From chemistry-request@server.ccl.net Tue Oct 23 02:54:44 2001 Received: from relay3.softcomca.com ([168.144.1.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9N6shB29835 for ; Tue, 23 Oct 2001 02:54:44 -0400 Received: from m2w068 ([168.144.108.68]) by relay3.softcomca.com with Microsoft SMTPSVC(5.0.2195.2966); Tue, 23 Oct 2001 02:57:45 -0400 X-Originating-IP: 202.185.72.119 X-URL: http://www.mail2web.com/ Subject: random pick of binding site? Sender: "nepenthes@vplaces.net" From: "nepenthes@vplaces.net" Date: Tue, 23 Oct 2001 02:57:33 -0400 To: "chemistry@ccl.net" Reply-To: nepenthes@vplaces.net X-Priority: 3 X-MSMail-Priority: Normal MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Mailer: JMail 3.7.0 by Dimac (www.dimac.net) Message-ID: X-OriginalArrivalTime: 23 Oct 2001 06:57:45.0175 (UTC) FILETIME=[047C2E70:01C15B90] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-Printable to 8bit by server.ccl.net id f9N6siB29836 Dear all, I would like to ask some opinions from you.I'm studying protein-ligand interactions computationally. I have a hexamer protein with six identical binding sites. These six sites bind to six of the same ligand. Since it's quite complicated to study all six at a time, it was suggested to me that I study only one site since they are all identical. I am not too sure whether I can just take a site at random to study the ligand interactions or are there some other classifications which I should take account in picking the site i want to study. I would be glad to hear some suggestions as I've not found the answer yet or some reference to where I might be able to get some answers. My grateful thanks in advance. Hope to hear from somebody. Rowyna K. Institute of Biological Sciences University of Malaya Kuala Lumpur -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From chemistry-request@server.ccl.net Tue Oct 23 08:20:38 2001 Received: from gate.boehringer-ingelheim.de ([148.188.1.36]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9NCKcB05245 for ; Tue, 23 Oct 2001 08:20:38 -0400 Received: from gscinghub2.ing.de.bic by gate.boehringer-ingelheim.de via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 23 Oct 2001 12:21:57 UT Received: by gscinghub2.ing.de.bic with Internet Mail Service (5.5.2653.19) id ; Tue, 23 Oct 2001 14:23:21 +0200 Message-ID: From: Christian.Pilger@bc.boehringer-ingelheim.com To: chemistry@ccl.net Subject: continuum regression Date: Tue, 23 Oct 2001 14:23:19 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain Dear CCLers, is anybody aware of software capable of what is called 'continuum regression' for statistical analysis ? Regards, Christian ________________________________________________________________ Dr. Christian Pilger Dept. Chemical Research / Structural Research J51-00-01 Boehringer Ingelheim Pharma KG D-88397 Biberach/Germany Phone: 07351-545749 Fax: 07351-5497924 mailto: christian.pilger@bc.boehringer-ingelheim.com From chemistry-request@server.ccl.net Tue Oct 23 06:46:48 2001 Received: from osiris.uah.es ([212.128.9.134]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9NAklB03682 for ; Tue, 23 Oct 2001 06:46:47 -0400 Received: from uah.es ([212.128.17.77]) by osiris.uah.es with Microsoft SMTPSVC(5.0.2195.3779); Tue, 23 Oct 2001 10:59:55 +0200 Message-ID: <3BD5319B.4030104@uah.es> Date: Tue, 23 Oct 2001 11:00:11 +0200 From: Antonio Morreale Reply-To: antonio.morreale@uah.es Organization: Universidad de =?ISO-8859-1?Q?Alcal=E1?= de Henares User-Agent: Mozilla/5.0 (Macintosh; U; PPC; en-US; rv:0.9.1) Gecko/20010607 Netscape6/6.1b1 X-Accept-Language: en,es-ES MIME-Version: 1.0 To: chemistry@ccl.net Subject: G98 ERROR Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-OriginalArrivalTime: 23 Oct 2001 08:59:55.0823 (UTC) FILETIME=[15E44BF0:01C15BA1] Dear all, When running gaussian 98 rev. A9 I get the following error: Entering Gaussian System, Link 0=g98 Initial command: /programas/g98A9/g98/l1.exe /home3/s3/g94-48674.inp -scrdir=/home3/s3/ 48660:/programas/g98A9/g98/l1.exe: rld: Error: unresolvable symbol in /programas/g98A9/g98/l1.exe: putprc_ 48660:/programas/g98A9/g98/l1.exe: rld: Error: unresolvable symbol in /programas/g98A9/g98/l1.exe: irtcmp_ 48660:/programas/g98A9/g98/l1.exe: rld: Fatal Error: this executable has unresolvable symbols Does somebody know to solve it? Thanks, Antonio -- ======================================= = Antonio Morreale = = Departamento de Química Orgánica = = Universidad de Alcalá = = Ctra. Madrid-Barcelona Km. 33,600 = = Alcalá de Henares = = 28871 Madrid = = Spain = = Tlf. + 34 91 885 46 49 = = Fax. + 34 91 885 46 86 = = email: antonio.morreale@uah.es = ======================================= From chemistry-request@server.ccl.net Tue Oct 23 06:02:26 2001 Received: from dobit2.rug.ac.be ([157.193.42.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9NA2QB02624 for ; Tue, 23 Oct 2001 06:02:26 -0400 Received: from hartree4.rug.ac.be (hartree4.rug.ac.be [157.193.91.12]) by dobit2.rug.ac.be (8.11.1/8.11.1) with ESMTP id f9NA5Gt21199 for ; Tue, 23 Oct 2001 12:05:16 +0200 (MEST) Received: (from tom@localhost) by hartree4.rug.ac.be (AIX4.2/UCB 8.7/8.7) id MAA09094; Tue, 23 Oct 2001 12:07:31 +0100 (NFT) Date: Tue, 23 Oct 2001 12:07:29 +0100 (NFT) From: Tom Kuppens To: chemistry@ccl.net Subject: RIMM vs SDRAM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi there, We have several linux machines that run Gaussian. Now we want to add some new power to our park i.e. a PIV - 1700MhZ with 512M RAM (SDRAM or RIMM). Is there someone who can provide me with some info on the Gaussian and/or overall performance with RIMM versus SDRAM modules. Thanks in advance, Tom Kuppens Ghent University -- tom@hartree4.ac.be http://studwww.rug.ac.be/~tkuppens/quantum/ --- It seems to me, Golan, that the advance of civilization is nothing but an exercise in the limiting of privacy. -- Janov Pelorat in Asimov's Foundation's Edge From chemistry-request@server.ccl.net Tue Oct 23 05:39:06 2001 Received: from mel.ruc.dk ([130.225.220.27]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9N9d5B01934 for ; Tue, 23 Oct 2001 05:39:06 -0400 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id LAA28085; Tue, 23 Oct 2001 11:41:56 +0200 (MET DST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id LAA26038; Tue, 23 Oct 2001 11:17:13 +0200 (MEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 23 Oct 01 11:41:56 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 23 Oct 01 11:41:45 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Shobe, Dave" Date: Tue, 23 Oct 2001 11:41:19 +0100 Subject: CCL:Is TD or Zindo better than CIS? CC: chemistry@ccl.net X-Confirm-Reading-To: "Jens Spanget-Larsen" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <15E90A03A45@virgil.ruc.dk> Hello Dave: > A question related to the last one. I'm aware that CIS has its > shortcomings and the results should be considered only a rough > sketch of the molecule's spectrum. Gaussian has two other methods > (neither of which I've used) for calculating excited states: Zindo > and TD. Are these significantly better than CIS? Zindo being a > semiempirical method, is it only good for certain kinds of > molecules? Should I be looking at programs other than Gaussian for > this type of calculation? I just wish to draw your attention to a recent paper by Juergen Fabian, where he presents an extensive comparison of the performances of ZINDO/S and TD-DFT in the prediction of electronic transitions for a variety of organic sulfur compounds: Jueregn Fabian: "Electronic excitation of sulfur-organic compounds - performance of time-dependent density functional theory", Theor. Chem. Acc. 106, 199-217 (2001). Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Cell-Phone: +45 2320 6246 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~jsl =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@server.ccl.net Tue Oct 23 02:48:30 2001 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9N6mIB29770 for ; Tue, 23 Oct 2001 02:48:19 -0400 Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.11.6/8.11.0) with ESMTP id f9N6od246337; Tue, 23 Oct 2001 08:50:39 +0200 (EET) (envelope-from tamulis@itpa.lt) Date: Tue, 23 Oct 2001 08:50:39 +0200 (EET) From: Arvydas Tamulis To: Geoff Hutchison cc: , , , Jelena Tamuliene Subject: Re: CCL:Is TD or Zindo better than CIS? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Professor Hutchison and other CCL contributors, Thank you for your professional explanation and making clear many aspects of comparison of ZINDO, HF-CIS and DFT-TD, HF-TD. Having in mind all your and your colleagues mentioned negative points of ZINDO, HF-CIS and HF-TD, DFT-TD, we started to write DFT-TD that should be suitable for the calculations of electron charge transfer in excited states in large supermolecules (molecular devices, see our WEBsite: www.itpa.lt/~tamulis/). I need your consultations: did we started right relaying on DFT-TD using gradient-corrected functionals (see C. Van Cailie, R.D. Amos, Chem. Phys. Lett., v. 317 (2000) p. 159-164)? Would you please to say that calculation algorithms of molecular integrals over Gaussian basis functions are correct in article: M. Dupuis, J. Rys, H. King, J. Chem. Phys. v. 65, p. 111-116, 1976, or presently exist better published algorithms? Finally we need well described publications on SCF DIIS algorithm and algorithm for convertion four centers integrals to three centers integrals. We plan to run this our writting program on our having heterogenic cluster: Alpha XP1000 + 6x(AMD 1.2 GHz; 512 Mb; 40 Gb) that should be extended in the future. With best regards, Arvydas Tamulis ************************************************ Arvydas Tamulis Doctor of Natural Sciences, senior research fellow Institute of Theoretical Physics and Astronomy, Theoretical Molecular Electronics Research Group, A. Gostauto 12, Vilnius 2600, Lithuania e-mail: TAMULIS@ITPA.lt; WEBsite: http://www.itpa.lt/~tamulis/ fax: +(370-2)-225361 or +(370-2)-224694 Phone: +(370-2)-620861 Home address: Didlaukio 27-40, Vilnius 2057, Lithuania Phone: +370-9919397 ***************************************************** On Mon, 22 Oct 2001, Geoff Hutchison wrote: > At 1:25 PM -0400 10/22/01, Shobe, Dave wrote: > >spectrum. Gaussian has two other methods (neither of which I've used) for > >calculating excited states: Zindo and TD. Are these significatnly better > >than CIS? Zindo being a semiempirical method, is it only good for certain > >kinds of molecules? Should I be looking at programs other than Gaussian for > >this type of calculation? > > It's strange this should come up as I'm working on a manuscript along > these lines for a certain set of molecules. But first there's a > nomenclature issue. Normally when people say "Zindo," they mean > "INDO/S CIS," and so you can't compare "Zindo" to "CIS." Also, I'm > not quite sure I know what you mean when you say "TD" since you > usually refer to TD-HF or TD-DFT for time-dependent HF or time > dependent DFT. > > If you compare Zindo CIS to HF-CIS for most neutral organic > molecules, you'll find Zindo is more accurate. If you compare TD-HF > (say the RPA) to HF-CIS, the HF-RPA is better--no surprise since the > RPA is one step past the Tamm-Dancoff approximation (CIS). But HF-RPA > is not as good as Zindo for most neutral organic molecules. > > TD-DFT seems to be slightly worse than Zindo for neutral organic > molecules, but not by much. > > Also keep in mind that Zindo CIS as a semiempirical method sometimes > incorrectly identifies the composition of certain excitations even if > the energy is pretty good. > > Can't say how Gaussian does on these sorts of things--we can't get it > here. As Mark Thompson pointed out, you can also go beyond CIS to > CISD, etc. The original ZINDO program from Zerner does let you do > things like this, though YMMV. Other programs as well have CISD, > CISDT and other higher-order methods. (Dalton springs to mind.) > > -- > -- > -Geoff Hutchison > Ratner/Marks Groups (847) 491-3295 > Northwestern Chemistry http://www.chem.nwu.edu/ > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Tue Oct 23 09:20:20 2001 Received: from server.ttpharma.com ([216.237.220.134]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9NDKKB06621 for ; Tue, 23 Oct 2001 09:20:20 -0400 Received: from jerome ([192.168.4.31]) by server.ttpharma.com (8.11.1/8.11.1) with SMTP id f9NDNhx20548; Tue, 23 Oct 2001 08:23:43 -0500 From: "Jerome Baudry" To: , Subject: RE: random pick of binding site? Date: Tue, 23 Oct 2001 09:23:41 -0400 Message-ID: <000401c15bc5$eeb663e0$1f04a8c0@ttpharma.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 In-Reply-To: Importance: Normal One thing that would give a rationale for yout choice is too have a look at the kinetics of the reaction. Do you have a cooperative effect (Hill kinetics)?, what is the Hill coefficient? If you see cooperative binding, it might means that binding of one ligand leads to protein conformational changes that would make the sites non-equivalent to their original conformations, or that ligand see each other when in the site. If you have an 'infinite' cooperation (Hill coeeficient = 6 in your case), they all bind at the same time. In that case, as if you obesrve pure Michaelis kinetics, you might want to go for one site. Hoe it helps, Jerome ***************************************** Jerome Baudry, Ph.D. Research Scientist, Computational Chemistry TransTech Pharma, Inc. 4170 Mendenhall Oaks Pwky, Suite 110 High Point, NC, 27265 http://www.ttpharma.com jbaudry@ttpharma.com tel: (336) 841-0300 #120 fax: (336) 841-0310 > -----Original Message----- > From: Computational Chemistry List > [mailto:chemistry-request@ccl.net]On > Behalf Of nepenthes@vplaces.net > Sent: Tuesday, October 23, 2001 2:58 AM > To: chemistry@ccl.net > Subject: CCL:random pick of binding site? > > > Dear all, > > I would like to ask some opinions from you.I'm studying > protein-ligand interactions computationally. I have a hexamer > protein with six identical binding sites. These six sites > bind to six of the same ligand. Since it's quite complicated > to study all six at a time, it was suggested to me that I > study only one site since they are all identical. I am not > too sure whether I can just take a site at random to study > the ligand interactions or are there some other > classifications which I should take account in picking the > site i want to study. I would be glad to hear some > suggestions as I've not found the answer yet or some > reference to where I might be able to get some answers. > > My grateful thanks in advance. Hope to hear from somebody. > > > Rowyna K. > Institute of Biological Sciences > University of Malaya > Kuala Lumpur > > > -------------------------------------------------------------------- > mail2web - Check your email from the web at > http://mail2web.com/ . > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: > gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | > Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Tue Oct 23 10:52:06 2001 Received: from sungod.ccs.yorku.ca ([130.63.236.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9NEq6B08752 for ; Tue, 23 Oct 2001 10:52:06 -0400 Received: from sunburn.ccs.yorku.ca (sunburn.ccs.yorku.ca [130.63.236.110]) by sungod.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id KAA11712; Tue, 23 Oct 2001 10:54:56 -0400 (EDT) Received: from localhost (serge@localhost) by sunburn.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id KAA04263; Tue, 23 Oct 2001 10:54:52 -0400 (EDT) X-Authentication-Warning: sunburn.ccs.yorku.ca: serge owned process doing -bs Date: Tue, 23 Oct 2001 10:54:49 -0400 (EDT) From: Serge Gorelsky X-X-Sender: To: Jens Spanget-Larsen cc: Subject: Is TD or Zindo better than CIS? In-Reply-To: <15E90A03A45@virgil.ruc.dk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Along the same topic: another recent paper Electronic Structure and Spectra of Ruthenium Diimine Complexes by Density Functional Theory and INDO/S. Comparison of the two methods. S.I. Gorelsky and A. B. P. Lever J. Organomet. Chem., 635, 187 - 196 (2001). Regards, Serge > I just wish to draw your attention to a recent paper by Juergen > Fabian, where he presents an extensive comparison of the performances > of ZINDO/S and TD-DFT in the prediction of electronic transitions for > a variety of organic sulfur compounds: > > Jueregn Fabian: "Electronic excitation of sulfur-organic compounds - > performance of time-dependent density functional theory", Theor. > Chem. Acc. 106, 199-217 (2001). > > Yours, Jens >--< > > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > JENS SPANGET-LARSEN Office: +45 4674 2710 > Department of Chemistry Fax: +45 4674 3011 > Roskilde University (RUC) Cell-Phone: +45 2320 6246 > P.O.Box 260 E-Mail: JSL@virgil.ruc.dk > DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~jsl > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > ________________________________________________________________ S. I. Gorelsky, M.Sc. Department of Chemistry, York University 4700 Keele Street, Toronto, Ontario M3J 1P3 Canada Phone: 416-736-2100 ext#70131 Fax: 416-736-5936 http://www.chem.yorku.ca/grad/SG/ ________________________________________________________________ From chemistry-request@server.ccl.net Tue Oct 23 09:10:20 2001 Received: from jivdhan.unipune.ernet.in ([196.1.114.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9NDAIB06340 for ; Tue, 23 Oct 2001 09:10:19 -0400 Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.11.1/8.11.1) with ESMTP id f9NDMBl13810 for ; Tue, 23 Oct 2001 18:52:16 +0530 Received: (from gadre@localhost) by chem.unipune.ernet.in (8.9.3/8.8.7) id SAA10438 for CHEMISTRY@www.ccl.net; Tue, 23 Oct 2001 18:43:23 +0530 Date: Tue, 23 Oct 2001 18:43:23 +0530 From: gadre@chem.unipune.ernet.in Message-Id: <200110231313.SAA10438@chem.unipune.ernet.in> To: CHEMISTRY@server.ccl.net Subject: AJP MARTIN Dear Sirs and Madams : Can anyone give me the present address of the discverer of chromatography, Professor A J P Martin? Thanks.................................Shridhar Gadre From chemistry-request@server.ccl.net Tue Oct 23 10:31:24 2001 Received: from chemistry.chem.utah.edu ([128.110.197.226]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9NEVOB08226 for ; Tue, 23 Oct 2001 10:31:24 -0400 Received: from ANDERSON5 (anderson5.chem.utah.edu [128.110.196.158]) by chemistry.chem.utah.edu (Switch-2.0.6/Switch-2.0.6) with SMTP id f9NETMt27350 for ; Tue, 23 Oct 2001 08:29:22 -0600 (MDT) Message-ID: <016901c15bcf$c9c7b1b0$9ec46e80@ANDERSON5> From: "Scott Anderson" To: References: Subject: Re: CCL:RIMM vs SDRAM Date: Tue, 23 Oct 2001 08:34:14 -0600 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear Tom: Regarding your question about RIMM (RDRAM) v.s. SDRAM (or DDR SDRAM) for Gaussian: I have done a fair bit of comparing machines for Gaussian, as I am planning to buy a bunch in the near future. I have been using an MP2 Opt Freq job that takes a few hours as my benchmark. I have also run much longer Direct Dynamics trajectory jobs on several different configurations. The MP2 job was deliberately chose to avoid a lot of disk i/o because I really wanted to focus on the computational speed. I have compared 1 and 1.4 GHz Athlons, PIIIs, and P4s. The conclusion is that for Gaussian, the P4 is 20-30% faster than the Athlons for the same clock speed, and since you can get P4s with faster clocks, the P4 ends up being substantially faster. This speed difference is quite surprising because the P4 floating point unit is substantially inferior to that of the Athlon, and as far as I have been able to determine, the rate deterimining step for these fast chips is memory speed. Here the RDRAM really shines. I have also compared Athlons with PC133 SDRAM and PC2100 DDR ram, which is theoretically substantially faster. For Gaussian jobs, I see no difference. One interesting thing to look at in this regard is the review in the Tom's Hardware review of the new Athlon XP. http://www6.tomshardware.com/cpu/01q4/011009/index.html They compare several different Athlons with different memory configurations, and also 2GHz P4s with both RDRAM and DDR memory. The Athlon XP looks great on most of the benchmarks -- equalling or exceeding the P4, even though the P4 clock speed is much higher. The one area where the XP fails, however, is memory speed. Note that the P4 with RDRAM does 50% better than the P4 with DDR, and nearly a factor of two better than the Athlons with either PC133 or DDR memory. My conclusions: 1. Gaussian is probably memory-bandwidth limited, and you should spend the extra money RDRAM. 2. DDR memory doesn't really make a huge difference -- certainly nothing like the factor of two you might expect. 3. The ideal configuration is very application dependent. For Gaussian, I would go with the P4. If you are running a mix of programs, you really have a tough decision. Have fun Prof. Scott L. Anderson Department of Chemistry University of Utah 315 S. 1400 E. Rm 1216 Salt Lake City, UT 84112 (801)585-7289 FAX(801)581-8433 www.chem.utah.edu/chemistry/faculty/anderson/anderson.html ----- Original Message ----- From: "Tom Kuppens" To: Sent: Tuesday, October 23, 2001 5:07 AM Subject: CCL:RIMM vs SDRAM > Hi there, > > We have several linux machines that run Gaussian. Now we want to add some new > power to our park i.e. a PIV - 1700MhZ with 512M RAM (SDRAM or RIMM). > > Is there someone who can provide me with some info on the Gaussian and/or > overall performance with RIMM versus SDRAM modules. > > Thanks in advance, > > Tom Kuppens > Ghent University > > -- > tom@hartree4.ac.be > http://studwww.rug.ac.be/~tkuppens/quantum/ > --- > It seems to me, Golan, that the advance of civilization is nothing > but an exercise in the limiting of privacy. > -- Janov Pelorat in Asimov's Foundation's Edge > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > From chemistry-request@server.ccl.net Tue Oct 23 10:25:47 2001 Received: from femail7.sdc1.sfba.home.com ([24.0.95.87]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9NEPlB08108 for ; Tue, 23 Oct 2001 10:25:47 -0400 Received: from C1353359A ([65.4.172.51]) by femail7.sdc1.sfba.home.com (InterMail vM.4.01.03.20 201-229-121-120-20010223) with SMTP id <20011023142837.PBOH610.femail7.sdc1.sfba.home.com@C1353359A>; Tue, 23 Oct 2001 07:28:37 -0700 Message-ID: <003901c15bce$a6c196a0$33ac0441@sttln1.wa.home.com> Reply-To: "Mark A. Thompson" From: "Mark A. Thompson" To: "Shobe, Dave" , "Geoff Hutchison" Cc: "'CCL'" References: <157A51F55AAAD3119CD70008C7B1629D01C15666@lvlxch01.unitedcatalysts.com> Subject: Re: CCL:Is TD or Zindo better than CIS? Date: Tue, 23 Oct 2001 07:26:05 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 The nomenclature issue surrounding Zindo is a bit confusing. Zindo originally was just a program name for the code produced by Mike Zerner's group. Over time, Zindo became synonymous with the INDO/s-CIS method that Mike and Joanna Ridley developed in the 70's. The Zindo Hamiltonian is a Hartree-Fock semiempirical method. It solves the same matrix equations as any other Hartree-Fock method, albeit with approximations in how the elements of the Fock matrix are generated and usually assuming the overlap matrix is unity. So, confusingly, Zindo means not only the ground state Hamiltonian, but the approach (INDO/s-CIS) to get the excited states. The more important issue to me, is that after all these years, the method has shown itself invaluable to an increasing number of chemistry problems from non-linear optical effects, organometallic systems, solvent effects, to the large calculations Mike and I did on the photosynthetic reaction center some years ago. Mark ------------------------------------------------------------------------- home page: http://members.home.net/markt158/ ----- Original Message ----- From: "Geoff Hutchison" To: "Shobe, Dave" Cc: "'CCL'" Sent: Monday, October 22, 2001 8:27 PM Subject: CCL:Is TD or Zindo better than CIS? > At 1:25 PM -0400 10/22/01, Shobe, Dave wrote: > >spectrum. Gaussian has two other methods (neither of which I've used) for > >calculating excited states: Zindo and TD. Are these significatnly better > >than CIS? Zindo being a semiempirical method, is it only good for certain > >kinds of molecules? Should I be looking at programs other than Gaussian for > >this type of calculation? > > It's strange this should come up as I'm working on a manuscript along > these lines for a certain set of molecules. But first there's a > nomenclature issue. Normally when people say "Zindo," they mean > "INDO/S CIS," and so you can't compare "Zindo" to "CIS." Also, I'm > not quite sure I know what you mean when you say "TD" since you > usually refer to TD-HF or TD-DFT for time-dependent HF or time > dependent DFT. > > If you compare Zindo CIS to HF-CIS for most neutral organic > molecules, you'll find Zindo is more accurate. If you compare TD-HF > (say the RPA) to HF-CIS, the HF-RPA is better--no surprise since the > RPA is one step past the Tamm-Dancoff approximation (CIS). But HF-RPA > is not as good as Zindo for most neutral organic molecules. > > TD-DFT seems to be slightly worse than Zindo for neutral organic > molecules, but not by much. > > Also keep in mind that Zindo CIS as a semiempirical method sometimes > incorrectly identifies the composition of certain excitations even if > the energy is pretty good. > > Can't say how Gaussian does on these sorts of things--we can't get it > here. As Mark Thompson pointed out, you can also go beyond CIS to > CISD, etc. The original ZINDO program from Zerner does let you do > things like this, though YMMV. Other programs as well have CISD, > CISDT and other higher-order methods. (Dalton springs to mind.) > > -- > -- > -Geoff Hutchison > Ratner/Marks Groups (847) 491-3295 > Northwestern Chemistry http://www.chem.nwu.edu/ > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Tue Oct 23 10:51:29 2001 Received: from gatekeeper.tripos.com (firewall-user@[192.160.145.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9NEpTB08725 for ; Tue, 23 Oct 2001 10:51:29 -0400 Received: (from uucp@localhost) by tripos.com (8.8.8+Sun) id JAA02486 for <@firewall.tripos.com:chemistry@ccl.net>; Tue, 23 Oct 2001 09:54:19 -0500 (CDT) Received: from elara.tripos.com(172.20.5.15) by gatekeeper.tripos.com via smap (V5.5) id xma001055; Tue, 23 Oct 01 09:50:57 -0500 Received: from tripos.com (thebe [172.20.6.145]) by tripos.com (980919.SGI.STAND) via ESMTP id JAA36544; Tue, 23 Oct 2001 09:50:56 -0500 (CDT) Sender: dlarson@elara.tripos.com Message-ID: <3BD583D0.ECBF4221@tripos.com> Date: Tue, 23 Oct 2001 09:50:56 -0500 From: David Larson Reply-To: bclark@tripos.com Organization: Tripos, Inc. http://www.tripos.com X-Mailer: Mozilla 4.7C-SGI [en] (X11; U; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Fall 2002 ACS Meeting: QSAR FROM CRADLE TO GRAVE Content-Type: multipart/mixed; boundary="------------025E460BFCDA121198633CF1" This is a multi-part message in MIME format. --------------025E460BFCDA121198633CF1 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit QSAR FROM CRADLE TO GRAVE Fall ACS meeting in Boston (August 18-22, 2002) Sponsored by the Division of Computers in Chemistry (COMP) The scope of QSAR includes analysis of all aspects of quantitative molecular design. At the "front end" of drug or pesticide design, for example, structure/property relationships (SPRs) are being elucidated for pharmaco- kinetic properties, and predictions that a compound will have ADME or toxicological problems will stop some compounds from being made at all. At the other extreme is the growing use of combinatorial approaches and experimental design to optimize process chemistry. In between lie analysis of high-throughput screening (HTS) data and "classical" lead optimization. In other areas of inquiry - e.g., odorant or taste characterization or pest deterrence - QSARs may serve to either generate hypotheses or to test existing hypotheses generated from earlier analyses. We are organizing a multi-session symposium for the 18-22 August 2002 American Cheimcal Society meeting in Boston. If you would like to present a paper on any aspect of QSARs, QSPRs or a related area of chemometrics, please contact one of us with a brief description of your topic by April 15, 2002. Abstracts will need to be submitted via OASys shortly thereafter. Bob Clark (bclark@tripos.com) Tripos, Inc. 1699 S. Hanley Road St. Louis MO 63144 Yvonne Martin (yvonne.c.martin@abbott.com) D-47E AP10/2 Abbott Laboratories 100 Abbott Park Road Abbott Park IL 60064-6100 --------------025E460BFCDA121198633CF1 Content-Type: text/x-vcard; charset=us-ascii; name="dlarson.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for David Larson Content-Disposition: attachment; filename="dlarson.vcf" begin:vcard n:Larson;David A. tel;fax:314-647-9241 tel;work:314-647-1099 x-mozilla-html:FALSE org:TRIPOS, Inc. adr:;;1699 S. Hanley Road;St. Louis;MO;63144; version:2.1 email;internet:dlarson@tripos.com title:Customer Support Scientist note;quoted-printable:Please Send Requests For Technical=0D=0ASupport to 'support@tripos.com'.=0D=0ASYBYL 6.7.2/UNITY 4.2.2 now available for download. x-mozilla-cpt:;-12224 fn:David Larson end:vcard --------------025E460BFCDA121198633CF1-- From chemistry-request@server.ccl.net Tue Oct 23 13:25:16 2001 Received: from server.mldnet.com (root@[212.56.192.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9NHPDB12492 for ; Tue, 23 Oct 2001 13:25:14 -0400 Received: from ppp-212.56.193.152.mldnet.com (ppp-212.56.193.152.mldnet.com [212.56.193.152]) by server.mldnet.com (8.9.3/8.9.3) with ESMTP id UAA10390 for ; Tue, 23 Oct 2001 20:27:57 +0300 Date: Tue, 23 Oct 2001 20:34:35 +0300 From: Mike Peleah X-Mailer: The Bat! (v1.53d) Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <12023800426.20011023203435@yahoo.com> To: chemistry@ccl.net Subject: Analytical Chemistry: Colour of Reagents MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I find two papers in Russian dated 1971 dealing with colour of organic reagents: E.L.Kuzin To the theory of action of coloured organic reagents 1. Introduction to the elementary quantum theory of the change of the sensitivity of colour analytical reactions // Zhurnal Analiticheskoi Khimii, 1971, Vol.26, No.2, pp.210-216 and 2. To the theory of the substituent effect on the contrast of colour indicator reactions // Zhurnal Analiticheskoi Khimii, 1971, Vol.26, No.2, pp.217-223 Could anybody point me out more recent papers on this topic? Thanks in advance. All informative answers will be summarised. Best regards, Mike mailto:MikePeleah@yahoo.com From chemistry-request@server.ccl.net Tue Oct 23 21:04:47 2001 Received: from deimos.email.Arizona.EDU (IDENT:root@[128.196.133.166]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9O14kB01424 for ; Tue, 23 Oct 2001 21:04:46 -0400 Received: from demetrio.u.arizona.edu (128.196.86.129) by deimos.email.Arizona.EDU (5.1.056) id 3BC7BE0B0010A7D3 for CHEMISTRY@ccl.net; Tue, 23 Oct 2001 18:07:35 -0700 Message-Id: <5.1.0.14.0.20011023180348.00b2bc20@deimos.email.arizona.edu> X-Sender: dasf@deimos.email.arizona.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 23 Oct 2001 18:07:17 -0700 To: CHEMISTRY@ccl.net From: Demetrio Antonio da Silva Filho Subject: Animate sequence of coordinates from TINKER Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL'ers, I am using TINKER to perform some MD calculations and I would like to animate the viewing of sequence of coordinates snapshots from a dynamic trajectory. Does anybody knows a free software able to read the TINKER .xyz files and animate them ? Thanks in advance, Demetrio Filho