.chimica.unimi.it (Postfix, from userid 500) id 912BB1504D; Wed, 15 Oct 2003 08:59:57 +0200 (CEST) Received: from localhost (localhost [127.0.0.1]) by heisenberg.chimica.unimi.it (Postfix) with ESMTP id 8B2AE1503F; Wed, 15 Oct 2003 08:59:57 +0200 (CEST) Date: Wed, 15 Oct 2003 08:59:57 +0200 (CEST) From: Alessandro Contini Subject: Re: CCL:AutoDock output file format In-reply-to: <3F8BCEEB.235046D~at~unisi.it> To: Stefano Forli Cc: chemistry~at~ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=UTF-7 References: <3F8BCEEB.235046D~at~unisi.it> X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id h9F6ngdH016645 Hi Stefano, I feel pretty good using AutodockTools, wich is free downloadable from the scripps site (http://www.scripps.edu/pub/olson-web/dock/autodock/). It can handle pdb and mol2 file formats in reading and writing and it can display docking results, surfaces, h bonds etc. Another nice program is VMD (http://www.ks.uiuc.edu/Research/vmd/), witch uses OpenBabel to handle many different file formats. Reguards, Alessandro 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 On Tue, 14 Oct 2003, Stefano Forli wrote: > Dear all, > what is the best way to analyze the output structures of autodock jobs? > I found some scripts (PDB_to_car.bcl and car2arc.awk) to convert pdb > files in arc files for insightII, but it's unformatted so all lines are > merged, and are unreadable. > I even tried babel to make some conversion, but I don't know what is the > best mix of formats to load protein and ligands (in our lab we have > Macromodel too). > Any suggestion will be appreciated... > Thanks > > Stefano > > -- > > *********************************** > Dr. Forli Stefano PhD Student > Dip. Farmaco Chimico Tecnologico > Universita' degli Studi di Siena > Via Aldo Moro > I-53100 Siena, Italy > Phone: ++39 0577 234307 > Fax: ++39 0577 234333 > *********************************** > > > -= This is automatically added to each message by the 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 Oct 15 03:18:41 2003 Received: from nankai.edu.cn (sun.nankai.edu.cn [202.113.16.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9F7I2dH017322 for ; Wed, 15 Oct 2003 03:18:05 -0400 Resent-Date: Wed, 15 Oct 2003 03:18:02 -0400 Resent-Message-Id: <200310150718.h9F7I2dH017322(at)server.ccl.net> Received: (eyou send program); Wed, 15 Oct 2003 15:18:46 +0800 Received: from unknown (HELO 192.168.0.101) (unknown@128.195.87.184) by 202.113.16.21 with SMTP; Wed, 15 Oct 2003 15:18:46 +0800 Date: Wed, 15 Oct 2003 00:17:41 -0700 From: John Lee X-Mailer: The Bat! (v1.62r) Reply-To: John Lee X-Priority: 3 (Normal) Message-ID: <1846911240.20031015001741(at)joyie.com> To: "Cust . Service Doug" CC: chemistry(at)ccl.net Subject: Re[2]: CCL:GDIIS and Z-MATRIX Resent-from: John Lee MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.3 required=7.0 tests=EMAIL_ATTRIBUTION,FROM_ENDS_IN_NUMS,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Cust., I the simulation of 4-8 water cluster, I want to keep all the distances between neighbor oxygen the same. However it was hard to converge with B3LYP 6-311++G** and tight if I didn't use GDIIS. If I use GDIIS the distances will not be the same. Thanks for your reply. John Tuesday, October 14, 2003, 5:27:52 PM, you wrote: CSD> John, CSD> Why do you need to use GDIIS? CSD> Note that this would break symmetry only if you are using the Z-matrix CSD> to define symmetry which is not really in the molecule? >> >> Hi CCLers, >> >> Z-matrix optimization only work with Berny algorithm. >> What if I have to use GDIIS and still want to control the zmatrix >> symmetry. Is there a way to do it? >> >> >> >> -- >> Best regards, >> John >> >> >> >> -= This is automatically added to each message by the 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) >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >> >> >> >> >> -- Best regards, John Lee From chemistry-request@ccl.net Wed Oct 15 07:44:21 2003 Received: from hqmail1.corp.aspentech.com ([192.160.187.80]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9FBhndH025007 for ; Wed, 15 Oct 2003 07:43:50 -0400 Received: by hqmail1.corp.aspentech.com with Internet Mail Service (5.5.2653.19) id <4ZR9M38R>; Wed, 15 Oct 2003 07:43:50 -0400 Message-ID: <63799630D1424545BB6E6B0E98FE2B5604968849_at_hqmail1.corp.aspentech.com> From: "Mathias, Paul" To: "'Andreas Klamt'" , chemistry_at_ccl.net Subject: RE: 2nd Industrial Fluids Properties Simulation Challenge Date: Wed, 15 Oct 2003 07:43:49 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=-0.1 required=7.0 tests=EMAIL_ATTRIBUTION,ORIGINAL_MESSAGE,QUOTED_EMAIL_TEXT, RCVD_IN_RFCI version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I second Andreas's opinion. The write-up for the 2nd Industrial Fluids Properties Simulation Challenge points out the importance of predicting fluid properties. I completely agree with that! But the sponsors of the contest are also limiting the methods to solve the problem. That's contrary to the way good technology is developed, which often is the benefit of favorable unintended consequences. The contest should be one of market pull. Define the problem, widely advertise the problem, but don't limit the solution approach. Perhaps a good creative scientist in a different field will propose an entirely new method. As Andreas writes, COSMO-RS makes different approximations than the MD/MC force-field methods where the approximation is in the intermolecular forces, the need for multi-body corrections, etc. etc. COSMO-RS calculations are much faster than the MD/MC force-field methods, and this is critically important to industrial applications. Which one is better? I don't know yet. Neither does anyone else. Why limit the development of either method? The real issue is that we need an open mind and more creative solutions to the problem. The contest sponsors are suppressing creativity by limiting the solution approach. Why not create a perturbative method from the vast existing database? The weather folks don't predict tomorrow's weather in Boston by calculations alone. We need quality of results, not some narrowly defined, subjective purity of approach. As one who makes his living from simulating real plants and processes, I know the value of good data and the need for better data and predictive methods. The currently defined contest does not encourage new creative predictive solutions. Paul Mathias Aspen Technology -----Original Message----- From: Andreas Klamt [mailto:klamt_at_cosmologic.de] Sent: Wednesday, October 15, 2003 1:51 AM To: chemistry_at_ccl.net Subject: CCL:2nd Industrial Fluids Properties Simulation Challenge Dear Colleagues, I just like to point out a small drawback of the 2nd challenge: For what reason ever the organization committee decided to exclude all methods > from the competition (or at least from the candidates to be winners) which do not obey their definition of molecular simulation given on their web page. This definition is constructed exactly in a way, that it excludes my COSMO-RS method, which happened to be winner of the VLE part of the first competition. Since all 3 problem sets given this time are VLE problems, there would have been a good chance for us to do a good job this time again. It would take us about a day to solve the given problems with our COSMO-RS method. But we do not want to participate as second class contributors. Therefore we will publish our results for the problem sets exactly on the day of the submission deadline on our homepage. So everybody who is interested to see our performance for the contest will be able to see them and compare them with the final submissions. If the goal of the contest really would be to "to obtain an in-depth and objective assessment of our current abilities and inabilities in the prediction of physical properties for industrially challenging fluids", then I do not see a good reason to exclude one proven powerful approach > from the contest. COSMO-RS is a combination of good quality quantum chemistry with good quality statistical thermodynamics, and we are just making our approximations at different points than the MD/MC force field methods. Regards Andreas Dr. Jan K Labanowski wrote: >---------- Forwarded message ---------- >Date: Wed, 24 Sep 2003 15:07:08 -0500 >From: rbross_at_mmm.com >To: jkl_at_ccl.net > >Topic: 2nd Industrial Fluids Properties Simulation Challenge > >It is with great pleasure we announce the Second Industrial Fluid >Properties Simulation Challenge. The second challenge follows the >successful conclusion of the first challenge which led to significant >assessment and advancements of simulation methodology via the application >to research challenge problems for prediction of vapor-liquid equilibria, >density, and viscosity. The Second Simulation Challenge will focus on >prediction of vapor pressures and heats of vaporization, gas solubility, >and enthalpies of mixing for materials. For details on Second Simulation >Challenge as well as on the results of the first competition and could you >please see the attached announcement and/or >http://www.cstl.nist.gov/FluidSimulationChallenge. > >The goal of the Industrial Fluid Properties Simulation Challenge (IFPSC) >is to obtain an in-depth and objective assessment of our current abilities >and inabilities in the prediction of physical properties for industrially >challenging fluids. > >The accuracy of property prediction is based on the choice of forcefield >and modeling technique. As a result, it is anticipated that the awardees >of each problem in this competition will develop or apply an accurate and >general forcefield that can model a range of different chemistries and >develop or apply a modeling technique that can handle materials in different >states (liquid/vapor), is precise and accurate, and computationally swift. > >Industrial and NIST Organizing Committee > > > > > > > > > > > > -- ---------------------------------------------------------------------------- ---- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt_at_cosmologic.de web: www.cosmologic.de ---------------------------------------------------------------------------- ---- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ---------------------------------------------------------------------------- ---- -= This is automatically added to each message by the 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 Oct 15 05:55:25 2003 Received: from gveu50.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9F9sqdH021471 for ; Wed, 15 Oct 2003 05:54:53 -0400 Subject: Re: CCL:meaning of Ph.D.? To: jerome:at:scs.uiuc.edu Cc: CHEMISTRY:at:ccl.net, chemistry-request:at:ccl.net, chieny:at:msu.edu X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: Andras.Borosy:at:givaudan.com Date: Wed, 15 Oct 2003 11:25:17 +0200 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.07a |May 14, 2001) at 15/10/2003 11:54:59 MIME-Version: 1.0 Content-type: text/plain; charset=UTF-8 X-Spam-Status: No, hits=1.9 required=7.0 tests=BASE64_ENC_TEXT,NO_REAL_NAME,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h9F9tPdH021495 Dear Colleagues, I suppose it is Philosophiae Doctor Philosophy actually comes from the ancient greek O N9N;N?O N?O N/N1 (philosophia) means love of wisdom. Medieval universities had four faculties: theology, philosophy, law and medicine. The highest degree of each faculty called Doctor. I do not know if Doctor of theology, law title exits in the Anglo-saxone world, however they do exit in many countries in Europe. Salve, AndrC!s Borosy Jerome Baudry edu> cc: Sent by: Subject: CCL:meaning of Ph.D.? "Computational Chemistry List" 15.10.2003 05:25 > > 2. What does Doctor mean? Compare and contrast with Master (as in MS or > MA), and Bachelor (as in BS or BA). > 4. Does AD (or DA, Doctor of Art) exist? > If we follow the format of MS = master of Science, MA = master of Art, > then PhD (= Doctor of Philosophy) should be DPh. See the following > pattern, BS, BA, MS, MA > DPh in Science, Engineer, etc. Where is Art? These titles are from Latin, not English: "Doctor": capable of teaching, from "docere": to teach BA: "Baccalaureus Artium," MA: "Magister Artium," BS: "Baccalaureus Scientiae," MD: "Medicinae Doctor," Ph.D: "Philosophia Doctor" Salvate omnes, Hieronymus Baudry ;-) ---------------------------------------------------------- Jerome Baudry, Ph.D. Senior Research Scientist, VizLab Manager. School of Chemical Sciences University of Illinois at Urbana-Champaign 505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801 Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120; e-mail: jerome:at:scs.uiuc.edu -= This is automatically added to each message by the 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 Oct 15 03:46:46 2003 Received: from kuzey.cc.boun.edu.tr (kuzey.cc.boun.edu.tr [193.140.192.30]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h9F7kAdH018133 for ; Wed, 15 Oct 2003 03:46:12 -0400 Received: (qmail 13270 invoked from network); 15 Oct 2003 07:40:50 -0000 Received: from unknown (HELO guardian2) (193.140.192.10) by 0 with SMTP; 15 Oct 2003 07:40:50 -0000 Received: from saritepe.cc.boun.edu.tr ([193.140.192.31]) by guardian2 (SAVSMTP 3.1.2.35) with SMTP id M2003101510442022269 for ; Wed, 15 Oct 2003 10:44:20 +0300 Received: (qmail 34903 invoked by uid 80); 15 Oct 2003 10:46:53 -0000 Received: from 193.140.211.203 ([193.140.211.203]) by webmail.boun.edu.tr (IMP) with HTTP for ; Wed, 15 Oct 2003 10:46:53 +0000 Message-ID: <1066214813.3f8d259d0f7ab/at/webmail.boun.edu.tr> Date: Wed, 15 Oct 2003 10:46:53 +0000 From: Alimet Sema Ozen To: Computational Chemistry List Subject: CCL:scrf (iefpcm) error: too many vertices in a tessera MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.1 X-Spam-Status: No, hits=-0.3 required=7.0 tests=USER_AGENT_IMP version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL members, At the end of an scrf calculation I got the following error. TESSERA: too many vertices in a tessera Error termination via Lnk1e in /usr/local/products/g98_a9/exe/l502.exe. Job cpu time: 0 days 2 hours 25 minutes 8.9 seconds. File lengths (MBytes): RWF= 168 Int= 0 D2E= 0 Chk= 3 Scr= 1 This was an B3LYP-iefpcm calculation in g98 with water as solvent where radii=bondi option for scrf was employed. The molecule is a radical anion. Do you have any suggestions on how to overcome this error? Best Regards Alimet -- Normal termination of e-mail message Bogazici University Chemistry Department Istanbul Turkey +90 212 3581540 - 2379 From chemistry-request@ccl.net Wed Oct 15 11:23:50 2003 Received: from electra.cc.umanitoba.ca (electra.cc.umanitoba.ca [130.179.16.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9FFNJdH000422 for ; Wed, 15 Oct 2003 11:23:19 -0400 Received: from hultin (hultin.chem.umanitoba.ca [130.179.48.60]) by electra.cc.umanitoba.ca (8.12.10/8.12.10) with SMTP id h9FFNFqq000525 for ; Wed, 15 Oct 2003 10:23:16 -0500 (CDT) From: "Phil Hultin" To: "Computational Chemistry List" Subject: PhD and Deep Questions Date: Wed, 15 Oct 2003 10:23:16 -0500 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00B8_01C39306.58CE5570" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-DCC-UofM-Metrics: electra 1032; IP=ok Body=1 Fuz1=1 Fuz2=1 X-Spam-Status: No, hits=2.0 required=7.0 tests=HTML_20_30,HTML_FONT_BIG,HTML_FONT_BIG_B, HTML_FONT_FACE_ODD,HTML_MESSAGE,MSGID_GOOD_EXCHANGE version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_00B8_01C39306.58CE5570 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Three cheers for Yao-Ying Chien's nephew! I have often said that if I could teach a class of students who had the knowledge and skills of 20-year olds combined with the intellectual drive of 3-year olds (I have a 3-year old) together we could do miracles. There are a variety of names for academic degrees depending on the country in question, and even the individual school. Thus, Oxford gives a D. Phil. degree, for example, which is similar to the PhD given elsewhere. The important question is not what the degrees are called, but what they actually MEAN. Yao-Ying's nephew had this bang on. Just what does it mean to be a "Doctor of Philosophy"? Unfortunately, for many science students this seems to be simply a certificate that they are really good at mixing the right chemicals, or tweaking the right knob on a machine, or writing code that actually runs. All of these things are good skills to have, and very important for specific areas of science, but they are of much less importance than what is implied by the word "Philosophy". Being a "Doctor of Philosophy" should (IMHO) mean that one is driven by a true love of knowledge and understanding of the world (universe) around us to become ever more skilled in the quest for more knowledge and understanding. It MAY also imply (and I think probably should also imply) that one is skilled in applying one's knowledge and understanding to improve the world around us, but since this involves a value judgement it is difficult to include in a definition. I think it is wonderful that most universities give the same Ph.D. degree to graduates in what we like to call "the Arts", "the Sciences", "Engineering", "the Social Sciences" etc etc. All of these artificial distinctions are no more than convenient ways to categorize the world around us in terms of specific classes of questions that may be asked. The true Philosopher recognizes the kinship of all branches of knowledge, and grants pre-eminence to no particular branch a priori. Because all of us have only a little time on this earth, we must by necessity specialize in order to achieve anything, but we should nonetheless strive (whether we hold the degree or not) to be true "Doctors of Philosophy" insofar as we are able. To Yao-Ying Chien: keep that nephew of yours asking these questions. Together, you and he are walking along the road to Philosophy. One of the first steps on this road is to realize how little one actually knows, and your posting shows that you and he are facing this realization - and it showed me that I also could not answer his questions except by indirection. Thank him for me, please. The gods did not reveal from the beginning All things to us; but in the course of time, Through seeking, men find that which is better. But as for certain truth, no man has known it. Nor will he know it. Xenophanes (6th Century B.C.) Dr. Philip G. Hultin Associate Department Head and Associate Professor of Chemistry University of Manitoba Winnipeg, MB, Canada R3T 2N2 (vox) 204-474-9814 (fax) 204-474-7608 mailto:hultin~at~cc.umanitoba.ca http://www.umanitoba.ca/chemistry/ ------=_NextPart_000_00B8_01C39306.58CE5570 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Three = cheers for=20 Yao-Ying Chien's nephew!  I have often said that if I could teach a = class=20 of students who had the knowledge and skills of 20-year olds combined = with the=20 intellectual drive of 3-year olds (I have a 3-year old) together we = could do=20 miracles.
 
There = are a variety=20 of names for academic degrees depending on the country in question, and = even the=20 individual school.  Thus, Oxford gives a D. Phil. degree, for = example,=20 which is similar to the PhD given elsewhere.
 
The = important=20 question is not what the degrees are called, but what they actually = MEAN. =20 Yao-Ying's nephew had this bang on.  Just what does it mean to be a = "Doctor=20 of Philosophy"?  Unfortunately, for many science students this = seems to be=20 simply a certificate that they are really good at mixing the right = chemicals, or=20 tweaking the right knob on a machine, or writing code that actually = runs. =20 All of these things are good skills to have, and very important for = specific=20 areas of science, but they are of much less importance than what is = implied by=20 the word "Philosophy".
 
Being = a "Doctor of=20 Philosophy" should (IMHO) mean that one is driven by a true love of = knowledge=20 and understanding of the world (universe) around us to become ever more = skilled=20 in the quest for more knowledge and understanding.  It MAY also = imply (and=20 I think probably should also imply) that one is skilled in applying = one's=20 knowledge and understanding to improve the world around us, but since = this=20 involves a value judgement it is difficult to include in a=20 definition.
 
I = think it is=20 wonderful that most universities give the same Ph.D. degree to graduates = in what=20 we like to call "the Arts", "the Sciences", "Engineering", "the Social = Sciences"=20 etc etc.  All of these artificial distinctions are no more than = convenient=20 ways to categorize the world around us in terms of specific classes of = questions=20 that may be asked.  The true Philosopher recognizes the kinship of = all=20 branches of knowledge, and grants pre-eminence to no particular = branch a=20 priori.
 
Because all of us=20 have only a little time on this earth, we must by necessity specialize = in order=20 to achieve anything, but we should nonetheless strive (whether we hold = the=20 degree or not) to be true "Doctors of Philosophy" insofar as we are=20 able.
 
To = Yao-Ying Chien:=20 keep that nephew of yours asking these questions.  Together, you = and he are=20 walking along the road to Philosophy.  One of the first steps on = this road=20 is to realize how little one actually knows, and your posting shows that = you and=20 he are facing this realization - and it showed me that I also could not = answer=20 his questions except by indirection.  Thank him for me,=20 please.
 

The=20 gods did not reveal from the beginning

All=20 things to us; but in the course of time,

Through seeking, men find that which is better.

But=20 as for certain truth, no man has known it.

Nor=20 will he know it.

    = Xenophanes (6th=20 Century B.C.)

Dr. Philip G. Hultin
Associate Department Head=20 and
Associate Professor of Chemistry
University of = Manitoba
Winnipeg,=20 MB, Canada R3T 2N2
(vox) 204-474-9814
(fax) 204-474-7608
mailto:hultin~at~cc.umanitoba.ca<= BR>http://www.umanitoba.ca/chemistry/

 
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