From chemistry-request@www.ccl.net Mon Mar 29 04:21:19 1999 Received: from faust27-s.rz.uni-frankfurt.de (pp@faust27-s.rz.uni-frankfurt.de [141.2.149.151]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id EAA23915 Mon, 29 Mar 1999 04:21:12 -0500 (EST) Received: from chemie.uni-frankfurt.de (actually eco.anorg.chemie.uni-frankfurt.de) by faust27-eth.rz.uni-frankfurt.de with Local SMTP (PP); Mon, 29 Mar 1999 11:20:15 +0000 Message-ID: <36FF43FE.273EB763@chemie.uni-frankfurt.de> Date: Mon, 29 Mar 1999 11:12:31 +0200 From: Georgios Tsantes X-Mailer: Mozilla 4.05 [en] (WinNT; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: AIMPAC binaries Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I have problems compiling the programs of the AIMPAC package. I tried this on three different platforms (SGI OCTANE IRIX 6.4, Digital UNIX 4.0D and Linux) and failed. If somebody has manage this on the mentioned platforms, please be so kind and contact me. Thanks George Georgios Tsantes tsantes@chemie.uni-frankfurt.de From chemistry-request@www.ccl.net Mon Mar 29 04:27:10 1999 Received: from pobox.csc.fi (pobox.csc.fi [128.214.46.62]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA23937 Mon, 29 Mar 1999 04:27:09 -0500 (EST) Received: from voxopm-e.csc.fi (voxopm-e.csc.fi [128.214.46.23]) by pobox.csc.fi (8.9.0.Beta5/8.9.0.Beta5/CSC/Rtrs-1.22) with ESMTP id MAA24256 for ; Mon, 29 Mar 1999 12:27:09 +0300 (EET DST) Date: Mon, 29 Mar 1999 12:27:09 +0300 From: Maija Lahtela X-Sender: mlahtela@voxopm.minedu.fi To: chemistry@www.ccl.net Subject: Problems with G98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL readers, We would greatly appreciate your help in our problem. We have tried to optimize geometry for peptide with several amino acids using G98 amber-option (# opt amber iop(4/68=3) iop(7/29=6) ). However, our calculations have been ended to following message == Energy= 1.340246963503 NIter= 0. Dipole moment= 0.000000 0.000000 0.000000 FrcOut-1 allocation failure: iend,mxcore= 314720624 104857600 Error termination via Lnk1e in /v/irix65_mips64/appl/chem/gaussian/G98RevA.3/g9 8/l716.exe. Job cpu time: 0 days 0 hours 7 minutes 5.1 seconds. File lengths (MBytes): RWF= 2462 Int= 0 D2E= 0 Chk= 1 Scr= 1 Thanks in advance! Sincerely Yours, Maija Lahtela-Kakkonen *************************************** Maija Lahtela-Kakkonen Researcher CSC-Center for Scientific Computing Tekniikantie 15 a D P.O.Box 405 FIN-02101 ESPOO FINLAND TEL 358-9-4572079 FAX 358-9-4572302 E-MAIL mlahtela@csc.fi *************************************** From chemistry-request@www.ccl.net Mon Mar 29 07:09:38 1999 Received: from nmrc.ucc.ie (nmrc.ucc.ie [143.239.64.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA24679 Mon, 29 Mar 1999 07:09:29 -0500 (EST) Received: from odessa.nmrc.ucc.ie (odessa.nmrc.ucc.ie [143.239.64.65]) by bastion.nmrc.ucc.ie (8.9.3/8.9.3) with ESMTP id NAA00698 for ; Mon, 29 Mar 1999 13:08:59 +0100 (BST) Date: Mon, 29 Mar 1999 13:09:34 +0100 From: Michael Nolan To: ccl Subject: apologies Message-ID: <19990329130933.B326@rennes.nmrc.ucc.ie> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.95.1i Dear netters, apologies to anyone who read a message form me...it was inadvertantly sent to CCL. apologies once more michael -- ************************************************************************** Mr. Michael Nolan Materials Modelling Section, Advanced Materials and Technologies Group National Microelectronics Research Centre Lee Maltings, Prospect Row Cork, IRELAND mail: mnolan@nmrc.ucc.ie Tel: + 353 21 90 4113 http://nmrc.ucc.ie/projects/ape/ http://nmrc.ucc.ie/groups/AMT/modellingRes.html *************************************************************************** From chemistry-request@www.ccl.net Mon Mar 29 07:47:50 1999 Received: from scsx01.sc.ehu.es (root@scsx01.sc.ehu.es [158.227.150.40]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA24835 Mon, 29 Mar 1999 07:47:47 -0500 (EST) Received: from scox01.sc.ehu.es (scox01.sc.ehu.es [158.227.150.10]) by scsx01.sc.ehu.es (8.9.3/8.9.1) with ESMTP id OAA17971 for ; Mon, 29 Mar 1999 14:47:42 +0200 (MET DST) Received: from sq.ehu.es (pobmelat@sqpx94.sq.ehu.es [158.227.108.94]) by scox01.sc.ehu.es (8.9.3/8.9.1) with ESMTP id OAA16081 for ; Mon, 29 Mar 1999 14:47:35 +0200 (MET DST) Sender: pobmelat@sc.ehu.es Message-ID: <36FF75E6.57B629A9@sq.ehu.es> Date: Mon, 29 Mar 1999 14:45:26 +0200 From: Txema Mercero Reply-To: pobmelat@sq.ehu.es Organization: E.H.U. X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.34 i586) X-Accept-Language: Spanish, es, en MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: jcc.bst file Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL readers, Does anybody know where could I find a BibTex *.bst file to format the bibliography for the journal of computational chemistry? thank you all! From chemistry-request@www.ccl.net Mon Mar 29 07:48:21 1999 Received: from opium.q1.fcen.uba.ar (root@opium.q1.fcen.uba.ar [157.92.31.21]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA24854 Mon, 29 Mar 1999 07:48:18 -0500 (EST) Received: from opium (churca@opium.q1.fcen.uba.ar [157.92.31.21]) by opium.q1.fcen.uba.ar (8.8.0/8.8.0) with SMTP id JAA03148 for ; Mon, 29 Mar 1999 09:09:10 -0300 Sender: churca@opium.q1.fcen.uba.ar Message-ID: <36FF6D66.6A448A55@q1.fcen.uba.ar> Date: Mon, 29 Mar 1999 09:09:10 -0300 From: Adrian Turjanski X-Mailer: Mozilla 3.0Gold (X11; I; Linux 2.0.0 i586) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Summary Xmol program. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Some days ago I posted the following question: > Hi: > does anybody know about Xmol program? Where can i download it? > > Thank you very much. > > Adrian Turjanski Thanks to all who answered it, here are the answers: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx I use it quite often. You used to be able to download it from the CCL's ftp server, but try going to http://www.chimie.fundp.ac.be/cms/cmsinfo/xmol.htm. I think you can dowload it there. Richard xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx http://www.msc.edu/msc/docs/xmol/XMol.html Maybe this site is of interest for you, too: http://www.chem.swin.edu.au/chem_ref.html Regards, Jens xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Hi Adrian Look at: http://www.msc.edu/msc/docs/xmol/XMol.htm (original source, USA) or: http://www.chm.tu-dresden.de/edv/xmol/xmol.html (a mirror in Germany) or simply use a search engine to get your favorite server , if those are not what you want for some reasons. Hope that helps BYe Elmar xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx hi adrian, try http://www.networkcs.com/msc/docs/xmol/ftp.html. there you can get the free version 1.3.1 for numerous unix-workstations. michael braunschweig xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx I'm not sure if you can actually get the source for Xmol anymore, only the binaries may be available, which isn't very useful. As an alternative, the source code of a fully supported, free, variant of Xmol called XMakemol can be downloaded from the following website: http://brian.ch.cam.ac.uk/~matt/XMakemol/XMakemol.html hope this helps, Tiffany Walsh xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Hi Adrian, try this site: http://www.msc.edu/msc/docs/xmol/ftp.html Good luck, Thomas. From chemistry-request@www.ccl.net Mon Mar 29 08:30:43 1999 Received: from rrzs2.rz.uni-regensburg.de (rrzs2.rz.uni-regensburg.de [132.199.1.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA25200 Mon, 29 Mar 1999 08:30:41 -0500 (EST) Received: from ngate.ngate.uni-regensburg.de (ngate.rz.uni-regensburg.de [132.199.3.13]) by rrzs2.rz.uni-regensburg.de (8.8.8/8.8.8) with SMTP id PAA00502 for ; Mon, 29 Mar 1999 15:30:40 +0200 (MET DST) Received: from daub.chemie.ngate.uni-regensburg.de by ngate.ngate.uni-regensburg.de; Mon, 29 Mar 99 14:30 MET Received: from ALF2/SpoolDir by alf2.ngate.uni-regensburg.de (Mercury 1.44); 29 Mar 99 15:30:36 +0100 Received: from SpoolDir by ALF2 (Mercury 1.44); 29 Mar 99 15:30:23 +0100 From: "Christian Stadler" Organization: Universitaet Regensburg To: chemistry@www.ccl.net Date: Mon, 29 Mar 1999 15:30:20 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: DFT with high-spin iron complexes Priority: normal X-mailer: Pegasus Mail for Windows (v2.54DE) Message-ID: <1E3A9B071AF@alf2.ngate.uni-regensburg.de> Dear CCLers First of all thanks for all the answers regarding my problem with "insufficiant memory ..." posted one week ago. (see: "technical problem with gaussian98 job") The problem really seems to be a "bug" in the G98 code regarding calculation of the amount of memory needed. I increased the %mem value only slightly and it worked. I did not try to decrease it as has been also suggested. Now for the "new" problem. For almost three months now I've been trying to perform DFT calculation on various iron complexes, escpecially tris(acetylacetonato)iron(III) Fe(acac)3 with Gaussian 98. I already tried B3LYP and SVWN with the LANL2DZ basis set - in one case also a mixed LANL2DZ/6-31G(d) basis set. Unfortunately, the mullikan and nbo population analyses yield rather strange results. All calculations are performed on C1 symmetric molecules since we discovered problems when C3 axes are present although the molecule should have D3 symmetry. One example: Fe(acac)3 with SVWN/LANL2DZ gives a charge of 5.3 on Fe after the first SCF and about -3.3 after the following SCFs according to NBO analysis. At the same time there are no major changes in the eigenvalues. However, some of them are pretty close and two of the alpha occ. eigenvalues are positive. In our opinion the result of the first SCF ist quite acceptable but the following SCFs seem to produce excited states. Is there a way to get further information about what's going on from the output files? Would it be useful to introduce f-functions or to use a triple zeta basis set? According to literature the chosen method should work but obviously it does not. :-( Thanks and greetings Christian Stadler ******************************* Christian Stadler c/o Prof. Dr. J. Daub Institut fuer Organische Chemie Universitaet Regensburg 93040 Regensburg Germany Phone: +49 941/943-4610 Fax: +49 941/943-4984 ******************************* From chemistry-request@www.ccl.net Mon Mar 29 11:42:02 1999 Received: from magnum.cooper.edu (magnum.cooper.edu [199.98.16.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA26950 Mon, 29 Mar 1999 11:42:00 -0500 (EST) Received: from robin.cooper.edu by magnum.cooper.edu with SMTP id AA29185 (5.65c/IDA-1.4.4 for ); Mon, 29 Mar 1999 11:40:43 -0500 Received: by robin.cooper.edu (SMI-8.6/SMI-SVR4) id LAA07414; Mon, 29 Mar 1999 11:41:30 -0500 Message-Id: <199903291641.LAA07414@robin.cooper.edu> Subject: CCL:Re: Computational Chemist vs Theoretical Chemist To: CHEMISTRY@www.ccl.net Date: Mon, 29 Mar 1999 11:41:29 -0500 (EST) From: "Prof. Robert Topper" X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Hello all I think Stefan's got it just right (especially about the need to have a sense of humor!). I was trained as a theoretical chemist. To me, what this means is that I was trained to push a pencil with the goal of developing certain mathematical aspects of chemistry. This includes making theoretical improvements to transition-state theory, developing new quantum path-integral representations, inventing a new theory of the liquid state, working out better ways to set up the integrals for 5th-order perturbation theory, and so forth. Of course, I eventually use computers to implement all of the above. But experimentalists use computers too. IMHO, this may also justifiably be called "computational chemistry" (I know, not everyone agrees, this is an old debate, just my $0.02, sincere apologies to all who find my heresy distasteful). Novices tend to divide science into theory and experiment, and therefore "computation must be theory." As Stefan mentions, this is a historical bias. Although computer simulation work is not experiment, it isn't exactly theory either. When I was a student we used to call computer simulations "numerical experiments" (these days, maybe "virtual experiments" would be trendier), which could be tested either against theory or experiment. In Einstein's day things were different, but science now consists of theory, experiment and simulation. Some people work in one, two or even all three of these areas (I myself get into the lab once in a blue moon). So am I a theoretical physical chemist? A computational chemist? A chemical physicist? A computational molecular thermodynamicist? Personally, I don't think of myself as any of the above. I'm a chemist. ***************************************************************************** Robert Q. Topper email: topper@cooper.edu Department of Chemistry phone: (212) 353-4378 School of Engineering fax: (212) 353-4341 The Cooper Union subway: take the 6 to Astor Place 51 Astor Place or the N/R to 8th street New York, NY 10003 and you're there! ***************************************************************************** http://www.cooper.edu/engineering/chemechem/ ***************************************************************************** From chemistry-request@www.ccl.net Mon Mar 29 11:59:32 1999 Received: from sgi.com (sgi-too.SGI.COM [204.94.211.39]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA27085 Mon, 29 Mar 1999 11:59:31 -0500 (EST) Received: from odin.corp.sgi.com (odin.corp.sgi.com [192.26.51.194]) by sgi.com (980327.SGI.8.8.8-aspam/980304.SGI-aspam: SGI does not authorize the use of its proprietary systems or networks for unsolicited or bulk email from the Internet.) via SMTP id IAA09406; Mon, 29 Mar 1999 08:59:32 -0800 (PST) mail_from (omar@boston.sgi.com) Received: from sgibos.boston.sgi.com by odin.corp.sgi.com via ESMTP (951211.SGI.8.6.12.PATCH1502/951211.SGI) id IAA18251; Mon, 29 Mar 1999 08:59:30 -0800 Received: from arkham.boston.sgi.com (arkham.boston.sgi.com [169.238.35.21]) by sgibos.boston.sgi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id LAA20052; Mon, 29 Mar 1999 11:59:28 -0500 (EST) Received: from localhost (omar@localhost) by arkham.boston.sgi.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via SMTP id LAA02048; Mon, 29 Mar 1999 11:59:25 -0500 (EST) Date: Mon, 29 Mar 1999 11:59:25 -0500 (EST) From: Omar Stradella To: Georgios Tsantes cc: chemistry@www.ccl.net Subject: Re: CCL:AIMPAC binaries In-Reply-To: <36FF43FE.273EB763@chemie.uni-frankfurt.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 29 Mar 1999, Georgios Tsantes wrote: > Hi, > > I have problems compiling the programs of the AIMPAC package. I tried > this on three different platforms > (SGI OCTANE IRIX 6.4, Digital UNIX 4.0D and Linux) and failed. > If somebody has manage this on the mentioned platforms, please be so > kind and contact me. > > Thanks > > George > > > > Georgios Tsantes > tsantes@chemie.uni-frankfurt.de Hi Giorgios, On SGI Octane IRIX 6.4 you can compile the AIMPAC package by simply using "f77 -O2". All versions of f77 from 7.1 up work. Omar. +---------------------------------------------------------------------+ Omar G. Stradella, Ph.D. Supercomputing Applications Silicon Graphics, Inc. Computational Chemistry One Cabot Road, Hudson, MA 01749, USA N 42 22'40" W 71 33'44" E-mail: omar@boston.sgi.com Phone: +1-978-567-2258 FAX: +1-978-562-4755 http://www.sgi.com/ChemBio http://reality.sgi.com/omar +-------- Ph-nglui mglw'nafh Cthulhu R'lyeh wgah'nagl fhtagn -------+ From chemistry-request@www.ccl.net Mon Mar 29 12:44:34 1999 Received: from lgsx01.lg.ehu.es (lgsx01.lg.ehu.es [158.227.2.34]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA27510 Mon, 29 Mar 1999 12:44:32 -0500 (EST) Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by lgsx01.lg.ehu.es (8.8.5/8.8.5) with SMTP id TAA17003 for ; Mon, 29 Mar 1999 19:45:47 +0200 (MET DST) Date: Mon, 29 Mar 1999 19:44:03 +0200 (MET DST) From: Pablo Vitoria Garcia To: ccl Subject: QM and Mathematica Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I am attending a graduate course in magnetism (molecular and extended), and I would like to do some work and exercises in Mathematica. I wonder if somewhere out there in the Net there is a Notebook (or package) with stuff like operators, spin functions, ... already defined. I mean, for example, a package to calculate matrix elements of Sz, LzSz,... or other operators. Thank you very much for any information Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lg.ehu.es Phone: +34 94 6012000 Ext. 5529 -------------------------------------------------------------------------------- From chemistry-request@www.ccl.net Mon Mar 29 15:26:24 1999 Received: from cerberus.ulaval.ca (cerberus.ulaval.ca [132.203.250.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA02768 Mon, 29 Mar 1999 15:26:23 -0500 (EST) Received: from fluor.chm.ulaval.ca (fluor.chm.ulaval.ca [132.203.70.9]) by cerberus.ulaval.ca (8.8.7/8.7.3) with ESMTP id PAA27522; Mon, 29 Mar 1999 15:33:14 -0500 (EST) Received: (from anh@localhost) by fluor.chm.ulaval.ca (8.6.12/8.6.12) id KAA14032; Mon, 29 Mar 1999 10:03:56 -0500 From: "Nguyen N. Anh" Message-Id: <9903291003.ZM14030@fluor.chm.ulaval.ca> Date: Mon, 29 Mar 1999 10:03:53 -0500 In-Reply-To: Pablo Vitoria Garcia "CCL:QM and Mathematica" (Mar 29, 7:44pm) References: X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: Pablo Vitoria Garcia Subject: Re: CCL:QM and Mathematica Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii > I would like to do some work and exercises in Mathematica. I wonder if > somewhere out there in the Net there is a Notebook (or package) with stuff > like operators, spin functions, ... already defined. I mean, for example, > a > package to calculate matrix elements of Sz, LzSz,... or other operators. Hi Pablo, Your request seems a little bit specific. I don't know of any package that fits your demand and do wonder to know if such a package exists at all. I think you should take a package you consider the best and then develop it to suit your goals. I have some sugetions: - A good book dealing with quantum mechanics using Mathematica is: J.M.Feagin, Quantum Methods with Mathematica (TELOS, Springer, New-York, 1994) - Take a look at the Computer Physics Communications program library http://www.cpc.cs.qub.ac.uk. There is a lot of symbolic packages wich may be useful - We're developing a package that deals with QM noncommutative operators, unitary transformations etc. With it we can define spin operators, ladder operators and do some rotations. The reference is: Computer Physics Communications 115(1998) 183-199 Good luck Best regards -- Nguyen Nam Anh Quebec, Canada E-mail: anh@chm.ulaval.ca WWW: http://promethium.chm.ulaval.ca/~anh/ From chemistry-request@www.ccl.net Mon Mar 29 15:31:05 1999 Received: from hugh.chem.uic.edu (HUGH.CHEM.UIC.EDU [131.193.195.93]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id PAA02835 Mon, 29 Mar 1999 15:31:05 -0500 (EST) Received: by hugh.chem.uic.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id OAA24122; Mon, 29 Mar 1999 14:46:44 -0600 Date: Mon, 29 Mar 1999 14:46:30 +36000 From: Richard Wood To: "Prof. Robert Topper" cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Computational Chemist vs Theoretical Chemist In-Reply-To: <199903291641.LAA07414@robin.cooper.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dr. Topper- While I agree with you when you say "I am a chemist", as I have several years of experience working in the IR/CD area, as well as three plus years of experience doing MD simulations, I must disagree with you when you imply that the distinction between being a "theoretical chemist" vs. a "computational chemist" doesn't matter. It matters to me (however, don't think that I lose sleep over it) because to me developing a theory and using it are two ENTIRELY different things. I think that most any chemist can USE a theory; only a special "bird" can develop theory. Let me give you an example. A few years back, I was measuring IR/CD spectra of some (chiral) tetrasubstituted biphenyls, and also attempting to calculate the observed IR/CD spectra by varying the angle between the two rings (in other words, trying to find the angle that gave me the closest match with my experimental results). We were using a simple coupled oscillator model to calculate the spectra, and my calculations of the spectra were too small, regardless of what angle I picked. I then came to the conclusion that the distance between the too dipoles was too small, and thus R+ and R- were cancelling out, decreasing their magnitude. I also concluded that my theory needed some modification. Lacking the necessary theoretical "ability", my project basically crashed and burned. I guess that you are probably aware being a physical chemist, that if you are going to try and publish experimental results, you better have very good agreement between experiment and calculations. Richard On Mon, 29 Mar 1999, Prof. Robert Topper wrote: > Hello all > > I think Stefan's got it just right (especially about the need > to have a sense of humor!). > > I was trained as a theoretical chemist. To me, what this means > is that I was trained to push a pencil with the goal of developing > certain mathematical aspects of chemistry. This includes making > theoretical improvements to transition-state theory, developing > new quantum path-integral representations, inventing a new theory > of the liquid state, working out better ways to set up > the integrals for 5th-order perturbation theory, and so forth. > > Of course, I eventually use computers to implement all of the above. > But experimentalists use computers too. IMHO, > this may also justifiably be called "computational chemistry" > (I know, not everyone agrees, this is an old debate, just my $0.02, > sincere apologies to all who find my heresy distasteful). > > Novices tend to divide science into theory and > experiment, and therefore "computation must be theory." > As Stefan mentions, this is a historical bias. > Although computer simulation work is not experiment, > it isn't exactly theory either. When I was a student we used to > call computer simulations "numerical experiments" (these > days, maybe "virtual experiments" would be trendier), which > could be tested either against theory or experiment. > > In Einstein's day things were different, but science now consists of > theory, experiment and simulation. Some people work in one, two or > even all three of these areas (I myself get into the lab once in > a blue moon). > > So am I a theoretical physical chemist? A computational chemist? > A chemical physicist? A computational molecular thermodynamicist? > Personally, I don't think of myself as any of the above. > I'm a chemist. > > ***************************************************************************** > Robert Q. Topper email: topper@cooper.edu > Department of Chemistry phone: (212) 353-4378 > School of Engineering fax: (212) 353-4341 > The Cooper Union subway: take the 6 to Astor Place > 51 Astor Place or the N/R to 8th street > New York, NY 10003 and you're there! > ***************************************************************************** > http://www.cooper.edu/engineering/chemechem/ > ***************************************************************************** > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: topper@cooper.edu > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From chemistry-request@www.ccl.net Mon Mar 29 18:17:12 1999 Received: from magnum.cooper.edu (magnum.cooper.edu [199.98.16.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id SAA03938 Mon, 29 Mar 1999 18:17:11 -0500 (EST) Received: from robin.cooper.edu by magnum.cooper.edu with SMTP id AA24357 (5.65c/IDA-1.4.4 for ); Mon, 29 Mar 1999 18:15:44 -0500 Received: by robin.cooper.edu (SMI-8.6/SMI-SVR4) id SAA20376; Mon, 29 Mar 1999 18:16:32 -0500 Message-Id: <199903292316.SAA20376@robin.cooper.edu> Subject: CCL:Computational Chemist vs Theoretical Chemist To: CHEMISTRY@www.ccl.net Date: Mon, 29 Mar 1999 18:16:32 -0500 (EST) From: "Prof. Robert Topper" X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Hi again all, Sorry for the bandwidth. Just want to point out that I personally feel that there is a very big difference between theoretical chemistry and computational chemistry, and that was in fact what I was trying to say - perhaps too obliquely. My parting comment was merely put in to point out that I have no particular axe to grind on this issue, as I have done work in all three areas (although I have done most of my work in the "theoretical" and "simulation" ends of things). Any inferences of other, guessed-at meanings are simply incorrect. Best, Robert ***************************************************************************** Robert Q. Topper email: topper@cooper.edu Department of Chemistry phone: (212) 353-4378 School of Engineering fax: (212) 353-4341 The Cooper Union subway: take the 6 to Astor Place 51 Astor Place or the N/R to 8th street New York, NY 10003 and you're there! ***************************************************************************** http://www.cooper.edu/engineering/chemechem/ ***************************************************************************** > > Dr. Topper- > While I agree with you when you say "I am a chemist", as I have > several years of experience working in the IR/CD area, as well as three > plus years of experience doing MD simulations, I must disagree with you > when you imply that the distinction between being a "theoretical chemist" > vs. a "computational chemist" doesn't matter. It matters to me (however, > don't think that I lose sleep over it) because to me developing a theory > and using it are two ENTIRELY different things. I think that most any > chemist can USE a theory; only a special "bird" can develop theory. > > Let me give you an example. A few years back, I was measuring IR/CD > spectra of some (chiral) tetrasubstituted biphenyls, and also attempting to > calculate the observed IR/CD spectra by varying the angle between the two > rings (in other words, trying to find the angle that gave me the closest > match with my experimental results). We were using a simple coupled > oscillator model to calculate the spectra, and my calculations of the > spectra were too small, regardless of what angle I picked. I then came > to the conclusion that the distance between the too dipoles was too > small, and thus R+ and R- were cancelling out, decreasing their > magnitude. I also concluded that my theory needed some modification. > Lacking the necessary theoretical "ability", my project basically crashed > and burned. I guess that you are probably aware being a physical > chemist, that if you are going to try and publish experimental results, > you better have very good agreement between experiment and calculations. > > Richard From chemistry-request@www.ccl.net Mon Mar 29 22:26:08 1999 Received: from post-ofc05.srv.cis.pitt.edu (root@post-ofc05.srv.cis.pitt.edu [136.142.185.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id WAA04536 Mon, 29 Mar 1999 22:26:08 -0500 (EST) Received: from hathi.chem.pitt.edu (hathi.chem.pitt.edu [136.142.109.10]) by post-ofc05.srv.cis.pitt.edu with SMTP (8.8.8/8.8.8/cispo-7.2.2.2) ID for <@smtp.pitt.edu:chemistry@www.ccl.net>; Mon, 29 Mar 1999 22:26:08 -0500 (EST) Received: by hathi.chem.pitt.edu (940816.SGI.8.6.9/920502.SGI.AUTO) for chemistry@www.ccl.net id WAA14837; Mon, 29 Mar 1999 22:26:08 -0500 From: "Gustavo Moura" Message-Id: <9903292226.ZM14835@hathi.chem.pitt.edu> Date: Mon, 29 Mar 1999 22:26:05 -0500 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Upgrading to Fortran 90/95 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL readers, can someone out there suggest a good book on upgrading to Fortran 90/95 for someone with a reasonable knowledge of Fortran 77? I am about to start writing a program and I would like to take advantage of the new capabilities of Fortran 90/95. I will summarize. Thank you very much in advance. Gustavo Moura gustavo@hathi.chem.pitt.edu