From chemistry-request@server.ccl.net Thu Apr 22 00:38:36 1999 Received: from pobox.csc.fi (pobox.csc.fi [128.214.46.62]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA29907 for ; Thu, 22 Apr 1999 00:38:35 -0400 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 HAA04795 for ; Thu, 22 Apr 1999 07:35:08 +0300 (EET DST) Date: Thu, 22 Apr 1999 07:35:08 +0300 From: Maija Lahtela X-Sender: mlahtela@voxopm.minedu.fi To: chemistry@ccl.net Subject: summary of teaching material Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, Thank you all for these web-pages dealing with teaching material for computational chemistry. I rwally appreciate your help. I have spend days just by wondering your beautiful pages. Thanks specially for Greg, Alex MacKerell, Kimberley Cousins, Donald B. Boyd, I.Novak and Frank. Thanks also John Marelius of summary about "Molecular modelling software in education". I have also some link that I want to share with you. Nice demos for PC; http://www.jbpub.com/disks/chemdownload.htm. Practical exercises in quantum chemistry, http://www.scsc.ethz.ch/~chem/QCII/qcii.html What's new in chemistry http://wwwsci.lib.uci.edu/~martindale/GradChemistry.html#WHATNEW Silicon graphics teaching laboratory http://www.ch.cam.ac.uk/SGTL/ ****************************************************************** there are some "self-paced" courses available from NetScience. See: http://www.netsci.org/ regards, Greg ********************************************************* check the course my web page. http://www.pharmacy.ab.umd.edu/~alex/www_alex/p531_syllabus.html it contains links to a variety of lecture notes, including Target Based Rational Drug Discovery which is a low level intro to comp. chemistry and Lab 2. Drug molecular modeling which is a computer based lab that uses the ChemSite program (although any modeling program would work). Alex ********************************************************** there's some stuff on my compchem page Soaring Bear Ph.D. Research Pharmacologist, Informatics, Chemistry & Biochemisty, Herbalist & Healthy Lifestyles http://www.dakotacom.net/~bear http://www.amfoundation.org ************************************************************ You might check out my web page (chem 500 during the 97/98 AY and my "cheminternet98 poster" describing my course). There are numerous links to other resources on the internet, as well as a few developed locally. Actually, several of the vendors have good stuff too--Wavefunction (Spartan family) and CAChe come to mind. You might search the online indices of J. Chem. Educ. as The Chemical Educator as well. kcousins@csusb.edu http://chem.csusb.edu/~kcousins ************************************************************** Self tutorials about computational chemistry and molecular modeling can be found in many chapters of Reviews in Computational Chemistry. Take at look at our website (http://chem.iupui.edu/rcc/rcc.html) for the topics covered. I hope you find them useful. Donald B. Boyd ******************************************************** I teach quantum chemistry in my Dept. and I find articles in J.Chem.Educ. to be very useful. You can use their on-line search facility to find specific topics. As an example I can also suggest(somewhat immodestly) that you look at my article in J.Chem.Educ.vol.76 (1999) 135. Bookwise, as a primer I would warmly recommend the book by J.M.Goodman, Chemical Applications of Molecular Modelling, published by Royal Society of Chemistry 1998 (ISBN 0-85404-579-1). I.Novak ******************************************************** I have collected some, and made links to others: http://bogense.chem.ou.dk/~icc If you get other useful responses I'll appreciate if you send a copy to me. Frank ********************************************************** Yours Sincerely, 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@server.ccl.net Thu Apr 22 01:03:47 1999 Received: from pobox.csc.fi (pobox.csc.fi [128.214.46.62]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA30133 for ; Thu, 22 Apr 1999 01:03:47 -0400 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 IAA05261 for ; Thu, 22 Apr 1999 08:00:20 +0300 (EET DST) Date: Thu, 22 Apr 1999 08:00:20 +0300 From: Maija Lahtela X-Sender: mlahtela@voxopm.minedu.fi To: chemistry@ccl.net Subject: Using ONIOM in G98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers We have tried 2-layer ONIOM, using AM1 or B3LYP/6-31G(d,p) one amino acid and the rest of protein using amber. The input file for G98 #p opt oniom(B3LYP/6-31G(d,p):amber) iop(5/6=3) test However, we have problems with parameters. We would greatly appreciate your guidance with ONIOM. I have contact also Dr.Stefan Dapprich with this problem. End of our G98 .log-file AMBER calculation of energy and first derivatives. MO and density RWFs will be updated. Recover connectivity from rwf. EGHMM: NBAlg=1 ICut=1 CutNB= 1.43D+03 I= 12 IAn= 7 Valence= 4. JB= 1 J= 13 IAn= 1 IBT= 1 Dist= 1.03D+00 JB= 2 J= 14 IAn= 1 IBT= 1 Dist= 1.03D+00 JB= 3 J= 15 IAn= 1 IBT= 1 Dist= 1.03D+00 JB= 4 J= 16 IAn= 6 IBT= 1 Dist= 1.45D+00 I= 26 IAn= 1 Valence= 3. JB= 1 J= 23 IAn= 6 IBT= 1 Dist= 1.58D+00 JB= 2 J= 27 IAn= 8 IBT= 1 Dist= 9.39D-01 JB= 3 J= 28 IAn= 8 IBT= 2 Dist= 2.25D+00 I= 29 IAn= 1 Valence= 6. JB= 1 J= 5 IAn= 6 IBT= 2 Dist= 1.08D+00 JB= 2 J= 30 IAn= 1 IBT= 1 Dist= 1.17D+00 JB= 3 J= 31 IAn= 6 IBT= 1 Dist= 1.62D+00 Missing atomic parameters for atom 12 IAtTyp= -1 Missing atomic parameters. Error termination via Lnk1e in /v/irix65_mips64/appl/chem/gaussian/G98RevA.3/$ Job cpu time: 0 days 0 hours 16 minutes 9.9 seconds. File lengths (MBytes): RWF= 15 Int= 0 D2E= 0 Chk= 1 Scr= 1 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@server.ccl.net Thu Apr 22 02:00:45 1999 Received: from punegate.mahindrabt.com (uucp@[203.197.95.162]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA30507 for ; Thu, 22 Apr 1999 02:00:25 -0400 Received: (from uucp@localhost) by punegate.mahindrabt.com (8.8.7/8.8.6) id LAA28017 for ; Thu, 22 Apr 1999 11:34:34 +0530 Received: from intranet.pune.mahindrabt.com(202.41.13.243) via SMTP by punegate.mahindrabt.com, id smtpda28005; Thu Apr 22 06:04:26 1999 Received: from mahindrabt.com (pc-172-24-7-180.pune.mahindrabt.com [172.24.7.180] (may be forged)) by intranet.pune.mahindrabt.com (8.8.7/8.8.7) with ESMTP id LAA22135 for ; Thu, 22 Apr 1999 11:26:16 +0530 Message-ID: <371EB8BB.71A56E0B@mahindrabt.com> Date: Thu, 22 Apr 1999 11:20:52 +0530 From: "Dr. Sudhir A. Kulkarni" X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Molecular recognition Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear colleagues, I am looking for recent experimental/theoretical methods that deals with the process of molecular recognition. Any references or reviews will be highly appreciated. I will summarize if there is sufficient interest. Thanks in advance. Sudhir Kulkarni MBT, Pune 411 018, India From chemistry-request@server.ccl.net Thu Apr 22 03:23:50 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA31205; Thu, 22 Apr 1999 03:23:50 -0400 Received: from fskru5.hre.hydro.com (fskru5.hre.hydro.com [163.34.32.82]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id DAA12058 Thu, 22 Apr 1999 03:20:20 -0400 (EDT) Received: (from msj@localhost) by fskru5.hre.hydro.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) id KAA20871 for chemistry@www.ccl.net; Thu, 22 Apr 1999 10:14:29 +0200 From: "Merethe Sjovoll" Message-Id: <9904221014.ZM20869@fskru5.hre.hydro.com> Date: Thu, 22 Apr 1999 10:14:29 -0600 Reply-To: Merethe.Sjovoll@hre.hydro.com X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Estimation of vapour pressure of organic liquids and solids Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi everybody, is there a way of estimating in a crude way the vapour pressure of organic liquids and solids? I have a whole bunch of molecules and I don't need absolute values, just look for tendencies. So I imagine some calculation formula which perhaps contains temperature, possibly boiling point and melting point, or perhaps dipole moment, molecular weight etc. (easily accessible quanities). Is this wishful thinking? Best regards Merethe Sjovoll -- ******************************************************** Merethe Sjovoll, Ph.D. * * Senior Research Scientist * * Norsk Hydro a.s Research Center * * * * P.O.Box 2560 * HYDRO * N-3907 Porsgrunn, * RESEARCH * Norway * * * ((( * email: Merethe.Sjovoll@hre.hydro.com * (=====) * Phone:+47 35 56 48 97 * * Fax :+47 35 56 27 22 * * ******************************************************** From chemistry-request@server.ccl.net Thu Apr 22 06:05:04 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA32632; Thu, 22 Apr 1999 06:05:04 -0400 Received: from galaad.citi2.fr (galaad.citi2.fr [192.70.98.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA12322 Thu, 22 Apr 1999 06:01:31 -0400 (EDT) Received: from bisance.citi2.fr (bisance.citi2.fr [192.70.98.30]) by galaad.citi2.fr (8.8.8/jtpda-5.3) with ESMTP id MAA01640 ; Thu, 22 Apr 1999 12:01:31 +0200 (MET DST) Received: from crimson (u40011.citi2.fr [193.51.81.70]) by bisance.citi2.fr (8.8.8/jtpda-5.3) with SMTP id MAA23105 ; Thu, 22 Apr 1999 12:01:29 +0200 (MET DST) Sender: jirka@citi2.fr Message-ID: <371F7205.41C6@citi2.fr> Date: Thu, 22 Apr 1999 12:01:25 -0700 From: Jirka Kozelka Organization: Universite Rene Descartes,CNRS Paris France X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP17) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: HOMO-LUMO gap in Pt(II) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL-members, I have carried out a number of SCF calculations on Pt(II) complexes with chloride, amine, and phosphine ligands, using Gaussian 94 and 98, with different basis sets, and find consistently HOMO-LUMO gaps of 0.3-0.4 Hartrees, i.e., 65000-90000 cm-1. This is roughly 3 times the excitation energies of spin-allowed d-d bands seen in solutions of these species. The difference seems too big to me to be explained by electron relaxation. I would very much appreciate comments and/or explications on/of this apparent discrepancy. We have seen that the bond lengths and dipole moment coming from HF calculations are quite wrong for these compounds, and one has to apply correlated methods to get these quantities right. But can it be that the difference in energies of the HF HOMO/LUMO one-electron orbitals is so far from the excitation energy? I shall summarize the answers. Thanks, Jirka Kozelka -- Jirka Kozelka Universite Rene Descartes URA CNRS 400 45 rue des Saints-Peres 75270 Paris 06 FRANCE Tel. +331 42 86 21 75 Fax +331 42 86 83 87 E-mail: kozelka@citi2.fr From chemistry-request@server.ccl.net Thu Apr 22 07:53:19 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA00875; Thu, 22 Apr 1999 07:53:19 -0400 Received: from mail2.uct.ac.za (mail2.uct.ac.za [137.158.128.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA12524 Thu, 22 Apr 1999 07:47:38 -0400 (EDT) Received: from mort by mail2.uct.ac.za with local (Exim 2.01 #1) for chemistry@www.ccl.net id 10aHtM-0000Zy-00; Thu, 22 Apr 1999 13:43:40 +0200 Received: by mail2.uct.ac.za (Mort 2.23alpha) id 536 from ACHIM@PSIPSY; Thu Apr 22 13:43:40 1999 From: "Achim Lienke" Organization: University of Cape Town To: chemistry@www.ccl.net Date: Thu, 22 Apr 1999 13:47:08 SAST-2 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Hydrogen bonds Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) Message-Id: Hi there, can anybody point me to a review which compares the accuracy of different DFT methods with respect to predicting the geometry and strength of hydrogen bonds, especially for interactions between water and simple anions. Thanks Achim ---------------------------------------------------------------------- Achim Lienke Department of Chemistry University of Cape Town Private Bag Rondebosch 7701 South Africa Phone: ++27-21-650-2325 or -2530 Fax: ++ 27-21-689-7499 email: achim@psipsy.uct.ac.za ---------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Apr 22 11:08:40 1999 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA03262 for ; Thu, 22 Apr 1999 11:08:39 -0400 Received: from sally.schrodinger.com (sally.schrodinger.com [206.231.140.227]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id IAA19611 for ; Thu, 22 Apr 1999 08:07:33 -0700 Received: from localhost (shenkin@localhost) by sally.schrodinger.com (8.8.5/8.8.5) with ESMTP id LAA04639 for ; Thu, 22 Apr 1999 11:06:58 -0400 X-Authentication-Warning: sally.schrodinger.com: shenkin owned process doing -bs Date: Thu, 22 Apr 1999 11:06:58 -0400 (EDT) From: Peter Shenkin To: chemistry@ccl.net Subject: Re: CCL:multi-processors and memory In-Reply-To: <371E8F56.D128CEB8@syr.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII For the answer to your question, "man runon". However, if GAMESS is like most quantum programs, it spends a lot of time in IO and cannot keep the CPU busy. The net effect of doing what you propose might be to give each charmm run 50% of a CPU and to increase the GAMESS CPU utilization by very little. Still, you could try and see. -P. On Wed, 21 Apr 1999, Deepak Singh wrote: > Hi folks > > This might be a little out of context but if someone could just point me > > in the right direction it would be great. > > I have a SGI OCTANE with 2 processors (and 1.5 GB of memory). I am not > running any parallel > applications and do not think runnign parallel versions would give me an > advantage with just 2 > processors, but is there any way I can assign a processor to e.g. a > gamess run (which is where I need that capability the most)? Right now > I have two charmm runs > underway and one gamess run. While the overall operation of my computer > is nto significantly affected, > I do not like the CPU utilization which is currently ~75% each for the > charmm runs and 21% for the > GAMESS run (at least that is what gr_top reports). Any idea how I can > make GAMESS utilize more of > the CPU? Is this a problem in my GAMESS input file ( I am new to > ab-inito stuff) or is there something I can do to teh computer? > > > If someone can refer me to a good resource it would be great. > > Thanks > > Deepak. > > -- > ********************************************************************** > Deepak Singh Tel : (315)443 1739 (w) > Graduate Student (315)472 9659 (h) > Dept. of Chemistry & Biochemistry Fax : (315)443 4070 > Syracuse University email : desingh@syr.edu > 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh > NY 13244 > > "Violence is the last refuge of the incompetent." --- Salvor Hardin > ********************************************************************** > > > > -= 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 > > > > > -- ********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** From chemistry-request@server.ccl.net Thu Apr 22 13:18:05 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA05301; Thu, 22 Apr 1999 13:18:04 -0400 Received: from zmaj.etf.bg.ac.yu (zmaj.etf.bg.ac.yu [147.91.8.62]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA13995 Thu, 22 Apr 1999 13:14:24 -0400 (EDT) Received: from nastava.tf.bor.ac.yu (nastava.bor.tf.ac.yu [160.99.193.1] (may be forged)) by zmaj.etf.bg.ac.yu (8.9.3/8.9.0) with SMTP id TAA11291 for ; Thu, 22 Apr 1999 19:14:02 +0200 Received: from NASTAVA/SpoolDir by nastava.tf.bor.ac.yu (Mercury 1.12); Thu, 22 Apr 99 18:36:28 GMT+01 Received: from SpoolDir by NASTAVA (Mercury 1.12); Fri, 9 Apr 99 16:37:03 GMT+01 From: "Milan Antonijevic" Organization: Tehnicki Fakultet u Boru To: chemistry@www.ccl.net Date: Fri, 9 Apr 1999 16:36:55 GMT+1 Subject: airstrike X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail v3.1 (R1) Message-ID: <867457697@nastava.tf.bor.ac.yu> Dear Sirs, I am calling from my country, YUGOSLAVIA which is under agressive NATO-airstrikes. AMERICA and NATO are trying to terminate Yugoslavian nation. Why?????? Our men ,women and CHILDREN are frantig with terror and a huge psihological preasure is being puted under us because of this situation, and I want to know your opinion about NATO's and Amricans decision to bomb our country and about the consequences of the bombing. You can send me your opinions on my personal e-mail. M.M. Antonijevic ======================================== Professor Dr Milan M. Antonijevic University of Belgrade Technical Faculty Bor 19210 BOR, Serbia, YUGOSLAVIA Tel: +381 30 24 555 Fax : +381 30 21 078 e-mail: amilan@nastava.tf.bor.ac.yu adanilo@ptt.yu ========================================== From chemistry-request@server.ccl.net Thu Apr 22 14:20:48 1999 Received: from swan2.uspnet.usp.br (swan2.uspnet.usp.br [143.107.253.69]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA06203 for ; Thu, 22 Apr 1999 14:20:32 -0400 Received: from ligquim ([143.107.194.89]) by swan2.uspnet.usp.br (8.9.1a/8.9.1) with SMTP id PAA23204 for ; Thu, 22 Apr 1999 15:13:34 -0300 (EST) Message-ID: <00c301be8cec$117fa0e0$0100005a@ligquim.ffclrp.usp.br> From: "Sergio Emanuel Galembeck" To: "CCL mail list" Subject: G98 and ZINDO Date: Thu, 22 Apr 1999 15:14:33 -0300 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 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Content-Transfer-Encoding: 7bit Dear All, Does ZINDO in G98 uses the new parametrization proposed recently by Broo and Zerner? Thanks a lot, Sergio ============================================== Sergio Emanuel Galembeck Assistant Professor in Physical Chemistry Laboratorio de Modelagem Molecular Departamento de Quimica Faculdade de Filosofia, Ciencias e Letras de Ribeirao Preto Universidade de Sao Paulo fax: +55-16-633-81-51 e-mail: segalemb@usp.br =============================================== From chemistry-request@server.ccl.net Thu Apr 22 18:30:19 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA08725; Thu, 22 Apr 1999 18:30:19 -0400 Received: from rutchem.rutgers.edu (rutchem.rutgers.edu [128.6.1.216]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA22562 Thu, 22 Apr 1999 18:26:38 -0400 (EDT) Received: from localhost (yong@localhost) by rutchem.rutgers.edu (8.8.8/8.6.10) with SMTP id WAA14730 for ; Thu, 22 Apr 1999 22:26:40 GMT Date: Thu, 22 Apr 1999 18:26:40 -0400 (EDT) From: Dayong He To: CHEMISTRY@www.ccl.net Subject: which company sell desktop or laptop with Redhat Linux. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello everybody. I am planing to buy a desktop with Redhat Linux installed, this machine will be mostly used for programming and scientific calculation, my budget is around $2000. Actually I know there are some companies on the web sell desktop with linux install, but do not remember the web site address, I will apprecite if you could point me to these sites or give me some suggestions. Thank you very much for your help. Dayong From chemistry-request@server.ccl.net Thu Apr 22 19:17:54 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA09284; Thu, 22 Apr 1999 19:17:54 -0400 Received: from relay2.scripps.edu (relay2.scripps.edu [137.131.200.30]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA22634 Thu, 22 Apr 1999 19:14:14 -0400 (EDT) Received: from redox.scripps.edu (redox.scripps.edu [137.131.240.50]) by relay2.scripps.edu (8.9.3/TSRI-3.0.2r) with ESMTP id QAA10597; Thu, 22 Apr 1999 16:14:10 -0700 (PDT) Received: from localhost by redox.scripps.edu (8.9.1/TSRI-2.8) with SMTP id QAA20871; Thu, 22 Apr 1999 16:13:44 -0700 (PDT) Date: Thu, 22 Apr 1999 16:13:44 -0700 (PDT) From: "Jesus M. Castagnetto" Sender: jesusmc@scripps.edu To: Dayong He cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:which company sell desktop or laptop with Redhat Linux. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A list of hardware vendors is at: http://www.linux.org/vendors/systems.html You can also go to the official Linux web site (the one above is not): http://www.li.org/resources/linuxlinks.html and check the HOWTO on installing Linux in systems w/ another OS. On Thu, 22 Apr 1999, Dayong He wrote: > I am planing to buy a desktop with Redhat Linux installed, this machine > will be mostly used for programming and scientific calculation, my > budget is around $2000. > > Actually I know there are some companies on the web sell desktop with > linux install, but do not remember the web site address, I will apprecite > if you could point me to these sites or give me some suggestions. > > Thank you very much for your help. > > Dayong -- Jesus M. Castagnetto - "Ken Zen Ichi-nyo" Program Project: http://www.scripps.edu/research/metallo/ Metalloprotein DB: http://metallo.scripps.edu/ Pilot Stuff: http://www.geocities.com/ResearchTriangle/Lab/1059/ From chemistry-request@server.ccl.net Wed Apr 21 05:43:59 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA17973; Wed, 21 Apr 1999 05:43:59 -0400 Received: from stan.ch.pwr.wroc.pl (stan.ch.pwr.wroc.pl [156.17.2.231]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA18036 Wed, 21 Apr 1999 05:40:39 -0400 (EDT) Received: from localhost (stanley@localhost) by stan.ch.pwr.wroc.pl (8.8.7/8.8.7) with ESMTP id LAA10676 for ; Wed, 21 Apr 1999 11:42:15 +0200 Date: Wed, 21 Apr 1999 11:42:14 +0200 (EEST) From: Stanislaw Kucharski To: chemistry@www.ccl.net Subject: G98 on SGI r5000 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I have some problem with getting a proper code of Gaussian 98 on SGI R5000, IRIX 6.3, F77 v.7.1, BLAS library - original. The compilation seemed to be successful, all modules were obtained. The test runs of selected at random test programs were in part OK. But, when running the test023.com, the program crushed with problems via link 9999. When trying optimization, the errors of initial Huckel guess (all values equal to zero), was always the case. I should be grateful for any helpful suggestion, as I am probably not the only person who met the above problem. With regards, Stan ********************************************************************* * Stanislaw Kucharski * Tel. +48 71 3202862 * * Institute of Organic and * +48 71 3202426 * * Polymer Technology * * * Wroclaw Technical University * Fax +48 71 3203678 * * ul. Wybrzeze Wyspianskiego 27 * * * 50-370 Wroclaw, Poland * * ********************************************************************* * E-mail: stanley@stan.ch.pwr.wroc.pl * * kucharski@itots.ch.pwr.wroc.pl * ********************************************************************* From chemistry-request@server.ccl.net Wed Apr 21 13:47:43 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA24217; Wed, 21 Apr 1999 13:47:43 -0400 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA28855 Wed, 21 Apr 1999 13:44:20 -0400 (EDT) Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id NAA08094 for ; Wed, 21 Apr 1999 13:44:17 -0400 (EDT) Received: (from daemon@localhost) by bioc1.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id KAA00034 for ; Wed, 21 Apr 1999 10:42:45 -0700 (PDT) Received: from dxg-pc.msi.com(146.202.11.19) by bioc1.msi.com via smap (V2.0) id xma000015; Wed, 21 Apr 99 10:42:14 -0700 Message-Id: <3.0.32.19990421104021.00a8f450@146.202.6.130> X-Sender: dgregory@146.202.6.130 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Wed, 21 Apr 1999 10:40:21 -0700 To: chemistry@ccl.net (Comp. Chem. List) From: Don Gregory Subject: Re: CCL:Benchmarks and software Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Warning: short, perhaps controversial response follows. ; ) >>On Mon, 19 Apr 1999, David Giesen wrote: >> I would like to add a second requirement of all commercial software if I >> may dream a little. > While Peter Shenkin replied ..... >Where there's life, there's hope. :-) A comment on a related statement made earlier, plus a small additional note of my own. It was pointed out that it is *very* difficult to get consensus from any significant number of people, on what 'banchmarks' are acceptable/ useful. This has been my experience, in the extreme. Secondly, people are looking for the commercial companies (note that I am, and have been an employee of MSI for quite some time) to do the benchmarks, and indeed, I can tell you that there has been for many years lively discussion within MSI regarding just that. But the first point keeps rearing its ugly head, and the more we bring in 'consultants' and outside-academics, the more convoluted things get. My additional note is this: there is a 'Consumers Union' and 'Consumers Report' that does analysis and 'benchmarking' for a reason. It is crucial, for them to be useful to the public at large, that such tests be run in an independent, objective, repeatable fashion (the hallmarks of good 'science', eh?) I am *definitely* not suggesting that MSI is shy about having our products tested and compared; we do that evey day as we go into companies world-wide. Of course, evey customer before they buy, wants to know how well you stack up against the competition. I'm not here to soap-box for MSI; I just don't want to give the silly impression that I'm trying to 'hide' where I work. But my main focus is, that given the recent fracas of linus 'benchmarks', one might think that the populace at large might have an interest in *establishing* what good benchmarks are, and how they are run and by what criteria they are judged. I think if that could be done, MSI would be thrilled to compete. But as with any 'reality check' the closer one looks, the more complicated things become. This is not to say that such efforts are not important, but that it isn't as simple as it implies to just say "someone should do it". Don Gregory Dr. Don Gregory (dgregory@msi.com) Asia Pacific Science Liaison Molecular Simulations Inc. 9685 Scranton Rd. San Diego, CA 92121 (619) 799-5331 http://www.msi.com From chemistry-request@server.ccl.net Wed Apr 21 19:43:42 1999 Received: from mailbox2.ucsd.edu (mailbox2.ucsd.edu [132.239.1.54]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA27279 for ; Wed, 21 Apr 1999 19:43:41 -0400 Received: from chemcca10.ucsd.edu (chemcca10.ucsd.edu [132.239.68.250]) by mailbox2.ucsd.edu (8.9.1a/8.9.1) with ESMTP id QAA10266 for <@mailbox.UCSD.EDU:chemistry@ccl.net>; Wed, 21 Apr 1999 16:40:18 -0700 (PDT) Received: (from hcarlson@localhost) by chemcca10.ucsd.edu (980427.SGI.8.8.8/970903.SGI.AUTOCF) id QAA26707; Wed, 21 Apr 1999 16:40:17 -0700 (PDT) Date: Wed, 21 Apr 1999 16:40:17 -0700 (PDT) From: hcarlson@chemcca10.ucsd.edu (Heather Carlson) Message-Id: <199904212340.QAA26707@chemcca10.ucsd.edu> To: chemistry@ccl.net Subject: SCF problem with G98 on T90 Cc: hcarlson@chemcca10.ucsd.edu Hello All, My students and I have a problem with the newly installed G98 on the T90 at the SDSC. In short, G94 gave us and energy of -397.85 H for our system, but G98 gives us -1E+145!!! (Yes, same input... and not an isolated incident/structure.) Does anyone know what is going on (full account below)??? Thank you, Heather ___________________________________________________________________ Dr. Heather A. Carlson, Ph.D. American Cancer Society Postdoctoral Fellow La Jolla Interfaces in Science Postdoctoral Fellow UCSD, Dept. of Chemistry and Biochemistry Phone: (619) 822-1469 9500 Gilman Drive, 4202 Urey Hall Fax: (619) 534-7042 La Jolla, CA 92093-0365 E-mail: hcarlson@chemcca10.ucsd.edu ___________________________________________________________________ > System: Alanine and one water molecule > > We tried to finish some IRCs that we had started with G94, and > they would not run. So we back-tracked the project to re- > calculating the TSs (we have 4). One ran properly, the other 3 > all fell victim to the same error... supposedly, our gradients > are out of range. > > Our command lines are: > #N 6-31+G* OPT=(TS,CalcAll,NoRaman) SCF=DIRECT > > Charge is zero; multiplicity is one. The code reads in the Zmat > input just fine, providing proper input and standard orientation > cartisian coordinates that perfectly match the structure in the > Zmat input: > > Standard orientation: > ---------------------------------------------------------------- > Center Atomic Atomic Coordinates (Angstroms) > Number Number Type X Y Z > ---------------------------------------------------------------- > 1 7 0 -0.383566 -1.364896 0.499169 > 2 6 0 0.550279 -0.546147 -0.342259 > 3 6 0 0.384693 0.957734 0.006937 > 4 8 0 1.380278 1.605834 0.160026 > 5 8 0 -0.814323 1.389658 0.087560 > 6 1 0 0.199639 -0.681904 -1.358544 > 7 6 0 1.977132 -1.045635 -0.196762 > 8 1 0 2.632312 -0.468463 -0.832898 > 9 1 0 2.332086 -0.932044 0.821286 > 10 1 0 2.049184 -2.091742 -0.483460 > 11 1 0 -1.676934 0.680044 -0.141141 > 12 1 0 -0.273038 -2.345158 0.301267 > 13 1 0 -0.202638 -1.231763 1.480958 > 14 8 0 -2.454641 -0.289740 -0.302798 > 15 1 0 -1.431265 -1.055390 0.264615 > 16 1 0 -3.307509 -0.161041 0.087933 > ---------------------------------------------------------------- > This is an exact match of the final output structure from the > original TS optimization with G94; rotational constants also > match. > > Though the structures are the same, the N-repulsion energies are > not: G94 gives 341.8720848317 H but G98 gives 341.8720849191 H. > Now for the interesting part... > > G94 gives the following SCF results > SCF Done: E(RHF) = -397.853912102 A.U. after 12 cycles > Convg = 0.4285E-08 -V/T = 2.0021 > S**2 = 0.0000 > G98 gives > SCF Done: E(RHF) = -0.104107509526+146 A.U. after 2 cycles > Convg = 0.2575E-12 -V/T = ******* > S**2 = 0.0000 > > Needless to say, all hell breaks loose at this point with out- > rageous eigenvalues and the following partial charges: > Total atomic charges: > 1 > 1 N -4.978340 > 2 C 0.639611 > 3 C 4.910643 > 4 O 6.155526 > 5 O 4.662892 > 6 H 0.136323 > 7 C -5.996997 > 8 H -0.166654 > 9 H 0.998955 > 10 H -0.078574 > 11 H -0.993813 > 12 H -0.590006 > 13 H 0.908727 > 14 O -3.981953 > 15 H -0.625232 > 16 H -1.001110 > Sum of Mulliken charges= 0.00000 >