From ccl@www.ccl.net Wed Mar 26 03:37:41 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id DAA11279; Wed, 26 Mar 1997 03:26:00 -0500 (EST) Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by bedrock.ccl.net (8.8.3/950822.1) id DAA02721; Wed, 26 Mar 1997 03:25:55 -0500 (EST) Received: from judy.ic.ac.uk [155.198.5.5] by romeo.ic.ac.uk with esmtp (Exim 0.57 #1) id 0w9o1p-0001af-00; Wed, 26 Mar 1997 08:25:53 +0000 Received: from cscmgb.cc.ic.ac.uk (sg1.cc.ic.ac.uk [155.198.63.8]) by judy.ic.ac.uk (8.7.5/8.7.5) with SMTP id IAA27648 for ; Wed, 26 Mar 1997 08:25:24 GMT Received: from [155.198.224.86] by cscmgb.cc.ic.ac.uk (940816.SGI.8.6.9/4.0) id IAA16256; Wed, 26 Mar 1997 08:25:23 GMT Date: Wed, 26 Mar 1997 08:25:23 GMT X-Sender: rzepa@155.198.63.8 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@ccl.net From: "Rzepa, Henry" Subject: ANNOUNCE: ECTOC-3 on Organometallic Chemistry An Electronic conference for discussing recent developments in Organometallic Chemistry Chemistry will be held during 30 June - 31 July 1997 on the Global Internet using the World-Wide Web and electronic mail as the delivery mechanisms. Scientific organisation will be under the auspices of the Royal Society of Chemistry. ECTOC-3 will continue the innovative style introduced with ECTOC-1 and ECTOC-2 (ECHET96) conferences in offering a low cost and near-instant mechanism for discussing chemistry, with features such as full colour structure diagrams, editable structures and reaction schemes, rotatable 3D molecular images, index searches of conference proceedings, contributed discussions by participants, up to date access statistics for articles, photographs submitted by participants and other novel features. The conference will take the form of keynote articles, contributed articles and posters and discussions on all aspects of organometallic chemistry, including synthetic and modelling areas. As with ECTOC-1 and ECHET96, we hope to publish a CD-ROM of the conference proceedings, comprising those accepted articles and posters whose authors have agreed to their inclusion. The deadline for submission of abstracts of articles or posters is Friday, April 25, 1997. For further information, including the submission process for abstracts, connect to http://www.ch.ic.ac.uk/ectoc/ectoc-3/ Or send a message to majordomo@ic.ac.uk with the single line message info ectoc-3 Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ From ccluser@chu.chem.nthu.edu.tw Wed Mar 26 22:32:02 1997 Received: from chu.chem.nthu.edu.tw for ccluser@chu.chem.nthu.edu.tw by www.ccl.net (8.8.3/950822.1) id VAA19040; Wed, 26 Mar 1997 21:55:51 -0500 (EST) From: Received: by chu.chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA18249; Thu, 27 Mar 1997 10:51:22 +0800 Message-Id: <9703270251.AA18249@chu.chem.nthu.edu.tw> Subject: H2 dissociation by UHF and DFT in G94? To: chemistry@www.ccl.net Date: Thu, 27 Mar 97 10:51:21 TAIST Dear CCL members, I tried to get energies of h2 (H atoms are seperated by 2 and 10 angstrom) by UHF/6-31g**, b3lyp/6-31g** and svwn/6-31g**, and all are set in singlet state, then I got energies as following, 2 angstrom, UHf/6-31g** -0.9167408 b3lyp/6-31g** -0.9959347 svwn/6-31g** -0.9167408 10 angstrom, UHf/6-31g** -0.7241629 b3lyp/6-31g** -0.8923662 svwn/6-31g** -0.4588643 I am so surprising at these results, does it mean these three methods can't describe the PES of h2 dissociation exactly? and we can't calculate TS involving H2 formation or dissociation? -- ===================================================================== Chiu-Ling Lin | E-mail: lin@chu.chem.nthu.edu.tw Department of chemistry | National Tsing Hua University | Phone: 886-35-721634 Hsinchu, Taiwan 30043 | Fax: 886-35-711082 ===================================================================== From noy@einstein.sc.mahidol.ac.th Thu Mar 27 11:32:13 1997 Received: from einstein.sc.mahidol.ac.th for noy@einstein.sc.mahidol.ac.th by www.ccl.net (8.8.3/950822.1) id KAA22644; Thu, 27 Mar 1997 10:55:05 -0500 (EST) Received: (from noy@localhost) by einstein.sc.mahidol.ac.th (8.7.4/8.7.3) id WAA14674 for chemistry@www.ccl.net; Thu, 27 Mar 1997 22:30:40 -0700 From: "Dr. Teerakiat Kerdcharoen" Message-Id: <199703280530.WAA14674@einstein.sc.mahidol.ac.th> Subject: Getting Started with Gaussian To: chemistry@www.ccl.net Date: Thu, 27 Mar 1997 22:30:40 -0700 (GMT+7) In-Reply-To: <199703261553.KAA29504@alchemy.chem.utoronto.ca> from "E. Lewars" at Mar 26, 97 10:53:03 am > H Y Jeong recently asked how he could get started using programs like > Gaussian. > > 1 General information on computational chemistry: > "Quantum Chemistry", by Ira N. Levine, 4th ed., Prentice Hall, 1991. > Very good introduction to QC, with problems (some answered). Chapters 15 and, > especially, 16 and 17 give a nice, brief overview of current computational May I added some here. A good new book just coming out to the shelf from Addison Wesley Longman Limited does worth your money. The title catches your eyes easily as "Molecular Modelling: Principles and Applications". The author is Andrew R. Leach and ISBN is 0-582-23933-9. Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen, Ph.D. Address: Department of Physics, Mahidol University, Bangkok 10400 Phone: 2461381 FAX 2461381 Cellular: 01-4906089 E-mail: noy@einstein.sc.mahidol.ac.th, noy@atc.atccu.chula.ac.th Homepage: http://www.sc.mahidol.ac.th/noy/ Research: Computer Aided Molecular Design (CAMD) ----------------------------------------------------------------------------- From dgregory@msi.com Thu Mar 27 12:32:12 1997 Received: from bioc1.msi.com for dgregory@msi.com by www.ccl.net (8.8.3/950822.1) id LAA23088; Thu, 27 Mar 1997 11:57:28 -0500 (EST) Received: by bioc1.msi.com (5.64/0.0) id AA16175; Thu, 27 Mar 97 08:56:56 -0800 Received: from biff.msi.com(146.202.0.225) by bioc1.msi.com via smap (V2.0) id xma016171; Thu, 27 Mar 97 08:56:45 -0800 Received: from [146.202.16.2] by biff.biosym.com (4.1/SMI-4.1) id AA24260; Thu, 27 Mar 97 08:56:35 PST X-Sender: dgregory@146.202.0.225 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 27 Mar 1997 08:57:40 -0800 To: chemistry@www.ccl.net From: dgregory@msi.com (Don Gregory) Subject: Re: CCL:How to prevent protein moving during dynamics? Hi Yun, If I read between your lines, my guess is that you have one very large sphere of surrounding water, with the protein in the middle ... ? and that when you did the SBMD the protein "diffused" to the boundary? Realize that the boundary potential has a lower-energy-well component in it, and that as one 'approaches' the boundary there is actually a bit of attraction, as there would be to numerous water molecules that the boundary is "representing" but then as one goes further and further into the boundary, there is a steep repulsive component, to keep molecules inside the boundary. So what you seeing is entierly .... understandable, if not desirable. I would think your only two alternatives at this point, would be to artifically restrain the protein, there are some ways one could think about doing this, but they all have the caveat of artificiallity. Some possibilities here might be the use of a droplet potential, or to add in a "dummy" atom at the center of your sphere, fix it, and put some weak distance constraints between it and some atoms near the center of the protein. Of course, you could also use a bigger sphere of water. Neither of these are optimal; in any case, it sounds like "starting" over in some manner will likely be necessary. Don Gregory At 6:08 AM 3/27/97, Yun Tang wrote: >Hi, everyone > >I tried to perform protein dynamics with deformable stochastic boundary >using CHARMM program. But during the dynamics process, the protein >gradually moved to the water sphere boundary and finally touched the >boundary. That meant I had to do it once more. > >Does anyone also meet this problem and how do you deal properly with it? >I mean how to prevent the protein moving during dynamics! Any >suggestions are appreciated! > >Thanks in advance and happy holiday to everyone! > >Yun Tang > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: yun.tang@csb.ki.se >-- Original Sender From: Address: yun.tang@csb.ki.se >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 Dr. Don Gregory (dgregory@msi.com) Molecular Simulations Inc. 9685 Scranton Rd. San Diego, CA 92121 (619) 546-5331 http://www.msi.com From SMILLER@RARUSRAEXS1.prius.jnj.com Thu Mar 27 14:39:29 1997 Received: from smtp-internet.jnj.com for SMILLER@RARUSRAEXS1.prius.jnj.com by www.ccl.net (8.8.3/950822.1) id NAA23554; Thu, 27 Mar 1997 13:34:23 -0500 (EST) Received: by smtp-internet.jnj.com id AA06263 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Thu, 27 Mar 1997 13:34:24 -0500 Received: by smtp-internet.jnj.com (Internal Mail Agent-2); Thu, 27 Mar 1997 13:34:24 -0500 Received: by smtp-internet.jnj.com (Internal Mail Agent-1); Thu, 27 Mar 1997 13:34:24 -0500 Date: Thu, 27 Mar 1997 13:35:58 -0500 From: "Miller, Susan [PRI]" Subject: Summary of answers to QSAR question To: "'chemistry@www.ccl.net'" Message-Id: Mime-Version: 1.0 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.993.5 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit Dear CCL'ers, Following is a summary of the replies I received to my question about how long it should take to perform a QSAR analysis of 120 compounds. First is the original question and then come the answers. Thanks very much to all who replied. Dear CCL'ers' I am about to start doing some QSAR on a set of 120 compounds. How long should I expect it to take to overlay all 120 compounds and adjust their conformations, to achieve maximal overlap? A range of times or an approximate number of hours will make a fine answer. Thanks alot. Susan gee, wouldn't that depend on what software and methods you're using?  ___ _ http://ellington.pharmacy.arizona.edu/~bear O-topo-O (___ |.) bear@.pharmacy.arizona.edu 5' : : .* ___)OARING |_)EAR, UA Pharmacy 404, Tucson 85721 |'*. .*'| | Computer Modeling for Medicinal Chemistry; SAR CAMD | | *.,* | | | Protein/DNA Structural Biology; Cancer Biochemistry 3',DNA helix|.* Pharmacognosy, Herbs, Nutrition, Natural Dentistry '***' '**  It depends on a lot of things. If these are near analogs, where a common scaffold has the same numbering, a Sybyl spl (there is one called align, or at least I have one) will do a rough atom-to-atom alignment in a matter of a minute or so. If the structures are dissimilar, a manual use (in Sybyl) of the orient command will give you a very rough alignment in probably 30 or 40 minutes, depending on how good you are with the keyboard. If you want to do something fancy, like alignments based on similarity of the ESP. . .this gets to be time consuming. If you are also taking into account multiple conformations, or tweaking the alignment given a first-pass CoMFA-QSAR. . .you just have to try it. I infer from your address (prius.jnj) that you are with Johnson and Johnson. Debbie Loughney (sp?) is well versed in Sybyl. Have you discussed this with her? Viel Vergnuegung! Steve Bowlus Hi there, It depends on the machine power, qsar software, compound size, parameter selecting .....Generally, as I am doing now for about 100 compounds(MW. 300) using a PowerMac8100 with CAChe Project leader, one month or 500 hrs around is the common expense. Maybe I am lazy. Any QSAR topic I am interesting in. Yours, Canping Pan --------------------------------- E-mail: pan_canp@agr.kyushu-u.ac.jp Tel: 092-611-7122(H) 092-642-2858(O) Fax: 092-642-2864 http://133.5.200.42/pan.html Hi Susan, I am afraid your question is impossible to answer considering the background information you supplied. None. First you need a very well planned working strategy. Do you now anything about the target protein. That is, do you now anything about the ligand-target protein interactions? How flexible are your compounds? You need to perform conformational analyses on most of them. You must align low energy conformations from all compounds. This is the most crucial step in order to obtain a reliable 3D QSAR model. Having all compounds aligned the most time consuming part is over and the real fun begins. Cheers /jonas My company offers two products that you may find VERY useful. The first is AMPAC, a semiempirical quantum mechanical package along with an easy to use graphical user interface. The second is CODESSA, and advanced QSAR/QSPR program that does much of what you are currently doing manually automatically when paired with AMPAC. There are a number of reference papers in the literature describing the sorts of correlations that are possible, and one of them (#1 below) sounds somewhat like what you want to do. If you are interested and will send me your regular mail address, I'll be happy to send some propaganda in the way of brochures along. Also, perhaps we can arrange a demo if you think that you might be further intrigued. Let me know. Best regards, Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER President Semichem, Inc. || Internet Addr: aholder@cctr.umkc.edu 7128 Summit || Phone Number: (913) 268-3271 Shawnee, KS, 66216 || FAX Number: (913) 268-3445 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dear CCL'ers, You have all rightly pointed out that I did not provide sufficient background information for an answer to my question. I will provide it now (I hope): I am doing everything manually, from the overlays to the conformational searches. The compounds I am aligning fall into about half a dozen structural categories (by my reckoning), within which there is not great structural variation but among which there is little similarity. There are large flat fused ring structures and spiro compounds, single phenyl rings with long aliphatic chains on either side (in some cases branched, in others, not) and pairs and larger sets of phenyl and non-aromatic rings connected by aliphatic chains and other moieties. I hope this clarifies the earlier question somewhat. Thanks for your replies, both future and those already sent. Susan -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: SMILLER@RARUSRAEXS1.prius.jnj.com -- Original Sender From: Address: SMILLER@RARUSRAEXS1.prius.jnj.com 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 Dear Susan, Please, post a summary with your answers. Which software are you using to do the QSAR study? Thanks, Ezequiel If you know the corresponding points then this is pretty easy. The cheapest way is to do ensemble distance geometry. I would use the most constrained analogue of each class. Generate 100 ensembles with that contain the chosen member of each class. Minimize the structures. Then see which ensembles (1) still match & how well and (2) contain mainly low energy conformations. You will discover either that you have only a few solutions (good) or 50 or so different solutions which will tell you that you will never have a unique choice of conformations so you might as well just pick one set and move on. Ensemble distance geometry is available in DGEOM from QCPE. Sheridan, R. P.; Nilakantan, R.; Dixon, J. S.; Venkataraghavan, R., J. Med. Chem. 1986, 29, 899-906. "The Ensemble Approach to Distance Geometry: Application to the Nicotinic Pharmacophore". If you don't know what atoms correspond in the different structures, you can run a bunch of DGEOM runs to see which give solutions. Or, you can use DISCO, an option with Sybyl. Martin, Y. C.; Bures, M. G.; Danaher, E. A.; DeLazzer, J.; Lico, I.; Pavlik, P. A., J. Comput.-Aided Mol. Design 1993, 7, 83-102. "A Fast New Approach to Pharmacophore Mapping and its Application to Dopaminergic and Benzodiazepine Agonists". It shouldn't take you a month to do what you want, except that you are apparently learning in the process with no good tutor. How do you plan to do the QSAR? Yvonne Martin, Senior Project Leader Computer Assisted Molecular Design Project D-47E, AP10 2fl Abbott Laboratories 100 Abbott Park Road Abbott Park, IL 60064-3500 Phone: 847 937-5362 FAX: 847 937-2625 yvonne.c.martin@abbott.com Susan, For the situation you have described, I highly recommend SEAL, an automatic alignment program, available from QCPE for a small fee. Forget manual alignments - it will take forever! With SEAL, you can align all 120 of your molecules (even if you have ~20 conformations of each) in <= a few hours. Good luck. Mary /*************************** * * * Mary Bradley * * Senior Research Scientist* * Rhone-Poulenc Ag Company * * * * bradleym@mindspring.com * * * ***************************/ *********************************** Mary Bradley * email: mbradley@mindspring.com * fone & fax: (919) 572-6599 * *********************************** Dear Suzan I don't know what you mean by hand... Could you tell me what are the modelling softwares available in you lab ? I see two problems to face : Conformer generation (it seems that you have very flexible compounds) and conformer fitting. I would suggest you to start with the more rigid compounds, do a conformational search (systematic, random, high temperature dynamic as you want or as you can). Keep structures in a range of 10-20 kCal above the minima (don't forget to investigate ring conformation). Then make hypothesis on what would be the pharmacophore (charged atom, hydrogen donnors or acceptors, aromatics, lipophilic groups etc...) or any common points available in your series or reported in literature. Then measure some key distances between these elements and try to cluster the molecules according to these parameters (with SAS) or make some sorts with excel to identify the common pharmacophore if you don't have any specific softwares to do that. Once you have identified the best clusters then you can superimpose the best conformations. Concerning the more flexible molecules, don't spend time to generate conformers but simply check that you can simply superimpose one reasonable conformation to the previously identified pharmacophore. To my opinion, and without any additional information, you have to plan some months to do the job. Hope this helps Don't hesitate to contact me for help Francois ------------------------------------------------------------------------ -- Dr. Francois CROIZET - Riom Laboratoires CERM - Chemistry Dept. (CMC) - ZI de la Varenne, Rue H. Goudier, BP 140 - 63203 RIOM Cedex - FRANCE - Phone: (33) 473 33 49 70 - Fax: (33) 473 33 49 97 E-mail: f.croizet@organon.akzonobel.nl ======================================================================== == For automated overlay of two molecule with conformational flexibility on PC, PowerFit may be useful. You can go to our web site to download a fully functional program to evaluate. Currently only Windows 95 and NT version is available for download. For automated overlay of two molecule with conformational flexibility on PC, PowerFit may be useful. You can go to our web site to download a fully functional program to evaluate. Currently only Windows 95 and NT version is available for download. Ms. (Dr.?) Miller: For the past few days, I have been following with interest your postings to the CCL concerning QSAR. (BTW, I haven't seen (most of) the responses to you show up in my mail, so I'm assuming they're going directly to you.) Since I do molecular modeling and algorithm design, I haven't felt competent to comment on your questions. After your last posting, however, I feel compelled to register extreme surprise (and to stick my nose in where it doesn't belong :-). Why, pray tell, would your mentor even suggest doing _all_ of the overlays by hand??? There is certainly value to doing a small, random set of overlays by hand, just to confirm that the results make sense. However, if you're needing to do anything more than a couple of handfuls of compounds, noninteractive fitting seems the only way to go. Otherwise, you end up wasting enormous amounts of human time doing things a mindless computer was invented for. On the other hand, if you're using Tripos software, I guess noninteractive isn't really a choice anyways? Ah well, good luck with your project. I hope you're able to finish in something approximating a reasonable amount of time. Sorry for butting into the middle of your more substantive discussion with people who actually do QSAR... Marti Head %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Martha S. Head, Ph.D. (Marti) Center for Advanced Research in Biotechnology 9600 Gudelsky Drive Rockville MD 20850 voice: (301)738-6104 email: mhead@indigo18.carb.nist.gov %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Hi all, Thanks again for all of your responses. I will post a summary in a couple of days when the discussion is over. All of the responses I've received so far have come to CCL and not to my personal mailbox, but if it is desired, I can still post a compilation of the responses. I forgot to mention 2 very important facts: 1) I am using SYBYL and have no access to anything else, save the free software on the net. I cannot use that however, for the second reason. 2) My mentor insists that I do the overlays by hand, that is, by using the fit module in SYBYL and picking points, with the mouse, to fit. I must also do torsion adjustments by hand, that is, by choosing a torsion angle for each bond and applying it, using either the twist widget in the upper left corner of the screen or the modify torsion command. Susan -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: SMILLER@RARUSRAEXS1.prius.jnj.com -- Original Sender From: Address: SMILLER@RARUSRAEXS1.prius.jnj.com 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 Susan, The superimposition procedure is performed due to that the 3D structure of the target protein is not known. You seek atoms or mutual points on your ligands that are most likely to interact with target protein. However, very often your fits will be much better if you also allow extension vectors to act as a fit point. For example, a basic nitrogen may interact through its lone pair of electrons or, if it is protonated, through the proton. Therefore, if you apply extension vectors in the direction of the lone pair of electrons , and use this vector as a fit point, much more reliable fits will occur. You use a UNIX machine and I suggest that you use Apollo or a similar program for this. Even SYBYL has a module. Your mentor does not allow you to perform conformational searches on your ligands? Then why bother at all. This is, one of the most crucial steps in 3D QSAR, especially if your ligands are flexible. In SYBYL I suggest you to use the random search procedure! The conformational search and the alignment proecedures are tedious and cost a lot of time, but must be performed rationally and thoroughly. Succes /jonas ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Jonas Nilsson e-mail: j.nilsson@farm.rug.nl Univ. Centre for Pharmacy tel: +31(0)503633302 Dept. of Med. Chemistry fax: +31(0)503636908 Antonius Deusinglaan 1 NL-9713 AV Groningen The Netherlands http://pc131.farm.rug.nl/main.htm ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ (In reply to your message dated Tuesday 11, March 1997) -- Something of interest for QSAR work. Accord for Excel can be used for structure relationships and Activities. Check out WWW.synopsys.co.uk Take care, all. Susan From jtgolab@amoco.com Thu Mar 27 18:32:13 1997 Received: from interlock.amoco.com for jtgolab@amoco.com by www.ccl.net (8.8.3/950822.1) id RAA25093; Thu, 27 Mar 1997 17:45:35 -0500 (EST) Received: by interlock.amoco.com id AA27857 (InterLock SMTP Gateway 3.0 for CHEMISTRY@www.ccl.net); Thu, 27 Mar 1997 16:45:34 -0600 Message-Id: <199703272245.AA27857@interlock.amoco.com> Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-3); Thu, 27 Mar 1997 16:45:34 -0600 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-2); Thu, 27 Mar 1997 16:45:34 -0600 Received: by interlock.amoco.com (Protected-side Proxy Mail Agent-1); Thu, 27 Mar 1997 16:45:34 -0600 From: jtgolab@amoco.com (Joe Golab) Date: Thu, 27 Mar 1997 16:44:42 -0600 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Summary of responses to "CCL: IRIX 6.2+ and MSC's XMOL" Cc: jtgolab@amoco.com Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii 3/27/97 RE: Summary of responses to "CCL: IRIX 6.2+ and MSC's XMOL" >-- Original Question >! Dear CCL: >! >! Recently, we upgraded our Silicon Graphics equipment to IRIX 6.2. After >! that, Xmol stopped working (% xmol - Exec format error) because Xmol uses >! the COFF binary format. According to Xmol's creators (Minnesota's SC), >! "There are not plans to produce a new XMol distribution". >! >! We have been looking for an alternative to Xmol. So far, we haven't had >! much luck to duplicate Xmol's "Extras/Animate" feature. We have found that >! feature very useful when looking at optimization runs, IRC runs, etc. The >! animation button basically reads and displays a series of geometries from an >! Xmol input file. >! >! Can anyone suggest an alternative software product for UNIX machines? >! We have tried Rasmol and have not had any luck getting it to do animation >! using a series of separate geometries. (Which should not be taken as a slam >! to Rasmol which we have found useful for Web presentations.) >! >! If any replies are received, I'll post the summary. Thank you. >! >! -- >! >! :Joe >! jtgolab@amoco.com >! (630) 961-7878 >-- Executive Summary 1) Source Code to Xmol is not available (to the best of my knowledge). It was only distributed via executable code. I (for one) wish one of the commerical software vendors would investigate the possibility of distributing a working copy of Xmol. As far as I know, MSC has no plans for it beyond what is on their web site now. (Hint, Hint, Knudge, Knudge, Wink, Wink - Know what I mean?) 2) Suggested Replacements a) VMD - http://www.ks.uiuc.edu/Research/vmd/ b) MOLDEN - http://www.caos.kun.nl/~schaft/molden/molden.html c) Chime - http://www.mdli.com/chemscape d) gOpenMol - http://laaksonen.csc.fi/gopenmol/gopenmol.htmls >-- Response *> Hi again Joe. I don't use Xmol, but would the MOLDEN program do what *> you need? I use it to visualize geometry optimizations, vibrational *> frequencies, and orbitals from Gaussian and sometimes GAMESS. It's *> free and has a web page: *> http://www.caos.kun.nl/~schaft/molden/molden.html *> *> Good luck! *> *> ---------------------------------------------- *> Dr. Karl K. Irikura *> Physical and Chemical Properties Division *> National Institute of Standards and Technology *> Gaithersburg, MD 20899 *> voice: 301-975-2510 fax: 301-975-3670 *> e-mail: karl.irikura@nist.gov *> ---------------------------------------------- >-- Response *> try using Chime as a plugin of a web page. It allows animations. *> You only will have to set up a web page to do the embedding. *> *> Chemscape Chime is free downloadable from http://www.mdli.com/chemscape *> *> Rene P.F. Kanters *> Chemistry Project Specialist *> Chemistry Department *> University of Richmond VA 23173 *> *> phone: (804) 287-6873 *> email: rkanters@richmond.edu *> www: http://www.richmond.edu/~rkanters *> http://www.science.richmond.edu/~kanters >-- Response *> You might want to try VMD, just released to the public on Mar 25. It's *> homepage is http://www.ks.uiuc.edu/Research/vmd/ *> *> David E. Reichert, Ph.D. *> Mallinckrodt Inst. of Radiology *> Div. Radiation Sciences *> phone: (314)362-8461 *> fax: (314)362-9940 *> e-mail: reichertd@mirlink.wustl.edu >-- Response *> I use vmd to display dynamics (results from MD and normal modes). *> I think vmd can use Xmol's xyz files, however I never tried that. *> Instead, I wrote a little program that generates dcd files that *> vmd can read. You are welcome to have it, if you want. *> I found that vmd makes very fast and very pretty animation. *> I you don't know where to find vmd on the net, I cal dig it up for you. *> *> Hope that helps, Gert *> *> Gert von Helden *> Dept. of molecular and Laser Physics, University of Nijmegen, Netherlands *> e-mail: gertvh@sci.kun.nl, phone: (+31) 24 3652179, fax: (+31) 24 3653311 >-- Response *> Did you tried the molden software ? *> I use it on IRIX6.2 but you should have gaussian output. *> Is it your case *> *> Dorothee Berthomieu *> ************************************************** *> Laboratoire des Materiaux et Procedes Membranaires *> UMR CNRS 5635 *> Ecole Nationale Superieure de Chimie de Montpellier *> 8, rue de l'Ecole Normale *> 34296 MONTPELLIER cedex 5 *> Tel : (33) 467 14 43 40 *> Telecopie : (33) 467 14 43 47 *> email : bertho@crit1.univ-montp2.fr *> http://www.dr13.cnrs.fr/lmpm/fequ.html#DEPOCVD >-- Response *> Have you tried MolDen? It can read various file types (e.g. Gaussian *> output) and animate things like structures and vibrational modes. *> *> Nick *> *> ============================================================================ *> Nicholas A. Nystrom, Ph.D. Pittsburgh Supercomputing Center *> Scientific Specialist Mellon Institute Building *> email: nystrom@psc.edu 4400 Fifth Avenue *> voice: +1 412-268-1592 fax: -5832 Pittsburgh, PA 15213 USA *> ============================================================================ >-- Response *> Can't you get the xmol source code? All you should *> need to do is to rebuild the executable. If the program *> is being distributed form an academic center, I would *> be surprised if they would not hand out the source. *> *> Good luck, *> *> Randy *> *> All opinions expressed here are mine, not my employer's *> *> ///////////////////////////////////////////////////////////////////////// *> \\ Randy J. Zauhar, PhD | E-mail: zauhar@tripos.com // *> \\ Tripos, Inc. | : zauhar@fastrans.net // *> \\ 1699 S. Hanley Rd., Suite 303 | Phone: (314) 647-1099 Ext. 3382 // *> \\ St. Louis, MO 63144 | // *> ///////////////////////////////////////////////////////////////////////// *> ** ** *> ** "If you have conceptions of things that you can have no conception ** *> ** of, then the conception and the thing appear to co-incide." ** *> ** --- C.G. Jung ** *> ************************************************************************* >-- Response *> Joe, I assume the source for XMol was never distributed? Does anybody own *> it currently? If they're not going to make a new distribution, what's *> happening to the program? *> *> All that's required is a recompile on an appropriate SGI... *> *> Joe *> *> -- *> *> Joe Leonard Phone: +1 314 647 8837 x3204 *> Tripos, Inc. Fax: +1 314 647 9241 *> 1699 S. Hanley Rd. email: jle@tripos.com *> St. Louis, MO 63144 USA after-hours: jle@world.std.com >-- Response *> We went through exactly the same process. We're presently using the package *> VMD. You can obtain a copy via http://www.ks.uiuc.edu/Research/vmd/ . It can *> read in multi-frame XYZ files. Might be worth a try.... *> *> Regards, *> Mike *> *> ------------------------------------------------------------------- *> | Mike Fearn, Tel : UK (01684) 896536 | *> | Room PA101, Fax : UK (01684) 896150 | *> | D.R.A, Malvern, | *> | Worcs. WR14 3PS Email : hp003@dra.hmg.gb | *> ------------------------------------------------------------------- >-- Response *> There are certainly a lot of options. Let me suggest one further: *> *> The gOpenMol program at: *> *> http://laaksonen.csc.fi/gopenmol/gopenmol.htmls *> *> Regards, *> *> -leif laaksonen *> *> ------------------------------------------------------------------- *> Leif Laaksonen | *> Center for Scientific Computing | Phone: 358 9 4572378 *> P.O. Box 405 | Mobile: 358 400425203 *> FIN-02101 Espoo | Telefax: 358 9 4572302 *> FINLAND | Mail: Leif.Laaksonen@csc.fi *> -------- URL: http://laaksonen.csc.fi/leif.laaksonen.html --------- >-- Response *> This seems to be a common question lately as more and more *> people upgrade to 6.x . You might want to look at our visualization *> program, VMD, at http://www.ks.uiuc.edu/Research/vmd/ . It was *> developed for, amoung other things, the visualization of MD *> trajectories. *> *> I doesn't read XYZ files directly, but if you have Babel *> installed (http://mercury.aichem.arizona.edu/babel.html) it VMD *> will call it and to the conversion to a set of PDB files automatically, *> then read them in. To the user, you wouldn't even notice the exchange. *> *> Andrew *> dalke@ks.uiuc.edu -- :Joe jtgolab@amoco.com (630) 961-7878 +----------------------------------------------------+ | Profanity - the one language all programmers know. | | After all, why do you think they call it a cursor? | +----------------------------------------------------+ From ccl@www.ccl.net Sun Mar 30 07:32:47 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id GAA18840; Sun, 30 Mar 1997 06:58:18 -0500 (EST) Received: from wchd18.chemie.uni-wuerzburg.de for s101264.k4.stud.uni-wuerzburg@wrzn12.rz.uni-wuerzburg.de by bedrock.ccl.net (8.8.3/950822.1) id GAA15597; Sun, 30 Mar 1997 06:58:16 -0500 (EST) Received: from claessen (wex026.extern.uni-wuerzburg.de [132.187.248.26]) by wchd18.chemie.uni-wuerzburg.de (8.6.9/8.6.9) with SMTP id UAA18165; Sun, 30 Mar 1997 20:57:15 +0200 Message-Id: <199703301857.UAA18165@wchd18.chemie.uni-wuerzburg.de> Comments: Authenticated sender is From: "Rolf Claessen" To: chemconf@umdd.umd.edu, CHEMED-L@UWF.CC.UWF.EDU, chemistry@ccl.net, CICOURSE@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu, ysn@crow-t-robot.stanford.edu Date: Sun, 30 Mar 1997 13:52:59 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Rolf Claessen's Chemistry Index (FREE Beilstein Netifre, FREE Me Reply-to: s101264@stud-mail.uni-wuerzburg.de Priority: normal X-mailer: Pegasus Mail for Win32 (v2.52) http://www.geocities.com/Tokyo/5243/index.htm (frames) http://www.geocities.com/Tokyo/5243home_en.htm (no frames - english) http://www.geocities.com/Tokyo/5243home_de.htm (no frames - german) Recently Added: TOP 5% CHEMISTRY SITE - Application Form Categories: ChemChat - Online Discussion Forum Journals - over 120 Journals Online Companies - Companies' URLs Databases - FREE Beilstein Netfire, FREE Medline, FREE CancerLit, FREE AIDSline, ... over 90 FREE Databases WebPublishing - All about Chemistry and VRML, Java, Chime, Online Education, ... 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Societies - Many national and international Societies Software - FREE Software with short Descriptions TOP 5% CHEMISTRY SITE - Application Form Search Engines - Search all the major Engines with one single Form Yours Rolf Claessen http://www.geocities.com/Tokyo/5243/index.htm s101264@stud-mail.uni-wuerzburg.de Rolf Claessen http://www.geocities.com/Tokyo/5243 s101264@stud-mail.uni-wuerzburg.de Tel. +49 931 701814 From schiffer@h1tw0036.hoechst.com Fri Apr 4 02:33:53 1997 Received: from backup.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id CAA05898; Fri, 4 Apr 1997 02:02:16 -0500 (EST) Received: by backup.hoechst.com (SMI-8.6/SMI-SVR4) id IAA14975; Fri, 4 Apr 1997 08:59:52 +0200 Received: from unknown(134.81.79.248) by backup via smap (V1.3) id sma014927; Fri Apr 4 08:52:24 1997 Received: from 134.81.76.36 by fra28.hiserv.de with SMTP (Microsoft Exchange Internet Mail Connector Version 4.0.994.63) id HV0NC1PN; Fri, 4 Apr 1997 08:58:42 +0200 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id IAA01570; Fri, 4 Apr 1997 08:53:35 +0200 Message-ID: <3344A56E.41C6@h1tw0036.hoechst.com> Date: Fri, 04 Apr 1997 08:53:34 +0200 From: "Dr. Heinz Schiffer" Organization: Hoechst Corporate Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: "M.Govender" , Computational Chemistry List Subject: Re: CCL:Temperature Calculations References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit M.Govender wrote: > > Dear Netters, > > I am interested in obtaining Rotational and Vibrational > temperature calculations on spherical top molecules. Can anyone > provide any info as to what programs are available?... > > Many Thanks > Magan Hi Magan, Look at Donald A. McQuarrie, Statistical Mechanics, Harper & Row 1976. All the relevant formulars are there. The vibrational temperature of the normal frequency nu_j is Theta_nu_j = h * nu_j / k The rotational temperatures of a general polyatomic molecule are : Theta_A = A / k Theta_B = B / k Theta_C = C / k A, B, and C are the rotational constants in Joule. Normally they are given in cm**(-1), that is as A_quer = A / ( h * c ). A, B, and C are defined as A = h**2 / ( 8 * pi**2 * I_A ) B = h**2 / ( 8 * pi**2 * I_B ) C = h**2 / ( 8 * pi**2 * I_C ) I_A, I_B, and I_C are the principle moments of inertia. You can get them by diagonalizing the moments of inertia tensor. The formalas in the McQuarrie book on page 134 are wrong : I_xy is missing a negative sign : I_xy = - sum_j .... and in the formulas for A_quer, B_quer, and C_quer the pi should be squared, see above. Ciao, Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main schiffer@msmwia.hoechst.com From ccl@www.ccl.net Mon Mar 31 11:33:02 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id LAA29430; Mon, 31 Mar 1997 11:28:46 -0500 (EST) Received: from admiral.umsl.edu for wwelsh@jinx.umsl.edu by bedrock.ccl.net (8.8.3/950822.1) id LAA05147; Mon, 31 Mar 1997 11:28:43 -0500 (EST) Received: from chewwels.umsl.edu ([134.124.77.29]) by admiral.umsl.edu (8.8.5/8.7.2) with SMTP id KAA05380 for ; Mon, 31 Mar 1997 10:28:40 -0600 (CST) Date: Mon, 31 Mar 1997 10:28:40 -0600 (CST) Message-Id: <199703311628.KAA05380@admiral.umsl.edu> X-Sender: wwelsh@jinx.umsl.edu X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: William Welsh Subject: band structures in 3D Dear Netters, Can someone point me to programs available for calculating electronic band structures in 1-, 2-, and 3- dimensions? I remember a few years back that a program known as VEH (Valence Effective Hamiltonian) was capable of doing this, but there may be others (or updated versions of VEH). I would be interested in both semi-empirical and ab initio programs. Thanks ... Prof. Bill Welsh Dept. of Chemistry University of Missouri-St. Louis From macrae@rikaxp.riken.go.jp Mon Mar 31 21:33:06 1997 Received: from ns.riken.go.jp for macrae@rikaxp.riken.go.jp by www.ccl.net (8.8.3/950822.1) id VAA03421; Mon, 31 Mar 1997 21:11:49 -0500 (EST) Received: from rikax1.riken.go.jp (rikax1.riken.go.jp [134.160.3.2]) by ns.riken.go.jp (8.8.5/8.8.5) with SMTP id LAA00643 for <@ns.riken.go.jp:CHEMISTRY@www.ccl.net>; Tue, 1 Apr 1997 11:11:48 +0900 (JST) Received: by rikaxp.riken.go.jp (MX V4.2 AXP) id 52; Tue, 01 Apr 1997 11:11:45 JST Date: Tue, 01 Apr 1997 11:11:45 JST From: "R. M. Macrae" To: CHEMISTRY@www.ccl.net Message-ID: <009B2215.F2A511D3.52@rikaxp.riken.go.jp> Subject: degenerate open shells Dear CCL subscribers Looking in the archive I saw some discussion from some considerable time back (around 1993) on the topic of G92 calculations on linear systems with x,y degenerate open shells, the point being that UHF gives the wrong result apparently even if nonstandard guess orbitals are used. (In some other programs apparently one can generate fractional occupancies with equally populated x and y components and this constraint will be retained throughout the calculation.) ROHF, on the other hand, will not of course give correct spin-dependent properties. There didn't seem to be a satisfactory outcome to this discussion at the time (unless, of course, i missed it). My question is, then: is there a satisfactory solution or workaround to this problem either in G92 or G94? Sincerely Rod * Rod Macrae * Muon Science Laboratory * macrae@rikaxp.riken.go.jp * From keruu@ifm.liu.se Tue Apr 1 11:33:15 1997 Received: from ifm.liu.se for keruu@ifm.liu.se by www.ccl.net (8.8.3/950822.1) id LAA07942; Tue, 1 Apr 1997 11:13:07 -0500 (EST) Received: from ike.ifm.liu.se (keruu@ike.ifm.liu.se [130.236.171.139]) by ifm.liu.se (8.8.5/8.8.5) with ESMTP id SAA20320 for ; Tue, 1 Apr 1997 18:13:06 +0200 (MET DST) From: Kenneth Ruud Received: (keruu@localhost) by ike.ifm.liu.se (SMI-8.6/8.6.9) id SAA09138 for chemistry@www.ccl.net; Tue, 1 Apr 1997 18:13:04 +0200 Date: Tue, 1 Apr 1997 18:13:04 +0200 Message-Id: <199704011613.SAA09138@ike.ifm.liu.se> To: chemistry@www.ccl.net Subject: Release of free quantum chemistry program: Dalton Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: 3Wwb5CD0UIR4duQfew8kFA== ANNOUNCEMENT We are happy to announce the release of the Dalton quantum chemistry program, Release 1.0 (1997) to the computational chemistry/physics community. Dalton is a complete, powerful quantum chemistry program for the calculation of molecular properties with SCF, MP2 or MCSCF wave functions. The strengths of the program are mainly in the areas of magnetic and (frequency-dependent) electric properties, and for studies of molecular potential energy surfaces, both for static and dynamical investigations, as well as stable algorithms for converging large MCSCF wave functions (also excited states). The program is distributed freely to all academic users, although we require all users to sign a copyright and license agreement. For more complete information on how to obtain a copy of the program, more information about what the program can and can not do, please check out our homepage at http://www.kjemi.uio.no/software/dalton/dalton.html, or send an e-mail to dalton-admin@kjemi.uio.no. The complete author list of the program is: T.Helgaker, H.J.Aa.Jensen, P.Joergensen, J.Olsen, K.Ruud, H.AAgren, T.Andersen, K.L.Bak, V.Bakken, O.Christiansen, P.Dahle, E.K.Dalskov, T.Enevoldsen, B.Fernandez, H.Heiberg, H.Hettema, D.Jonsson, S.Kirpekar, R.Kobayashi, H.Koch, K.V.Mikkelsen, P.Norman, M.J.Packer, T.Saue, P.R.Taylor, and O.Vahtras On behalf of the authors, Kenneth _______________________________________________________________________________ Kenneth Ruud, Ph.D.-student in Chemical Physics at the Department of Chemistry, University of Oslo, Norway. E-mail: kenneth.ruud@kjemi.uio.no I don't know what the computer language of the year 2000 will look like, but I know it will be called FORTRAN. _______________________________________________________________________________ From ccl@www.ccl.net Thu Apr 3 12:33:42 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA00189; Thu, 3 Apr 1997 12:27:55 -0500 (EST) Received: from shannon.sissa.it for demaria@sissa.it by bedrock.ccl.net (8.8.3/950822.1) id MAA07997; Thu, 3 Apr 1997 12:26:44 -0500 (EST) Received: (from demaria@localhost) by shannon.sissa.it (8.8.2/8.8.2) id TAA31876 for chemistry@ccl.net; Thu, 3 Apr 1997 19:26:10 +0200 From: Leonardo Demaria Message-Id: <199704031726.TAA31876@shannon.sissa.it> Subject: STO two-center overlap integrals. To: chemistry@ccl.net Date: Thu, 3 Apr 1997 19:26:10 +22310718 (MET_DST) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Hi everybody, I need to calculate STO two-center overlap integrals between s and p type orbitals for general n. Does any one know about a Fortran 77 subroutine that does this task? I thank you all in advance. Best regards, Leonardo De Maria From John_Beckerle@quickmail.clemson.edu Thu Apr 3 12:33:49 1997 Received: from CLEMSON.EDU for John_Beckerle@quickmail.clemson.edu by www.ccl.net (8.8.3/950822.1) id MAA00141; Thu, 3 Apr 1997 12:23:23 -0500 (EST) Received: from quickmail.clemson.edu (quickmail.clemson.edu [130.127.8.57]) by CLEMSON.EDU (8.7.5/8.7.3) with SMTP id MAA21730 for ; Thu, 3 Apr 1997 12:23:00 -0500 (EST) Message-ID: Date: 3 Apr 1997 12:23:29 -0500 From: "John Beckerle" Subject: "Best" Multiprocessor Platf To: "List CCL" X-Mailer: Mail*Link SMTP-QM 3.0.2 We are seriously considering investing in a multiprocessor compute server. The candidates include the IBM SP2, SGI Origin2000, Sun Ultra HPC, DEC Alphaserver and other similar machines. We are probably looking at something on the order of 8 processors and 2GB of memory, although expandability and upgradability are important. The system is supposed to serve a variety of engineering and scientific high performance computing needs, not just computational chemistry. I would like to poll the collective experience of CCL as to what is the best platform, and even more importantly, which platforms should be avoided for computational chemistry applications. I am interested in hearing about real experience with software availability, incompatibilities, and performance surprises (including effective use of parallelism), both good and bad. We are interested in the full range of computational chemistry applications including SCF and MD. I would like to stress that I am looking for good and bad experiences with effectively using any of these multiprocessor machines and the roadblocks others have encountered. I am not so interested in relatively minor differences in performance of the individual CPUs, benchmarks, etc. I want to know if they can be used effectively without miracles. I am already familiar with the extensive evaluation of workstation performance by Martyn Guest, as well as Milan Hodoscek's comparison for parallel MD speedups. As I don't subscribe to CCL at this time, please respond directly to: beckerj@clemson.edu I will summarize to the list if their is interest. John Beckerle Clemson University beckerj@clemson.edu From ccl@www.ccl.net Thu Apr 3 17:37:48 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id RAA02236; Thu, 3 Apr 1997 17:10:24 -0500 (EST) Received: from interlock.lubrizol.com for chaka@lubrizol.com by bedrock.ccl.net (8.8.3/950822.1) id RAA20640; Thu, 3 Apr 1997 17:10:23 -0500 (EST) From: Received: by interlock.lubrizol.com id AA12651 (InterLock SMTP Gateway 3.0 for CHEMISTRY@ccl.net); Thu, 3 Apr 1997 17:10:24 -0500 Message-Id: <199704032210.AA12651@interlock.lubrizol.com> Received: by interlock.lubrizol.com (Protected-side Proxy Mail Agent-1); Thu, 3 Apr 1997 17:10:24 -0500 Date: Thu, 3 Apr 1997 16:23:24 -0500 To: CHEMISTRY@ccl.net Subject: Comp. Chem. Reception at ACS in San Francisco Cc: chaka@lubrizol.com RECEPTION ANNOUNCEMENT INDUSTRIAL APPLICATIONS OF COMPUTATIONAL CHEMISTRY RECEPTION American Chemical Society Meeting in San Francisco Sunday evening, 6 - 9 pm April 13, 1997 ANA Hotel Metropolitan I Suite "Bring Your Unsolved Problems to the Experts" At the reception there will be an opportunity to informally present a poster and/or 2 minute oral presentation about an unsolved problem you wish to discuss with your colleagues. Then mingle with the experts from industry and academia and enjoy the refreshments! *********************************************************************** RECEPTION AND SYMPOSIUM ARE SPONSORED BY IBM CORPORATION MOLECULAR SIMULATIONS, INC. *********************************************************************** For more information, please contact the organizers: Anne Chaka Rick Ross The Lubrizol Corp. PPG Industries chaka@lubrizol.com rbross@ppg.com 216-943-1200 x2027 412-492-5359 ************SYMPOSIUM TECHNICAL PROGRAM************************ The Symposium on Industrial Applications of Computational Chemistry in the Computers in Chemistry Division comprises seven sessions from Sunday morning, April 13, through Wedensday morning, April 16. The sessions are as follows: Materials Properties Polymers Catalysis Automotive, Coatings, and the Petroleum Industry Molecular Properties Process Simulation Solvation and Surfactants Sunday Morning Industrial Applications of Computational Chemistry: Materials Properties Moscone Center Room 123, Exhibit Level 9:00--22. Computational materials science applications at the Hughes Research Laboratories. M. F. Gyure, R. N. Schwartz . Hughes Research Labs 9:30--23. Glass-densification under 193-nm laser exposure:Experiment and theory. D. C. Allan, C. Smith, N. F. Borrelli, T. P. Seward III . Corning Incorporated 10:00--24. Industrial applications of polymorph prediction. F. J. Leusen 10:30--25. Local density-functional theory study of paramagnetic ion-doped BaLiF3 for information storage applications. F. Tsobnang, I. Lado, A. Le Mhaut, J. C. Fayet . Universite du Maine 11:00--26. Industrial applications of computational materials science:Current status and future directions. S. J. Mumby . Molecular Simulations 11:30--27. A framework for approaching industrial problems by molecular simulation. J. M. Newsam. Molecular Simulations Sunday Afternoon Industrial Applications of Computational Chemistry: Polymers Moscone Center Room 123, Exhibit Level 1:30--48. Molecular modeling of polymers. S. H. Jacobson. Hoechst Celanese 2:00--49. Applications of molecular dynamics to the study of thermal degradation in polymers. M. R. Nyden. NIST 2:30--50. Prediction of stress-strain curves of semicrystalline polymers with rubbery amorphous phase. J. Bicerano, N. Grant, J. Seitz, K. Pant, Dow Chemical 3:00--51. Physical properties of PEN by amorphous cell simulation. J. M. O'Reilly, D. R. Perchak. Eastman Kodak. 3:30--52. Acyl and alkyl attack in the imidization reaction of poly(methyl methacrylate) (PMMA):A computational study. S. Fitzwater. Rohm and Haas 4:00--53. Rational design of next generation polycarbonates. C. W. Ulmer II, D. A. Smith, N. Teich, K. Miaskiewicz, P. Nagy, B. G. Sumpter, D. W. Noid. The DAS Group 4:30--54. Density functional study of initiators for polymerization of -caprolactones. P. W-C. Kung, N. Tanpipat, J. Andzelm. Molecular Simulations Sunday Evening Reception 6:00-9:00 pm Industrial Applications of Computational Chemistry Reception RBring Your Unsolved or Almost Solved Problems to the ExpertsS Optional Informal Poster and/or 2 minute oral presentation for your topic, then mingle with the experts and enjoy the refreshments Monday Morning Industrial Applications of Computational Chemistry: Catalysis Moscone Center Room 120, Exhibit Level 9:00--65. A computational study of the nature of Ti(IV) active sites in mesoporous titanosilicate catalysts. P. E. Sinclair, C. R. A. Catlow, G. Sankar, J. M. Thomas, T. Maschmeyer. The Royal Institution of Great Britain. 9:30--66. Activation of carbon-hydrogen bonds at transition-metal surfaces. S. Clemendot, C. Guerra, Z. Liu, J. Harris 10:00--67. Modeling of homogeneous catalysis by density-functional molecular dynamics. P. M. Margl, T. K. Woo, L. Deng, T. Ziegler, P. E. Bl¨ochl 10:30--68. Combined quantum mechanical/molecular mechanics (QM/MM) studies of homogeneous catalysis: Static and ab initio molecular dynamics investigations. T. K. Woo, P. M. Margl, L. Deng, T. Ziegler 11:00--69. Catalysts and sorbents:Industrial modeling applications and opportunities. C. M. Freeman, A. M. Gorman, C. M. K¨olmel 11:30--70. New reactors based on heat-tense catalytic surfaces. V. I. Anikeev, N. A. Kuzin, A. V. Gudkov Monday Afternoon Industrial Applications of Computational Chemistry: Automotive, Coatings, and Petroleum Moscone Center Room 130, Exhibit Level 1:30--104. Universal behavior in adhesion. J. R. Smith 2:00--105. Theoretical results on the mechanism of catalytic NO decomposition over Cu zeolites. W. F. Schneider, K. C. Hass, R. Ramprasad, J. B. Adams 2:30--106. Computational studies of the photochemistry of benzotriazole UV stabilizers. K. C. Hass, W. F. Schneider, C. M. Estevez, R. D. Bach 3:00--107. Theoretical study of the reaction of the chlorine atom with hydrocarbons. A. M. Chaka 3:30--108. Computational chemistry applications in an industrial coatings research laboratory. R. B. Ross 4:00--109. A joint QSAR project between LZ and Purdue University employing neural networks and first principles modeling. D. T. Daly, A. M. Chaka, V. Venkatasubramanian, A. Sundarum, J. Carruthers 4:30--110. Thermodynamical study of factors influencing polysulfides C-S and S-S bonds heterolytic scissions, Presulfiding agents for the oil refinery industry. J. Joffre, C. Moreau, J. C. Duchet, J. Leglise Tuesday Morning Industrial Applications of Computational Chemistry: Molecular Properties Moscone Center Room 130, Exhibit Level 9:00--144. High-performance electronic structure methods: Practicable techniques. G. Fitzgerald 9:45--145. Accurate thermochemistry:The parameterized multireference perturbation PMPx approach. M. Dupuis, K. Hirao, M. Yamanishi 10:15--146. Theoretical insight into the scaling of third-order nonlinear optical properties for polyenes and cyanines. B. M. Pierce 10:45--147. Binding energy calculations of HIV-2 protease inhibitors. P. H. Lee, G. M. Maggiora, W. J. Howe, K. W. Watenpaugh, P. K. Tomich, B. Honig 11:15--148. Experimental and theoretical studies of LED-compatible fluorogenic K+ sensing molecules. S-H. Chou, J. G. Bentsen, E. M. Cross, C. C. Nagel, J. E. Trend Tuesday Afternoon Industrial Applications of Computational Chemistry: Process Simulation Moscone Center Room 110, Exhibit Level 2:00--173. Industrial applications of modeling. N. Quirke 2:45--174. Making better technical business decisions with chemistry modeling. J. T. Golab, M. R. Green 3:15--175. Calculating chemical reaction equilibria using the reaction ensemble method. W. R. Smith, I. Nezbeda, M. Strnad 3:45--176. Kinetic parameters for hydrocarbon conversion reactions. J. K. Perry, W. A. Goddard III, A. Patel, N. Reynolds, J. Shinn, R. Frazier 4:15--177. Kinetic theory of transport in molecular sieve catalysts. S. M. Auerbach 4:45--178. Mathematical modeling of gas-phase catalytic copolymerization of propylene with ethylene in a system with two reactors. V. I. Anikeev Wednesday Morning Industrial Applications of Computational Chemistry: Solvation and Surfactants Moscone Center Room 110, Exhibit Level 9:00--296. Mesoscale dynamics of polymer surfactant solutions. J. G. E. M Fraaije, B. A. C. van Vlimmeren, N. M. Maurits 9:30--297. Correlation modeling of surfactants and surface active molecules in solution. M. J. Doyle, D. Rogers 10:00--298. Direct methods for calculating lipophilicity:Application to industrial chemicals. S. A. Best, K. M. Merz Jr., C. H. Reynolds 10:30--299. Molecular modeling studies of solvent solubility parameters and their components. D. Rigby 11:00--300. Parameterization and validation of atomic nonbonded parameters. H. Sun 11:30--301. Materials modeling on the corporate intranet. J. D. Honeycutt From CHZLIN@usthk.ust.hk Fri Apr 4 03:33:54 1997 Received: from usthk.ust.hk for CHZLIN@usthk.ust.hk by www.ccl.net (8.8.3/950822.1) id DAA07213; Fri, 4 Apr 1997 03:15:17 -0500 (EST) From: Received: from usthk.ust.hk by usthk.ust.hk (PMDF V5.0-7 #8150) id <01IHB8LXVO74922MA6@usthk.ust.hk> for chemistry@www.ccl.net; Fri, 04 Apr 1997 15:12:28 +0800 Date: Fri, 04 Apr 1997 15:12:28 +0800 Subject: Seeking assistance To: chemistry@www.ccl.net Message-id: <01IHB8LXYCN6922MA6@usthk.ust.hk> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Colleagues, We did MP2 calculation for a metal complex using G94. The job went through the SCF stage successfully, but it immediately failed after l906.exe has started with the message: Logic failure, MDV= 7440563 NBuf= -10 but FulOut=F Anyone has ever come across this kind of error message? I'd be very grateful if anyone could provide assistance. Thanks. Zhenyang LIN Chemistry/HKUST From h.rzepa@ic.ac.uk Fri Apr 4 03:39:58 1997 Received: from romeo.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.8.3/950822.1) id CAA06940; Fri, 4 Apr 1997 02:46:26 -0500 (EST) Received: from judy.ic.ac.uk [155.198.5.5] by romeo.ic.ac.uk with esmtp (Exim 0.57 #1) id 0wD3hV-0002oV-00; Fri, 4 Apr 1997 08:46:21 +0100 Received: from cscmgb.cc.ic.ac.uk (sg1.cc.ic.ac.uk [155.198.63.8]) by judy.ic.ac.uk (8.7.5/8.7.5) with SMTP id IAA10596 for ; Fri, 4 Apr 1997 08:46:18 +0100 (BST) Received: from [155.198.224.86] by cscmgb.cc.ic.ac.uk (940816.SGI.8.6.9/4.0) id IAA03796; Fri, 4 Apr 1997 08:46:17 +0100 Date: Fri, 4 Apr 1997 08:46:17 +0100 X-Sender: rzepa@155.198.63.8 Message-Id: Return-Receipt-To: Disposition-Notification-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: "Rzepa, Henry" Subject: ANNOUNCE: ECTOC-3 Organometallic Conf. Abstracts We would be grateful if you could bring to the attention of any "organometallic" chemists in your organisation who might be interested in submitting an article or poster to the ECTOC-3 conference that the registration process for abstracts is now open; http://www.ch.ic.ac.uk/ectoc/ectoc-3/ectoc_sub.html The deadline for submitting an abstract is April 25th, 1997. full details are on http://www.ch.ic.ac.uk/ectoc/ectoc-3/ Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk; Tel (44) 171 594 5774; Fax: (44) 171 594 5804. URL: http://www.ch.ic.ac.uk/rzepa/ From vrc@ems.ncl.res.in Fri Apr 4 04:33:54 1997 Received: from ems.ncl.res.in for vrc@ems.ncl.res.in by www.ccl.net (8.8.3/950822.1) id EAA07850; Fri, 4 Apr 1997 04:16:00 -0500 (EST) Date: Fri, 4 Apr 1997 14:13:24 +0530 (IST) From: Dr V R Choudhari To: "Dr. Bruno Manunza" cc: castejon@kbw350.chem.yale.edu, chemistry@www.ccl.net Subject: Re: CCL:real memory checking on IBM-errata- In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: vrc@ems.ncl.res.in I guess "top" command would do the trick or df -k in kilobytes or df -u with regards sivadinarayana naa@ems.ncl.res.in On Mon, 31 Mar 1997, Dr. Bruno Manunza wrote: > > > On Sun, 30 Mar 1997 castejon@kbw350.chem.yale.edu wrote: > > > > > Hi everyone. > > > > I have a simple question. Does anyon know how to check how > > much physical memory a computer has by using a unix command. > > I have an IBM RS/6000. Iknow how much memory it has but I want > > to be able to check it. > > > > > > > Dear Henry, sorry for my previous misleading message, and let me > apologize for this errata > > The right answer is: lsdev -C -c memory > > bye > Bruno > > > > > Dr Bruno Manunza > > DISAABA (Dept. of Agricultural Environm. Sci) > > University of Sassari > > V.le Italia 39 > > 07100 Sassari, ITALY > > phone: 39 79 229215 > > fax: 39 79 229276 > > e-mail: bruno@antas.agraria.uniss.it > > e-mail: bruno@tharros.dipchim.uniss.it > > e-mail: gx6bot81@cray.cineca.it > > web: http://antas.agraria.uniss.it > > > > > > -------This is added Automatically by the Software-------- > > -- Original Sender Envelope Address: bruno@antas.agraria.uniss.it > > -- Original Sender From: Address: bruno@antas.agraria.uniss.it > > 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 > > > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: bruno@antas.agraria.uniss.it > -- Original Sender From: Address: bruno@antas.agraria.uniss.it > 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 Sylvie.Joanteguy@univ-pau.fr Fri Apr 4 09:33:55 1997 Received: from crisv2.univ-pau.fr for Sylvie.Joanteguy@univ-pau.fr by www.ccl.net (8.8.3/950822.1) id IAA09404; Fri, 4 Apr 1997 08:42:25 -0500 (EST) From: Received: from crisv3.univ-pau.fr by crisv2.univ-pau.fr; Fri, 4 Apr 1997 15:42:03 +0200 Received: by crisv3.univ-pau.fr; Fri, 4 Apr 1997 15:42:03 +0200 Message-Id: <199704041342.PAA59434@crisv3.univ-pau.fr> Subject: electronic correlation To: chemistry@www.ccl.net Date: Fri, 4 Apr 1997 15:42:03 +0200 (MET DST) X-Mailer: ELM [version 2.4ME+ PL16 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCL, My question is short: What's exactely the electronic correlation (dynamic and no dynamic correlation)? Many thanks for your help Sylvie Joanteguy From david.decorte@unifr.ch Fri Apr 4 09:35:37 1997 Received: from swifr9 for david.decorte@unifr.ch by www.ccl.net (8.8.3/950822.1) id JAA09874; Fri, 4 Apr 1997 09:20:30 -0500 (EST) Received: from UFPER6.UNIFR.CH by swifr9 with SMTP (PP); Fri, 4 Apr 1997 16:20:15 +0200 Received: from sgich3.unifr.ch by UFPER6.UNIFR.CH via Pony Express SMTP with TCP (v8.1.1-dmr001); Fri, 4 Apr 97 16:20:10 MET Sender: decorte@sgich3.unifr.ch Message-ID: <33451BE9.2781@unifr.ch> Date: Fri, 04 Apr 1997 16:19:05 +0100 From: David De Corte Organization: Universite de Fribourg X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Gaussian94 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, A few days ago I posted the following problem. > Hello, > > I've got a small g94 problem. When doing a Scan=Opt calculation, the > calculation stops after the first optimisation and does not perform a > scan....No error messages are listed... Does anybody know how to prevent > this problem? > Kind regards, > David Here is a condensated version of the answer I received. The Scan=Opt keyword doesn't work! So it's better to perform an Opt=Addredundant or an Opt=Z-matrix calculation. It works..... Thanks to everybodz who responded to my mail. David -- David De Corte Institute of Inorganic Chemistry Tel: 0041-26-300.87.52(49) University Fribourg Fax: 0041-26-300.97.38 CH-1700 Switzerland mailto:David.Decorte@unifr.ch http://www.unifr.ch/ From schiffer@h1tw0036.hoechst.com Fri Apr 4 10:34:01 1997 Received: from backup.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id KAA10683; Fri, 4 Apr 1997 10:31:17 -0500 (EST) Received: by backup.hoechst.com (SMI-8.6/SMI-SVR4) id RAA24874; Fri, 4 Apr 1997 17:28:50 +0200 Received: from unknown(134.81.79.248) by backup via smap (V1.3) id sma024865; Fri Apr 4 17:28:16 1997 Received: from 134.81.76.36 by fra28.hiserv.de with SMTP (Microsoft Exchange Internet Mail Connector Version 4.0.994.63) id HW84MA1S; Fri, 4 Apr 1997 17:34:36 +0200 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id RAA02752; Fri, 4 Apr 1997 17:29:16 +0200 Message-ID: <33451E4C.7DE1@h1tw0036.hoechst.com> Date: Fri, 04 Apr 1997 17:29:16 +0200 From: "Dr. Heinz Schiffer" Organization: Hoechst Corporate Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Sylvie.Joanteguy@univ-pau.fr, Computational Chemistry List Subject: Re: CCL:electronic correlation References: <199704041342.PAA59434@crisv3.univ-pau.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Sylvie.Joanteguy@univ-pau.fr wrote: > > Dear CCL, > > My question is short: What's exactely the electronic correlation (dynamic and no dynamic correlation)? > > Many thanks for your help > > Sylvie Joanteguy Hi Sylvie, the definition of the correlation energy is E_corr = E_exact - E_HF E_exact is the exact nonrelativistic energy eigenvalue of the electronic Schroedinger equation. E_HF is the corresponding Hartree-Fock energy (basis set limit !). That definition goes back to Loewdin. Sinanoglu was the first who introduced the terms 'dynamic' and 'non-dynamic' correlation, the latter one arises because of degeneracies or near-degeneracies of electronic systems. A good and very recent discussion of this subject can be found in the paper Daniel K. W. Mok, Ralf Neumann, and Nicholaus C. Handy J. Phys. Chem. 100 (1996) 6225-6230 Ciao, Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main schiffer@msmwia.hoechst.com From gaussian.com!moses@lorentzian.com Fri Apr 4 11:34:13 1997 Received: from relay5.UU.NET for gaussian.com!moses@lorentzian.com by www.ccl.net (8.8.3/950822.1) id KAA10895; Fri, 4 Apr 1997 10:45:48 -0500 (EST) Received: from uucp4.UU.NET by relay5.UU.NET with SMTP (peer crosschecked as: uucp4.UU.NET [192.48.96.35]) id QQcjvj18036; Fri, 4 Apr 1997 10:45:56 -0500 (EST) Message-Id: Received: from m10.UUCP by uucp4.UU.NET with UUCP/RMAIL ; Fri, 4 Apr 1997 10:45:48 -0500 Received: by m10.lorentzian.com; Fri, 4 Apr 1997 10:48:27 -0500 Received: by mousse.gaussian.com; Fri, 4 Apr 1997 09:53:47 -0500 From: gaussian.com!moses@lorentzian.com (David Moses) Subject: NCSA/Gaussian Workshop in June To: CHEMISTRY@www.ccl.net Date: Fri, 4 Apr 1997 09:53:47 -0500 (EST) X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit **************************************************************************** The National Center for Supercomputing Applications and Gaussian, Inc. are pleased to announce: Quantum Chemistry for Engineers and Chemists in the Chemical Process Industry Date: June 3-6, 1997 Location: National Center for Supercomputing Applications Urbana-Champaign, IL The National Center for Supercomputing Applications (NCSA) in conjunction with Gaussian, Inc. are pleased announce a workshop tuned to address the needs of researchers in the chemical process industry who need to add electronic structure methods to their arsenal of research tools. State of the art electronic structure methods and main stream chemical process industry (CPI) applications are converging at a rapid pace. Computational models now have the accuracy and reliability to predict physical properties at costs and time frames competitive with experimental approaches. This course will lay out the methods of electronic structure theory and describe how to extract physical properties from calculations. While this workshop is oriented to chemical engineering topics we encourage you to consider sending chemist/chemical engineer teams to gain optimal benefit. Instructors: Dr. Michael J. Frisch Gaussian, Inc. Prof. Phillip Westmoreland Univ. of Massachusetts Prof. Matthew Neurock Univ. of Virginia Dr. Douglas J. Fox Gaussian, Inc. Tentative Agenda Topics: Computational Chemistry: A CPI Perspective Introduction to Electronic Structure Theory Predicting Thermodynamics with Model Chemistries Geometry Optimization Techniques Electron Correlation Methods Density Functional Theory Methods Theoretical Methods for Optical and UV Spectra Predicting Molecular Properties Continuum Models for Solvation Case Studies: Electronic Structure Methods in Process Design : Model Assessment for Physical Properties There will be hands-on sessions each day between the morning and afternoon lectures. Additional hands-on sessions will be available until the building closes. Workshop participants will be provided with use of an SGI workstation to complete exercises, experiment and/or conduct short research topics. Each workshop participant will also be provided a copy of the lecture notes, a copy of Exploring Chemistry with Electronic Structure Methods (2nd. Ed.) and a copy of the Gaussian 94 User's Reference. For Application please contact: Workshop Coordinator Gaussian, Inc. Carnegie Office Park Bldg. 6, Suite 230 Pittsburgh, PA 15106 USA Additional information can be obtained from Telephone: (412) 279-6700 Fax: (412) 279-2118 Email: info@gaussian.com DEADLINES: Receipt of Registration Materials: May 2, 1997 This notice is sent without warranty of any kind, expressed or implied by Gaussian, Inc. or NCSA. Gaussian is a registered trademark of Gaussian, Inc. **************************************************************************** From korkin@qtp.ufl.edu Fri Apr 4 13:33:59 1997 Received: from qtp.ufl.edu for korkin@qtp.ufl.edu by www.ccl.net (8.8.3/950822.1) id NAA11961; Fri, 4 Apr 1997 13:33:11 -0500 (EST) Received: from orange by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id NAA02130; Fri, 4 Apr 1997 13:32:54 -0500 Date: Fri, 4 Apr 1997 13:32:54 -0500 (EST) From: Anatoli Korkin Reply-To: Anatoli Korkin Subject: Re: CCL:electronic correlation To: Sylvie.Joanteguy@univ-pau.fr Cc: chemistry@www.ccl.net, rjbgroup@qtp.ufl.edu Message-ID: MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: sh/dj0ugqIiFPQIqh9WbKA== X-Mailer: dtmail 1.2.0 CDE Version 1.2_22 SunOS 5.6 sun4d sparc > > Dear CCL, > > My question is short: What's exactely the electronic correlation (dynamic and no dynamic correlation)? > > Many thanks for your help > > Sylvie Joanteguy > Dear Silvie, As you as a short question, I will give you a short answer :-) The definition of the electronic correlation is simple - it is what you get above single-determinant SCF method. Of course, you should remeber that your result depends of the basis set you use. Only full CI with infinite number of basis functions will give you an exact solution for the energy and the wave fuction within Born-Oppenheimer approximation. The definition of the dymanic and non-dynamic correlation is less accurate. If you have a good SCF solution, and you do a perturbation calculation on top of it, your correction to the energy, structure and other properties is considered to be an effect of dynamic correlation. If you need a few determinants to get a good first approximation for the wave function, it is what people call non-dynamic correlation. Of course, the destingtion between "good" and "bad" is rather uncertain, as it happens to all qualitative concepts. The coupled cluster (CC) method [1] provides both dynamic and non-dynamic correlation effects, and if the number of electrons is equal to the level of CC (e.g. CCSDT for 3 electrons) you will get the total correlation, as the full CI does. Anatoli Korkin [1] see, for example, R.J. Bartlett & J.F. Stanton, Applications of Post-Hartree-Fock Methods: A Tutorial, in Reviews in Computational Chemistry, Vol. 5, VCH Publishers, 1994)