From chemistry-request@server.ccl.net Wed Mar 14 15:54:05 2001 Received: from athe.wustl.edu ([128.252.146.60]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2EKs5D10309 for ; Wed, 14 Mar 2001 15:54:05 -0500 Received: (from toni@localhost) by athe.wustl.edu (8.9.3/8.9.3) id OAA15220; Wed, 14 Mar 2001 14:53:30 -0600 (CST) Date: Wed, 14 Mar 2001 14:53:30 -0600 (CST) From: Toni Kazic Message-Id: <200103142053.OAA15220@athe.wustl.edu> To: fgonzale@lauca.usach.cl CC: CHEMISTRY@ccl.net In-reply-to: <3AAF7C55.A72EF514@lauca.usach.cl> (message from Danilo Gonzalez on Wed, 14 Mar 2001 10:12:37 -0400) Subject: Re: CCL:Linux-Softwares Hello all, Not quite knowing what you mean by "molecular modeling" ---- We have been using VMD 1.6 from Klaus Schulten's group at the University of Illinois for several months now. We run it on Solaris8/Sparc and on RedHat 7.0/Intel. I have been absolutely delighted with its speed and capabilities on both platforms. The URL is http://www.ks.uiuc.edu/Research/vmd. Schulten's group are also the authors of NAMD, a molecular dynamics code particularly targeted at large ensembles of molecules. I have no direct experience with it, so cannot comment further. NWChem runs on Linux on a number of platforms (http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html) and GAMESS runs on Linux/Intel at least (http://www.msg.ameslab.gov/GAMESS/GAMESS.html). NWChem is a combined molecular dynamics/quantum mechanics code, and GAMESS is a quantum mechanics code. We use the semi-empirical part of GAMESS (hardly high-powered for most of you) and have been quite happy with it. I have no direct experience with NWChem, so cannot comment further (Theresa can comment if she's listening ;-)). We run GAMESS on Solaris8/Sparc. All these codes are FREE, sign the distinctly civilized license agreeements and enjoy. cheers, Toni From chemistry-request@server.ccl.net Wed Mar 14 16:01:41 2001 Received: from gate-sl1.mdli.com ([208.200.221.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2EL1fD10370 for ; Wed, 14 Mar 2001 16:01:41 -0500 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id NAA11725 for ; Wed, 14 Mar 2001 13:01:42 -0800 (PST) Received: from puffin.mdli.com(172.16.1.12) by gate-sl1.mdli.com via smap (V2.1) id xma011723; Wed, 14 Mar 01 13:01:41 -0800 Received: from shepherd.mdli.com by puffin.mdli.com (980427.SGI.8.8.8/BCH1.0) id NAA52487; Wed, 14 Mar 2001 13:01:41 -0800 (PST) Received: by shepherd.mdli.com with Internet Mail Service (5.5.2650.21) id ; Wed, 14 Mar 2001 13:01:40 -0800 Message-ID: <8E13FBBA26A9DA119ED400A0C9AB2CE50694B3C0@shepherd.mdli.com> From: Guenter Grethe To: "'Computational Chemistry List'" Cc: Guenter Grethe Subject: CSA Trust 2001 Award Date: Wed, 14 Mar 2001 13:01:39 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" CHEMICAL STRUCTURE ASSOCIATION TRUST - YEAR 2001 AWARD The Chemical Structure Association Trust is an internationally recognised Trust established to promote education, research or development in the area of systems and methods for the storage, processing and retrieval of information about chemical structures, reactions and compounds. Applications are invited for the Year 2001 Chemical Structure Association Trust Award. The Trust is offering an Award of up to two thousand pounds sterling for the best applicant seeking funds for education or research in chemical information. Anyone working in the field of chemical information research can apply and application can be made for funds to attend a relevant conference, for travel (e.g. to collaborate with another research group) or for hardware or software to assist with the research project. The award is unlikely to be given exclusively for hardware and software. The application should include: 1. A statement of academic qualifications 2. Details of relevant work and a statement of research recently completed by the applicant 3. The purpose for which the award is required. The clarity and relevance of this statement will be crucial in the evaluation of the applicants 4. Letters from two academic references to support the application. Award winners are expected to write a short report, within one year of receiving the money, giving details of how the money was spent. The Trust has previously supported the continuation of research studies in biomedical interactions including molecular recognition processes and drug design; a novel combination of reaction indexing and synthesis planning; clustering of chemical structures for property prediction; and investigation of reaction mechanisms. The work of younger scientists in developing countries has also been made possible in conjunction with some of the awards. Recent award winners, and their areas of research, are as follows: - Marina Molchanova, Zelinsky Institute of Organic Chemistry, Moscow (use graph theoretical and combinatorial algorithms in structure generation) - Weifan Zheng, University of North Carolina (QSAR and combinatorial chemistry) - Aniko Simon, University of Leeds (chemical literature data extraction) - Eugene Babaev, Moscow State University (computer-assisted synthesis) - Gareth Jones, University of Sheffield (for presentation of paper on genetic algorithms at an ACS National Meeting) - Vladimir Kvasnicka, Slovak Technical University (neural networks for prediction of physiochemical properties) - Rainer Herges, University of Erlangen-Nuernberg (reaction databases and quantum chemistry) - Michael Wright, Imperial College London, UK (chemical document system based on Chemical Markup Language) - Dr. Zaneta Nikolovska-Coleska, University of Saints Cyril and Methodius in Skopje, Republic of Macedonia (molecular modelling methods aimed at the de novo design of enzyme inhibitors) Applications must be submitted by 30 May 2001, preferably by e-mail, to the Chairman of the Awards sub-committee, Professor Michael Lynch, at: Michael F Lynch Any postal applications should be sent to: Dr Clive Weeks, Secretary of the Chemical Structure Association Trust 39 Rounton Road, Church Crookham, Fleet, Hants GU52 6JH, UK The Award will be announced and presented at the International Chemical Information Meeting in Annecy in October. From chemistry-request@server.ccl.net Wed Mar 14 15:42:00 2001 Received: from web13202.mail.yahoo.com ([216.136.174.187]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f2EKfxD10241 for ; Wed, 14 Mar 2001 15:42:00 -0500 Message-ID: <20010314202839.82539.qmail@web13202.mail.yahoo.com> Received: from [65.6.48.45] by web13202.mail.yahoo.com; Wed, 14 Mar 2001 12:28:39 PST Date: Wed, 14 Mar 2001 12:28:39 -0800 (PST) From: mike smith Subject: experiment of H-bond strength in solution To: chemistry@ccl.net In-Reply-To: <200103141548.f2EFmCL08089@server.ccl.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all, Since it's well-known that the H-bond strength will be highly weaken in solution, compared with that in gap phase, I am curious if there is any experimental evidence or hint available. Also, I found two papers on the potential enrgy curves of H-bond in gas-phase and solution: (1)Dang, L X; Kollman, P. A, J Am Chem Soc, 1990, 112,503 AT base pair (H-bond & stacking) from 12kcal/mol(gas) to 0.8kcal/mol (solution) (2)Osapay, K; Young W S; Brooks C L; Case D A J Phys Chem 1996, 100, 2698 Updated in Annu Rev Phys Chem, 2000, 51, 129 formamide dimer from 6.7 kcal/mol to 0.8 kcal/mol Here, I am wondering if any of you could provide me more related reference. Also, any discussion on the method to simulate this accurately would be highly appreciated. Thanks for your attention! --Mike __________________________________________________ Do You Yahoo!? Yahoo! Auctions - Buy the things you want at great prices. http://auctions.yahoo.com/ From chemistry-request@server.ccl.net Thu Mar 15 03:23:04 2001 Received: from vytautas.vdu.lt (mail@[193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2F8MwD12749 for ; Thu, 15 Mar 2001 03:23:00 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp id 14dT1I-0002Vi-00; Thu, 15 Mar 2001 10:22:04 +0200 Received: from vaidila.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id KAA21322; Thu, 15 Mar 2001 10:22:02 +0200 (GMT) Message-ID: <3AAFE11C.A7692042@vaidila.vdu.lt> Date: Wed, 14 Mar 2001 22:22:37 +0100 From: "art'" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: Yubo Fan CC: Familia Esguerra Neira , chemistry@ccl.net Subject: Re: CCL:Short Budget References: <1916920013213172720263@mentecolectiva.com> <3AAE843E.23AC887C@mail.chem.tamu.edu> <3AAEA27A.8D405713@vaidila.vdu.lt> <3AAFA8CE.D222E367@mail.chem.tamu.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, The bottleneck, usually, is the M/B bus, RAM and L2 Cache. If to choose the best and the most expensive CPU with highest core performance, what is the overall performance when M/B and RAM are far behind with speed and performance ? Athlon has better choice choosing M/B and Cache. So DDRAM, which performs two r or wr functions per clock, could serve well increasing the total performance too. Maybe I am wrong somethere, but let me know ;) Good day A.Ziemys > I don't think DDR memory is much faster than PC133 SDRAM. You can find the comparison > data on the homepage of www.amd.com. CPU is always the most important for > calculations. > > > > > DDR memory shoud be very quick as r/wr functions are performed in another way from > > SDRAM's. The 1.2 GHz Athlon is about $ 280 and mauch cheaper than PIII or P4 .... > > and Athlons usually have higher performance about 20 %. Espetially in floating > > point intensive calculations. > > > > I agree Athlon is faster and cheaper than PIII but there isn't dual processor > supported motherboard available now. Maybe two months later, this type of motherboard > is available commercially. Double speed is always better than 20% faster. From chemistry-request@server.ccl.net Thu Mar 15 05:14:29 2001 Received: from localhost.ox.ac.uk (root@[163.1.16.24]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FAETD13222 for ; Thu, 15 Mar 2001 05:14:29 -0500 Received: from smplinux.de (baaden@localhost [127.0.0.1]) by localhost.ox.ac.uk (8.9.3/8.9.3/Debian 8.9.3-21) with ESMTP id KAA05383 for ; Thu, 15 Mar 2001 10:14:29 GMT Message-Id: <200103151014.KAA05383@localhost.ox.ac.uk> X-Authentication-Warning: localhost.ox.ac.uk: Host baaden@localhost [127.0.0.1] claimed to be smplinux.de X-Mailer: exmh version 2.1.1 10/15/1999 (debian) To: CHEMISTRY@ccl.net Subject: Anaglyphic stereo in real time ? X-image-url: http://crypt.u-strasbg.fr/marc/m-baaden.gif X-url: X-Face: -Nz&SN]%I8g9WFR#/!fe9se!_G_OndNloj@t+6jrGsoZ"z)?an0n P!Nls~*o?u7fy:]1N|^^(KX*uE>Nk{bHaCJ)(hXF~E#5)j.k0n4hgfIzpmn,[VY'\7X:;VOZ\CItIq G!2f8,k2`VLrkXQ:<.3LxEQ'E-;d:A)V# Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Thu, 15 Mar 2001 10:14:29 +0000 From: Marc BAADEN Hi, yet another question. Having discovered the power of anaglyphic stereo representations (those images which use red/blue glasses) recently, I wonder why there are no molecular viewers out there, which support such a display in real time (except SwissPDBviewer, see note below). In fact I have tried (and succeeded) to create a 3D anaglyphic image of a molecule from VMD, and it proved very easy and the result was very convincing. The only problem is that it is not interactive and you thus get a static view only. Is anybody aware of a molecular viewer with real-time display in anaglyphic stereo ? Would anybody be interested in including such a feature in an existing viewer ? (I would like to do it, but I think it exceeds my programming capacities/available time). NOTE 1: ------- For those who are interested, here how to get an anaglyphic stereo image from VMD: Step-by-step instructions (with VMD) 1.Display your system in the view you like. 2.choose Stereo/Left in the Display menu 3.choose snapshot in the Render menu 4.save e.g. as left.rgb 5.choose Stereo/Right in the Display menu 6.choose snapshot in the Render menu 7.save e.g. as right.rgb 8.on the command line, type combine -stereo left.rgb right.rgb snap.rgb (this requires that ImageMagick is installed) 9.convert to any format you like, for example gif convert snap.rgb snap.gif (this requires that ImageMagick is installed) NOTE 2: ------- SwissPDBViewer This viewer has an option to display anaglyphic stereo in realtime. Two things annoyed me very much: a) The stereo image is only monochrome, and very "basic" concerning the display features. b) The quality was VERY bad (especially compared to a stereo image from VMD), and I couldn't figure out how to possibly adjust the stereo red/blue color settings to improve it. Thank you in advance, Marc Baaden -- Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University mailto:baaden@smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de FAX/Voice +49 40333 968508 - Tel: +44 1865 275380 or +33 609 843217 From chemistry-request@server.ccl.net Thu Mar 15 05:15:38 2001 Received: from sv2.ictp.trieste.it ([140.105.16.62]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FAFbD13241 for ; Thu, 15 Mar 2001 05:15:38 -0500 Received: from condense-39.ictp.trieste.it (IDENT:sekkal@condense-39.ictp.trieste.it [140.105.17.99]) by sv2.ictp.trieste.it (8.11.0/8.11.0) with ESMTP id f2FAMVR26862 for ; Thu, 15 Mar 2001 11:22:32 +0100 (MET) Date: Thu, 15 Mar 2001 11:22:31 +0100 (CET) From: "Dr. Wassila SEKKAL" To: chemistry@server.ccl.net Subject: MOPAC software Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear sir, I am very interesting with the MOPAC software, and I would like to ask you if there is an available version of MOPAC, please tell me where I could obtain it. Best regards W. SEKKAL From chemistry-request@server.ccl.net Thu Mar 15 05:51:06 2001 Received: from musset.lpct.u-bordeaux.fr ([147.210.56.51]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FAp5D13448 for ; Thu, 15 Mar 2001 05:51:06 -0500 Received: from lpct.u-bordeaux.fr (localhost [127.0.0.1]) by musset.lpct.u-bordeaux.fr (8.9.3/jtpda-5.3.2) with ESMTP id LAA17602 for ; Thu, 15 Mar 2001 11:56:38 +0100 (MET) Sender: fleurat@lpct.u-bordeaux.fr Message-ID: <3AB09FE5.C375C0B2@lpct.u-bordeaux.fr> Date: Thu, 15 Mar 2001 11:56:37 +0100 From: Paul Fleurat-Lessard Reply-To: fleurat@lpct.u-bordeaux.fr Organization: LPCM X-Mailer: Mozilla 4.61 [en] (X11; I; HP-UX B.10.01 9000/735) X-Accept-Language: fr-FR, en MIME-Version: 1.0 To: CCL Subject: PC Rack and Queuing System Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 7bit Hi All, We are using a bunch of PC (PIII) for computational chemistry research (using mainly Gaussian, Molpro, Molcas and Gamess). We are going to buy a 10 PIII rack. For now, we use NQS (Generic Network Queuing System) to dispatch and control jobs over our processors. However as we have physically different PC, it is difficult to prevent a same user from using all the processors... (you can easily do that on ONE PC). So, I was wondering : what are you using ? I will summarize the answers. Thanks in advance, Best regards, Paul. -- ------------------------------------------------------------------------- Fleurat-Lessard Paul | fleurat@lpct.u-bordeaux.fr Laboratoire de Physico Chimie Moleculaire, | Phone: (33)(0)5 56 84 63 09 Universite Bordeaux I, 33400 Talence, FRANCE| Fax : (33)(0) 5 56 84 66 45 _________________________________________________________________________ From chemistry-request@server.ccl.net Thu Mar 15 07:24:14 2001 Received: from furgoneta.uv.es ([147.156.1.46]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FCO6D14770 for ; Thu, 15 Mar 2001 07:24:13 -0500 Received: from tigris.uv.es (eufrates.ci.uv.es [147.156.1.50]) by furgoneta.uv.es (8.9.0/8.9.0) with ESMTP id NAA00933; Thu, 15 Mar 2001 13:24:02 +0100 Received: from nebot22.quifis.uv.es (nebot22.quifis.uv.es [147.156.122.126]) by tigris.uv.es (8.9.3/8.9.3) with ESMTP id NAA24917; Thu, 15 Mar 2001 13:24:01 +0100 (MET) Message-ID: X-Mailer: XFMail 1.3 [p0] on Linux X-Priority: 3 (Normal) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit MIME-Version: 1.0 In-Reply-To: <01031422353901.00713@borussia> Date: Thu, 15 Mar 2001 13:23:58 +0100 (CET) X-Face: #xC]}[!{&$YZ%].QkfGy2*$u;~^n"}zj!(D3hj|-YBq|EVdf&O'~z%Ctr?g(g:9=:ZXb*~: r^'Zp'FlBd{h)=4}~8&Bh'PCv\sYAZ|I2|j2l$\f.2G(4M{-qK]~vQtOunlCS'ooZ=]DJiC1'/$wo, Z30jx8Hy}[vAxGW%oQ\w3bCbQAs2@-Ouf.h]GzZ6$F0"Ecf9E1L(s|[26sU9\z?4z7C7{2@z7"5#: Reply-To: Ignacio.Nebot@uv.es Organization: Instituto de Ciencia Molecular, Universidad de Valencia Sender: nebot@nebot22.quifis.uv.es From: Ignacio Nebot-Gil To: Wibke Sudholt Subject: RE: CCL:Citation Cc: CHEMISTRY@ccl.net You can find the complete Dirac's sentence and very interesting comments on it at: Werner Kutzelnigg: perspective: Perspective on "Quantum mechanics of many-electron systems" Dirac PAM (1929) Proc R Soc Lond Ser A 123: 714 Theor Chem Acc 103 (2000) 3/4, 182-186 This article is accesible on the Springer webpage http://link.springer.de/link/service/journals/00214/tocs/t0103003.htm Prof. Ignacio Nebot-Gil ______________________________________________________ Inst. de Ciencia Molecular & Dept. de Quimica Fisica Univ. de Valencia E-mail: Ignacio.Nebot@uv.es Dr. Moliner, 50 Tel: +34 96 386 4333 46100-BURJASSOT (Valencia) FAX: +34 96 398 3156 Spain ______________________________________________________ From chemistry-request@server.ccl.net Thu Mar 15 07:38:08 2001 Received: from alpha.luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FCc7D14868 for ; Thu, 15 Mar 2001 07:38:08 -0500 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id NAA24557; Thu, 15 Mar 2001 13:38:05 +0100 (MET) Date: Thu, 15 Mar 2001 13:38:05 +0100 (MET) Message-Id: <200103151238.NAA24557@alpha.luc.ac.be> X-Sender: lucp1381@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: "Dr. Wassila SEKKAL" , chemistry@server.ccl.net From: sergiusz kwasniewski Subject: Re: CCL:MOPAC software Hi, you could take a look at http://www.fqspl.com.pl/winmopac Serge At 11:22 AM 3/15/01 +0100, Dr. Wassila SEKKAL wrote: >Dear sir, > >I am very interesting with the MOPAC software, and I would like to ask you >if there is an available version of MOPAC, please tell me where I could >obtain it. > >Best regards >W. SEKKAL > > >-= 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 > > > > > > ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Thu Mar 15 03:10:39 2001 Received: from mel.ruc.dk ([130.225.220.27]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2F8AcD12706 for ; Thu, 15 Mar 2001 03:10:38 -0500 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id JAA14885; Thu, 15 Mar 2001 09:10:39 +0100 (MET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id IAA08455; Thu, 15 Mar 2001 08:54:10 +0100 (MET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 15 Mar 01 09:10:38 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 15 Mar 01 09:10:33 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Wibke Sudholt Date: Thu, 15 Mar 2001 09:10:32 +0100 Subject: Re: CCL:Citation CC: CHEMISTRY@ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: Wibke Sudholt: > could anybody give me - for educational purposes - the sentence Dirac - I > think - said about that "in principle one can calculate the whole chemistry" - > if possible in German - and where and when he stated this? P. A. M. Dirac, Proceedings of the Royal Society of London, Series A, Vol. CXXIII, April 1929, pp 714: "... The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble. It therefore becomes desireable that approximate practical methods of applying quantum mechanics should be developed, which can lead to an explanation of the main features of complex atomic systems without too much computation." Hence, Dirac only stated that "the underlying physical laws ... for the whole of chemistry are complete known". He did NOT claim that all aspects of chemistry could be derived from these fundamental laws. Knowledge of the "underlying physical laws" does not, in general, allow us to anticipate all aspects of 'reduced' sciences. More or less like the concept of 'chaos' is not easily anticipated solely from a knowledge of Newton's classical mechanics, or the phenomenon 'life' is not easily derived from a knowledge of chemistry, and so on. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~jsl/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Mar 15 05:05:49 2001 Received: from localhost.ox.ac.uk (root@[163.1.16.24]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FA5mD13186 for ; Thu, 15 Mar 2001 05:05:49 -0500 Received: from smplinux.de (baaden@localhost [127.0.0.1]) by localhost.ox.ac.uk (8.9.3/8.9.3/Debian 8.9.3-21) with ESMTP id KAA05340; Thu, 15 Mar 2001 10:05:36 GMT Message-Id: <200103151005.KAA05340@localhost.ox.ac.uk> X-Authentication-Warning: localhost.ox.ac.uk: Host baaden@localhost [127.0.0.1] claimed to be smplinux.de X-Mailer: exmh version 2.1.1 10/15/1999 (debian) To: CHEMISTRY@ccl.net Subject: "SUMMARY" Re: CCL:Hardware question: dials for Linux ? Cc: warren@sunesis-pharma.com, sangeeta@bioinfo.ernet.in X-image-url: http://crypt.u-strasbg.fr/marc/m-baaden.gif X-url: X-Face: -Nz&SN]%I8g9WFR#/!fe9se!_G_OndNloj@t+6jrGsoZ"z)?an0n P!Nls~*o?u7fy:]1N|^^(KX*uE>Nk{bHaCJ)(hXF~E#5)j.k0n4hgfIzpmn,[VY'\7X:;VOZ\CItIq G!2f8,k2`VLrkXQ:<.3LxEQ'E-;d:A)V# Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Thu, 15 Mar 2001 10:05:36 +0000 From: Marc BAADEN Hi, some weeks ago I posted the question attached at the end of this message. Several people asked for a summary. It will be very short though: I did not receive any (positive or negative) answers. My conclusion is thus, nobody seems to use dials with Linux. Cheers, Marc === Original question was: > Hi, > > as I have almost completely switched to a Linux based workstation, > I wonder wether SGI-like dial boxes are available and supported for > these platforms. > > I am particularly interested in using them with rasmol, so if anybody > can report wether dial boxes under linux work successfully with that > software, I would be very grateful. > > Reports for any other (mainly visualisation/mol. modeling) software > under linux which supports dial box hardware would also be appreciated. -- Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University mailto:baaden@smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de FAX/Voice +49 40333 968508 - Tel: +44 1865 275380 or +33 609 843217 From chemistry-request@server.ccl.net Thu Mar 15 06:05:33 2001 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FB5XD13596 for ; Thu, 15 Mar 2001 06:05:33 -0500 Received: from sun1.lrz-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP; Thu, 15 Mar 2001 12:05:32 +0100 Received: from localhost (ui22204@localhost) by sun1.lrz-muenchen.de (8.8.8+Sun/8.8.8) with ESMTP id MAA23296; Thu, 15 Mar 2001 12:05:30 +0100 (MET) X-Authentication-Warning: sun1.lrz-muenchen.de: ui22204 owned process doing -bs Date: Thu, 15 Mar 2001 12:05:30 +0100 (MET) From: Eugene Leitl X-Sender: ui22204@sun1.lrz-muenchen.de To: "art'" cc: Yubo Fan , Familia Esguerra Neira , chemistry@ccl.net Subject: Re: CCL:Short Budget In-Reply-To: <3AAFE11C.A7692042@vaidila.vdu.lt> Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 14 Mar 2001, art' wrote: > The bottleneck, usually, is the M/B bus, RAM and L2 Cache. If to choose the best and the The bottleneck is specific to the problem. Some codes run entirely within L2 (or even L1) cache, some thrash cache, so bandwith to memory becomes relevant, some stream a lot to nonvolatile storage or across network (where latency or bandwidth may be the bottleneck). The only meaningful benchmark is your application. > most expensive CPU with highest core performance, what is the overall performance when > M/B and RAM are far behind with speed and performance ? Athlon has better choice choosing > M/B and Cache. So DDRAM, which performs two r or wr functions per clock, could serve well > increasing the total performance too. From chemistry-request@server.ccl.net Thu Mar 15 09:01:16 2001 Received: from lithium.theochem.uni-duesseldorf.de ([134.99.82.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FE1GD15333 for ; Thu, 15 Mar 2001 09:01:16 -0500 Received: from borussia.theochem.uni-duesseldorf.de (borussia.theochem.uni-duesseldorf.de [134.99.82.13]) by lithium.theochem.uni-duesseldorf.de (8.11.1/8.11.1) with ESMTP id f2FDloQ09979; Thu, 15 Mar 2001 14:47:51 +0100 Received: from localhost (localhost [[UNIX: localhost]]) by borussia.theochem.uni-duesseldorf.de (8.11.1/8.11.1) id f2FDlpP01318; Thu, 15 Mar 2001 14:47:51 +0100 From: Wibke Sudholt Reply-To: wibke@theochem.uni-duesseldorf.de To: CHEMISTRY@ccl.net Subject: Dirac Citation - Summary Date: Thu, 15 Mar 2001 14:08:23 +0100 X-Mailer: KMail [version 1.0.29] Content-Type: text/plain Cc: martinas@khroma.colorado.edu, chrirena@techunix.technion.ac.il, martin.mueller@iuct.fhg.de, jsl@virgil.ruc.dk, lars@theophys.kth.se, grimmes@uni-muenster.de, vdroogen@uia.ua.ac.be, "h.g.schreckenbach"@dl.ac.uk, Tucker.Carrington@UMontreal.CA, Christoph.vanWullen@tu-berlin.de, Ignacio.Nebot@uv.es MIME-Version: 1.0 Message-Id: <01031514475100.01292@borussia> Content-Transfer-Encoding: 8bit Hello CCLers, thank you very much for your quick response, Tucker Carrington, Irena Efremenko, Stefan Grimme, Sara Martinez, Martin Mueller, Ignacio Nebot-Gil, Lars Sandberg, Georg Schreckenbach, Jens Spanget-Larsen, Joris Van Droogenbroeck and Christoph van Wüllen! The original question was: "Could anybody give me - for educational purposes - the sentence Dirac - I think - said about that "in principle one can calculate the whole chemistry" - if possible in German - and where and when he stated this?" The most extended version of the citation sent to me was: "§1. Introduction The general theory of quantum mechanics is now almost complete, the imperfections that still remain being in connection with the exact fitting in of the theory with relativity ideas. These give rise to difficulties only when high-speed particles are involved, and are therefore of no importance in the consideration of atomic and molecular structure and ordinary chemical reactions, in which it is, indeed, usually sufficiently accurate if one neglects relativity variation of mass with velocity and assumes only Coulomb forces between the various electrons and atomic nuclei. The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these equations leads to equations much too complicated to be soluble. It therefore becomes desireable that approximate practical methods of applying quantum mechanics should be developed, which can lead to an explanation of the main features of complex atomic systems without too much computation." The original reference is: P. A. M. Dirac, "Quantum Mechanics of Many-Electron Systems", Proceedings of the Royal Society of London, Series A, Vol. CXXIII (123), April 1929, pp 714. Stefan Grimme and Ignacio Nebot-Gil point to a discussion article: Werner Kutzelnigg, "Perspective on "Quantum mechanics of many-electron systems" Dirac PAM (1929) Proc R Soc Lond Ser A 123: 714", Theor Chem Acc 103 (2000) 3/4, 182-186 http://link.springer.de/link/service/journals/00214/tocs/t0103003.htm Martin Mueller gave the weblink: http://www.linux-magazin.de/ausgabe/1999/01/Quantenchemie/quantenchemie.html Georg Schreckenbach added: "It is worthwhile, perhaps, to look up the context - the paragraphs before are quite interesting, too. Often, only the first sentence is cited. I find that the rest is important as well: It describes pretty well what many of the CCL readers are doing, 'developing approximate practical methods of applying quantum mechanics.' The ideas of what 'too much computation' might mean has changed a bit since Dirac's time but the task as such is still the same!" Jens Spanget-Larsen gave the comment: "Hence, Dirac only stated that "the underlying physical laws ... for the whole of chemistry are complete known". He did NOT claim that all aspects of chemistry could be derived from these fundamental laws. Knowledge of the "underlying physical laws" does not, in general, allow us to anticipate all aspects of 'reduced' sciences. More or less like the concept of 'chaos' is not easily anticipated solely from a knowledge of Newton's classical mechanics, or the phenomenon 'life' is not easily derived from a knowledge of chemistry, and so on." Thank you very much once again! Best regards, Wibke Sudholt Institute of Theoretical Chemistry Heinrich-Heine-University Duesseldorf, Germany wibke@theochem.uni-duesseldorf.de From chemistry-request@server.ccl.net Thu Mar 15 10:28:10 2001 Received: from usc.edu (root@[128.125.253.136]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FFS5D16901 for ; Thu, 15 Mar 2001 10:28:05 -0500 Received: from rcf-fs.usc.edu (root@rcf-fs.usc.edu [128.125.253.166]) by usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id HAA17080; Thu, 15 Mar 2001 07:28:05 -0800 (PST) Received: from usc.edu (IDENT:jorgevil@futura.usc.edu [128.125.14.59]) by rcf-fs.usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id HAA14566; Thu, 15 Mar 2001 07:28:04 -0800 (PST) Sender: jorgevil@rcf-fs.usc.edu Message-ID: <3AB0DF85.9A30AE1E@usc.edu> Date: Thu, 15 Mar 2001 07:28:05 -0800 From: Jordi Villa X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en MIME-Version: 1.0 To: mike smith , chemistry@ccl.net Subject: Re: CCL:experiment of H-bond strength in solution References: <20010314202839.82539.qmail@web13202.mail.yahoo.com> Content-Type: multipart/alternative; boundary="------------0CF7E9CD40008477BEBEEF9D" --------------0CF7E9CD40008477BEBEEF9D Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Mike, One of the best ways to simulate this is by using the EVB method by Warshel in, for example: An Empirical Valence Bond Approach for Comparing Reactions in Solutions and in Enzymes, A. Warshel and R. M. Weiss, J. Am. Chem. Soc. 102, 6218 (1980). Simulation of Enzyme Reactions Using Valence Bond Force Fields and Other Hybrid Quantum/Classical Approaches, J. Åqvist and A. Warshel, Chem. Rev. 93, 2523 (1993). and specifically, on the strength of HB's, a clear explanation is given in: On Low-Barrier Hydrogen Bonds and Enzyme Catalysis, A. Warshel, A. Papazyan and P. A. Kollman, Science 269, 102 (1995). Also, a simplified version of the use of the EVB for HB's can be found at http://www.tanchi.com/tufts/ Hope this helps Jordi mike smith wrote: > Dear all, > > Since it's well-known that the H-bond strength will be > highly weaken in solution, compared with that in gap > phase, I am curious if there is any experimental > evidence or hint available. > > Also, I found two papers on the potential enrgy curves > of H-bond in gas-phase and solution: > (1)Dang, L X; Kollman, P. A, > J Am Chem Soc, 1990, 112,503 > > AT base pair (H-bond & stacking) > from 12kcal/mol(gas) to 0.8kcal/mol (solution) > > (2)Osapay, K; Young W S; Brooks C L; Case D A > J Phys Chem 1996, 100, 2698 > Updated in Annu Rev Phys Chem, 2000, 51, 129 > > formamide dimer > from 6.7 kcal/mol to 0.8 kcal/mol > > Here, I am wondering if any of you could provide me > more related reference. Also, any discussion on the > method to simulate this accurately would be highly > appreciated. > > Thanks for your attention! > > --Mike > > __________________________________________________ > Do You Yahoo!? > Yahoo! Auctions - Buy the things you want at great prices. > http://auctions.yahoo.com/ > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Jordi Villa i Freixa jorgevil@usc.edu http://laetro.usc.edu/wgroup/people/jorgevil Department of Chemistry, University of Southern California Los Angeles, CA, USA, 90089-1062 Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 --------------0CF7E9CD40008477BEBEEF9D Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Mike,

One of the best ways to simulate this is by using the EVB method by Warshel in, for example:

An Empirical Valence Bond Approach for Comparing Reactions in Solutions and in Enzymes, A. Warshel and R. M. Weiss, J. Am. Chem. Soc. 102, 6218 (1980).
Simulation of Enzyme Reactions Using Valence Bond Force Fields and Other Hybrid Quantum/Classical Approaches, J. Åqvist and A. Warshel, Chem. Rev. 93, 2523
     (1993).

and specifically, on the strength of HB's, a clear explanation is given in:

On Low-Barrier Hydrogen Bonds and Enzyme Catalysis, A. Warshel, A. Papazyan and P. A. Kollman, Science 269, 102 (1995).

Also, a simplified version of the use of the EVB for HB's can be found at http://www.tanchi.com/tufts/

Hope this helps

Jordi
 

mike smith wrote:

Dear all,

Since it's well-known that the H-bond strength will be
highly weaken in solution, compared with that in gap
phase, I am curious if there is any experimental
evidence or hint available.

Also, I found two papers on the potential enrgy curves
of H-bond in gas-phase and solution:
  (1)Dang, L X; Kollman, P. A,
          J Am Chem Soc, 1990, 112,503

       AT base pair (H-bond & stacking)
        from 12kcal/mol(gas) to 0.8kcal/mol (solution)

   (2)Osapay, K; Young W S; Brooks C L; Case D A
          J Phys Chem 1996, 100, 2698
      Updated in Annu Rev Phys Chem, 2000, 51, 129

         formamide dimer
        from 6.7 kcal/mol to 0.8 kcal/mol

Here, I am wondering if any of you could provide me
more related reference. Also, any discussion on the
method to simulate this accurately would be highly
appreciated.

Thanks for your attention!

--Mike

__________________________________________________
Do You Yahoo!?
Yahoo! Auctions - Buy the things you want at great prices.
http://auctions.yahoo.com/

-= This is automatically added to each message by mailing script =-
CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To Admins
MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
CHEMISTRY-SEARCH@ccl.net -- archive search    |    Gopher: gopher.ccl.net 70
Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net

-- 
Jordi Villa i Freixa                  
jorgevil@usc.edu   http://laetro.usc.edu/wgroup/people/jorgevil
Department of Chemistry, University of Southern California
Los Angeles, CA, USA, 90089-1062
Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701
  --------------0CF7E9CD40008477BEBEEF9D-- From chemistry-request@server.ccl.net Thu Mar 15 11:16:46 2001 Received: from havana.ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FGGjD18323 for ; Thu, 15 Mar 2001 11:16:45 -0500 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id KAA06372; Thu, 15 Mar 2001 10:16:40 -0600 (CST) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.3+Sun/8.9.1) id KAA18247; Thu, 15 Mar 2001 10:15:26 -0600 (CST) Date: Thu, 15 Mar 2001 10:15:26 -0600 From: John Stone To: Marc BAADEN Cc: CHEMISTRY@ccl.net, vmd@ks.uiuc.edu Subject: Re: CCL:Anaglyphic stereo in real time ? Message-ID: <20010315101525.C18152@geneseo.ks.uiuc.edu> Mail-Followup-To: Marc BAADEN , CHEMISTRY@ccl.net, vmd@ks.uiuc.edu References: <200103151014.KAA05383@localhost.ox.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0i In-Reply-To: <200103151014.KAA05383@localhost.ox.ac.uk>; from baaden@smplinux.de on Thu, Mar 15, 2001 at 10:14:29AM +0000 Dear Marc, CCL, It is indeed possible to do anaglyph stereo in real-time as you've already seen. There are a few challenges which make implementation a little tricky as you mentioned in your commentary on the colors in SwissPDBviewer: 1) One can use the OpenGL accumulation buffer along with glColorMask() to draw the scene with the blue/red filtering enabled for each eye. This solution has the disadvantage that not all OpenGL implementations provide a workable accumulation buffer. Some implement the accumulation buffer entirely in software, which can be _very_ slow. Paul Bourke has a web page that discusses this: http://astronomy.swin.edu.au/pbourke/opengl/redblue/ 2) One could use a fully-stereo-capable video board, with quad-buffered stereo (front/back/left/right color buffers) and simply enable the color mask using glColorMask() before drawing the left and right images respectively. This solution assumes that the video hardware can do quad-buffered stereo, but I believe there are more boards that support stereo in hardware than support an accumulation buffer in hardware. This solution would probably be easy to implement in an existing stereo-capable molecular visualization program, I will try it out in VMD when I get back from a conference next week and if it works out, It'll show up in the next release of VMD. 3) There is a problem with both of these solutions in that certain color combinations in your molecule will look very bad when viewed in anaglyph stereo. Only grayscale images will appear entirely correct in both eyes, but this is a big sacrifice to make, to give up all coloring of the molecule. Perhaps its "ok" to color your molecule semi-normally and allow glColorMask() to chop out the red/blue components. As long as the user has fine control over the coloring of her molecule, it should be possible to tweak the scene to look good even in anaglyph mode. Here is another web page which has some brief coverage of color issues with anaglyph stereo: http://www.cs.jhu.edu/~acw3f/cg/project/intro.html#problems Making the colors look passable in anaglyph stereo is probably a bigger challenge than the actual rendering techniques in 1) and 2). It sounds like SwissPDBviewer takes the approach of forcing the molecule to grayscale as a first step. Does SwissPDBviewer pass the green color channel at all when it draws, or does it only pass red and blue? Those details matter a fair amount. This is where I'd expect the trouble to arise with implementing in VMD, making the colors look half-decent. I'll make an attempt at implementing 2) in VMD, and see if it works well, it should be a small hack to the existing CrystalEyes stereo mode, and should be able to render at 100% full-speed on any machine that has quad-buffered stereo. The accumulation buffer technique on Paul Bourke's page could also be implemented, but VMD isn't smart enough to manage an accumulation buffer well at present, and most current video boards do not implement the accumulation buffer in hardware. I strongly encourage any other molecular visualization software developers to chime in on this topic, I'd be curious to hear what other solutions people have for doing anaglyph stereo in real-time... Thanks, John Stone vmd@ks.uiuc.edu On Thu, Mar 15, 2001 at 10:14:29AM +0000, Marc BAADEN wrote: > > Hi, > > yet another question. > > Having discovered the power of anaglyphic stereo representations > (those images which use red/blue glasses) recently, I wonder why > there are no molecular viewers out there, which support such a > display in real time (except SwissPDBviewer, see note below). > > In fact I have tried (and succeeded) to create a 3D anaglyphic image > of a molecule from VMD, and it proved very easy and the result was > very convincing. The only problem is that it is not interactive and > you thus get a static view only. > > Is anybody aware of a molecular viewer with real-time display in > anaglyphic stereo ? > > Would anybody be interested in including such a feature in an existing > viewer ? (I would like to do it, but I think it exceeds my programming > capacities/available time). > > NOTE 1: > ------- > > For those who are interested, here how to get an anaglyphic stereo > image from VMD: > > Step-by-step instructions (with VMD) > > 1.Display your system in the view you like. > 2.choose Stereo/Left in the Display menu > 3.choose snapshot in the Render menu > 4.save e.g. as left.rgb > 5.choose Stereo/Right in the Display menu > 6.choose snapshot in the Render menu > 7.save e.g. as right.rgb > 8.on the command line, type > combine -stereo left.rgb right.rgb snap.rgb > (this requires that ImageMagick is installed) > 9.convert to any format you like, for example gif > convert snap.rgb snap.gif > (this requires that ImageMagick is installed) > > NOTE 2: > ------- > > SwissPDBViewer > > This viewer has an option to display anaglyphic stereo in realtime. > Two things annoyed me very much: > > a) The stereo image is only monochrome, and very "basic" concerning the > display features. > > b) The quality was VERY bad (especially compared to a stereo image from > VMD), and I couldn't figure out how to possibly adjust the stereo > red/blue color settings to improve it. > > > Thank you in advance, > > Marc Baaden > > -- > Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University > mailto:baaden@smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de > FAX/Voice +49 40333 968508 - Tel: +44 1865 275380 or +33 609 843217 > > > > -= 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 > > > > > > -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns@ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From chemistry-request@server.ccl.net Thu Mar 15 11:56:30 2001 Received: from hotmail.com ([64.4.9.60]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FGuUD18845 for ; Thu, 15 Mar 2001 11:56:30 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 15 Mar 2001 08:53:30 -0800 Received: from 193.55.61.191 by lw9fd.law9.hotmail.msn.com with HTTP; Thu, 15 Mar 2001 16:53:30 GMT X-Originating-IP: [193.55.61.191] From: "Alexandre Hocquet" To: jsl@virgil.ruc.dk Cc: CHEMISTRY@ccl.net Subject: Dirac Citation, reductionism and an advertisement Date: Thu, 15 Mar 2001 16:53:30 -0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 15 Mar 2001 16:53:30.0797 (UTC) FILETIME=[76D4BDD0:01C0AD70] Dear Jens, >Knowledge of the >"underlying physical laws" does not, in general, allow us to anticipate > >all aspects of 'reduced' sciences. It is certainly wise to consider that there exist aspects of chemistry that are not reduced to physics. Among the philosophers of science interested in those questions, i dont think many would dare to say the contrary. >Hence, Dirac only stated that "the underlying physical laws ... for the > >whole of chemistry are complete known". He did NOT claim that all > >aspects of chemistry could be derived from these fundamental laws. To say that Dirac did NOT claim this, is certainly correct stricto sensu. To imply that Dirac did not believe in a reductionist approach of chemistry is another matter. Among the historians of science that interested themselves to the subject, i cannot think of someone not seeing Dirac as a strong reductionnist. Now, what WE (the community of computational chemists) think about reductionism and Dirac is still another matter, and is also the oportunity for me to advertise for ECCC7 poster number ten "the epistemological status of computational chemistry". Please come on in and comment on the subject. Last, the cited paper by Werner Kutzelnigg certainly led to consider new aspects in how Dirac and his quotation are seen in our community. Yours, ------------------------------------------------------------ Alexandre HOCQUET Laboratoire de Physicochimie Biomoléculaire et Cellulaire ESA CNRS 7033 hocquet@lpbc.jussieu.fr Fax: 33 1 44277560 LPBC, case courrier 138 4 Place Jussieu, 75252 PARIS Cedex 05 France ------------------------------------------------------------ _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From chemistry-request@server.ccl.net Thu Mar 15 12:05:38 2001 Received: from havana.ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FH5bD18915 for ; Thu, 15 Mar 2001 12:05:37 -0500 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id LAA06689; Thu, 15 Mar 2001 11:05:31 -0600 (CST) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.3+Sun/8.9.1) id LAA18364; Thu, 15 Mar 2001 11:05:31 -0600 (CST) Date: Thu, 15 Mar 2001 11:05:31 -0600 From: John Stone To: Marc BAADEN , CHEMISTRY@ccl.net, vmd@ks.uiuc.edu Subject: Re: CCL:Anaglyphic stereo in real time ? Message-ID: <20010315110530.G18152@geneseo.ks.uiuc.edu> Mail-Followup-To: Marc BAADEN , CHEMISTRY@ccl.net, vmd@ks.uiuc.edu References: <200103151014.KAA05383@localhost.ox.ac.uk> <20010315101525.C18152@geneseo.ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0i In-Reply-To: <20010315101525.C18152@geneseo.ks.uiuc.edu>; from johns@ks.uiuc.edu on Thu, Mar 15, 2001 at 10:15:26AM -0600 Dear Marc and CCL, Although I should be preparing slides for a talk, I found it hard to resist attempting the implementation of Anaglyph stereo in VMD using method 2) below. :-) I got it to work, and it looks fairly decent. As expected, it runs very well speed-wise, but requires the machine to have quad-buffered stereo. So this solution only really helps those that have all of the equipment except for the stereo glasses. If your computer doesn't do quad-buffered stereo, then the implementation in I just wrote for VMD still isn't enough for your needs. While I'd like to implement an accumulation-buffer-based technique, this will have to wait for another time. I do feel that a VMD user would want to modify some of the default colors it uses for drawing in order to get better looking pictures when using anaglyph stereo, but the technique for method 2) is straightforward, its just a matter of getting the glColorMask() calls in the right places in the existing stereo code. So now a question to CCL: - what colors are the lenses in your anaglyph glasses?? - Paul Bourke's accumulation-buffer-based example code implements several different possible color combinations for people that have Cyan/Magenta, Red/Green, Red/Blue and other color combinations on their glasses. - To make the code I just wrote for VMD useful to more people it would be nice to hear back as to what color lenses people _actually_ have, then I won't clutter up menus with color combinations that nobody will ever use. I'll be checking in the first version of this code today for anyone that wants to see it. (We have a read-only CVS access for those that would like to see it before we release the next alpha/beta version of VMD 1.6.1...) Thanks, John Stone vmd@ks.uiuc.edu On Thu, Mar 15, 2001 at 10:15:26AM -0600, John Stone wrote: > > Dear Marc, CCL, > It is indeed possible to do anaglyph stereo in real-time as > you've already seen. There are a few challenges which make > implementation a little tricky as you mentioned in your > commentary on the colors in SwissPDBviewer: > > 1) One can use the OpenGL accumulation buffer along with glColorMask() > to draw the scene with the blue/red filtering enabled for each eye. > This solution has the disadvantage that not all OpenGL implementations > provide a workable accumulation buffer. Some implement the accumulation > buffer entirely in software, which can be _very_ slow. Paul Bourke has > a web page that discusses this: > http://astronomy.swin.edu.au/pbourke/opengl/redblue/ > > 2) One could use a fully-stereo-capable video board, with quad-buffered > stereo (front/back/left/right color buffers) and simply enable the > color mask using glColorMask() before drawing the left and right images > respectively. This solution assumes that the video hardware can do > quad-buffered stereo, but I believe there are more boards that support > stereo in hardware than support an accumulation buffer in hardware. > This solution would probably be easy to implement in an existing > stereo-capable molecular visualization program, I will try it out > in VMD when I get back from a conference next week and if it works out, > It'll show up in the next release of VMD. > > 3) There is a problem with both of these solutions in that certain color > combinations in your molecule will look very bad when viewed in anaglyph > stereo. Only grayscale images will appear entirely correct in both eyes, > but this is a big sacrifice to make, to give up all coloring of the > molecule. Perhaps its "ok" to color your molecule semi-normally and > allow glColorMask() to chop out the red/blue components. As long as > the user has fine control over the coloring of her molecule, it should > be possible to tweak the scene to look good even in anaglyph mode. > Here is another web page which has some brief coverage of color issues > with anaglyph stereo: > http://www.cs.jhu.edu/~acw3f/cg/project/intro.html#problems > Making the colors look passable in anaglyph stereo is probably a > bigger challenge than the actual rendering techniques in 1) and 2). > It sounds like SwissPDBviewer takes the approach of forcing the > molecule to grayscale as a first step. Does SwissPDBviewer pass the > green color channel at all when it draws, or does it only pass red > and blue? Those details matter a fair amount. This is where I'd > expect the trouble to arise with implementing in VMD, making the colors > look half-decent. > > I'll make an attempt at implementing 2) in VMD, and see if it works well, > it should be a small hack to the existing CrystalEyes stereo mode, and > should be able to render at 100% full-speed on any machine that has > quad-buffered stereo. The accumulation buffer technique on Paul Bourke's > page could also be implemented, but VMD isn't smart enough to manage an > accumulation buffer well at present, and most current video boards do not > implement the accumulation buffer in hardware. > > I strongly encourage any other molecular visualization software developers > to chime in on this topic, I'd be curious to hear what other solutions people > have for doing anaglyph stereo in real-time... > > Thanks, > John Stone > vmd@ks.uiuc.edu > > > On Thu, Mar 15, 2001 at 10:14:29AM +0000, Marc BAADEN wrote: > > > > Hi, > > > > yet another question. > > > > Having discovered the power of anaglyphic stereo representations > > (those images which use red/blue glasses) recently, I wonder why > > there are no molecular viewers out there, which support such a > > display in real time (except SwissPDBviewer, see note below). > > > > In fact I have tried (and succeeded) to create a 3D anaglyphic image > > of a molecule from VMD, and it proved very easy and the result was > > very convincing. The only problem is that it is not interactive and > > you thus get a static view only. > > > > Is anybody aware of a molecular viewer with real-time display in > > anaglyphic stereo ? > > > > Would anybody be interested in including such a feature in an existing > > viewer ? (I would like to do it, but I think it exceeds my programming > > capacities/available time). > > > > NOTE 1: > > ------- > > > > For those who are interested, here how to get an anaglyphic stereo > > image from VMD: > > > > Step-by-step instructions (with VMD) > > > > 1.Display your system in the view you like. > > 2.choose Stereo/Left in the Display menu > > 3.choose snapshot in the Render menu > > 4.save e.g. as left.rgb > > 5.choose Stereo/Right in the Display menu > > 6.choose snapshot in the Render menu > > 7.save e.g. as right.rgb > > 8.on the command line, type > > combine -stereo left.rgb right.rgb snap.rgb > > (this requires that ImageMagick is installed) > > 9.convert to any format you like, for example gif > > convert snap.rgb snap.gif > > (this requires that ImageMagick is installed) > > > > NOTE 2: > > ------- > > > > SwissPDBViewer > > > > This viewer has an option to display anaglyphic stereo in realtime. > > Two things annoyed me very much: > > > > a) The stereo image is only monochrome, and very "basic" concerning the > > display features. > > > > b) The quality was VERY bad (especially compared to a stereo image from > > VMD), and I couldn't figure out how to possibly adjust the stereo > > red/blue color settings to improve it. > > > > > > Thank you in advance, > > > > Marc Baaden > > > > -- > > Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University > > mailto:baaden@smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de > > FAX/Voice +49 40333 968508 - Tel: +44 1865 275380 or +33 609 843217 > > > > > > > > -= 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 > > > > > > > > > > > > > > -- > NIH Resource for Macromolecular Modeling and Bioinformatics > Beckman Institute for Advanced Science and Technology > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 > Email: johns@ks.uiuc.edu Phone: 217-244-3349 > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns@ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From chemistry-request@server.ccl.net Thu Mar 15 12:38:57 2001 Received: from alien.biochem.wfubmc.edu ([152.11.118.46]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FHcvD19156 for ; Thu, 15 Mar 2001 12:38:57 -0500 Received: from localhost (zhangxd@localhost) by alien.biochem.wfubmc.edu (SGI-8.9.3/8.9.3) with ESMTP id MAA36007; Thu, 15 Mar 2001 12:37:56 -0500 (EST) Date: Thu, 15 Mar 2001 12:37:56 -0500 From: Zhangxd To: Marc BAADEN cc: CHEMISTRY@ccl.net, warren@sunesis-pharma.com, sangeeta@bioinfo.ernet.in Subject: about sybyl In-Reply-To: <200103151005.KAA05340@localhost.ox.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi, everyone I build a small molecule with xleap in AMBER, then save the pdb file, then use to SYBYL to save mol2 file for the AUTODOCK. But when I use SYBYL (I am newer for SYBYL) to generate the mol2 file, it says: 33 16 36 1 34 19 20 2 35 19 21 1 36 21 37 1 37 21 38 1 38 21 39 1 @SUBSTRUCTURE 1 **** 1 TEMP 0 **** **** 0 ROOT @SET UNK_ATOMS STATIC ATOMS AMSOM **** Atom types guessed for these atoms 22 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 \ 20 21 22 When I used the build/edit in sybyl, I did not find out the error. Thank you for your reply and suggestion. With best regards, xiaodong From chemistry-request@server.ccl.net Thu Mar 15 13:34:01 2001 Received: from cougar.it.wsu.edu (root@[134.121.1.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FIY0D19402 for ; Thu, 15 Mar 2001 13:34:00 -0500 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cougar.it.wsu.edu (8.9.3/8.9.3) with SMTP id KAA14721; Thu, 15 Mar 2001 10:32:19 -0800 (PST) Message-ID: <006501c0ad7e$404a0050$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: "Eugene Leitl" , "art'" Cc: "Yubo Fan" , "Familia Esguerra Neira" , References: Subject: Re: CCL:Short Budget Date: Thu, 15 Mar 2001 10:32:12 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hi Eugene, > (where latency or bandwidth may be the bottleneck). The only meaningful > benchmark is your application. Not to start a flamer here or anything, but this thread has a very specific application in mind - Gaussian98. All of this discussion (at least what I've seen thus far) is all related to the hardware factors that affect G98 computation efficiency. So your post is correct in that it doesn't say anything that is incorrect, but at the same time give us credit for knowing what the topic is for what we are still talking about. Respectfully, Phillip Matz ----- Original Message ----- From: "Eugene Leitl" To: "art'" Cc: "Yubo Fan" ; "Familia Esguerra Neira" ; Sent: Thursday, March 15, 2001 3:05 AM Subject: CCL:Short Budget > On Wed, 14 Mar 2001, art' wrote: > > > The bottleneck, usually, is the M/B bus, RAM and L2 Cache. If to choose the best and the > > The bottleneck is specific to the problem. Some codes run entirely within > L2 (or even L1) cache, some thrash cache, so bandwith to memory becomes > relevant, some stream a lot to nonvolatile storage or across network > (where latency or bandwidth may be the bottleneck). The only meaningful > benchmark is your application. > > > most expensive CPU with highest core performance, what is the overall performance when > > M/B and RAM are far behind with speed and performance ? Athlon has better choice choosing > > M/B and Cache. So DDRAM, which performs two r or wr functions per clock, could serve well > > increasing the total performance too. > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Mar 15 15:23:39 2001 Received: from mail.chem.tamu.edu ([165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FKNdD20384 for ; Thu, 15 Mar 2001 15:23:39 -0500 Received: from mail.chem.tamu.edu ([165.91.177.32]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu; Thu, 15 Mar 2001 14:24:05 -0600 Sender: yubo@ccl.net Message-ID: <3AB12566.A0444B6A@mail.chem.tamu.edu> Date: Thu, 15 Mar 2001 20:26:14 +0000 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: zh-CN, en MIME-Version: 1.0 To: "Phillip D. Matz" CC: Eugene Leitl , "art'" , Familia Esguerra Neira , chemistry@ccl.net Subject: Re: CCL:Short Budget References: <006501c0ad7e$404a0050$b4297986@chem.wsu.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I really agree with Phillip. PC is a very good choice to do QM computations. But there are still some problems when you run jobs on Linux and PC. Sometimes, the system will jammed or respond very very slowly if you run some large DFT jobs (> 1000 basis functions) for a long time. Anyway, UNIX workstations can finish some jobs more efficiently than PCs. I love PCs because it's far cheaper and the speed of running DFT calculations is good. Yubo "Phillip D. Matz" wrote: > Hi Eugene, > > > (where latency or bandwidth may be the bottleneck). The only meaningful > > benchmark is your application. > > Not to start a flamer here or anything, but this thread has a very specific > application in mind - Gaussian98. All of this discussion (at least what > I've seen thus far) is all related to the hardware factors that affect G98 > computation efficiency. So your post is correct in that it doesn't say > anything that is incorrect, but at the same time give us credit for knowing > what the topic is for what we are still talking about. > > Respectfully, > > Phillip Matz > > ----- Original Message ----- > From: "Eugene Leitl" > To: "art'" > Cc: "Yubo Fan" ; "Familia Esguerra Neira" > ; > Sent: Thursday, March 15, 2001 3:05 AM > Subject: CCL:Short Budget > > > On Wed, 14 Mar 2001, art' wrote: > > > > > The bottleneck, usually, is the M/B bus, RAM and L2 Cache. If to choose > the best and the > > > > The bottleneck is specific to the problem. Some codes run entirely within > > L2 (or even L1) cache, some thrash cache, so bandwith to memory becomes > > relevant, some stream a lot to nonvolatile storage or across network > > (where latency or bandwidth may be the bottleneck). The only meaningful > > benchmark is your application. > > > > > most expensive CPU with highest core performance, what is the overall > performance when > > > M/B and RAM are far behind with speed and performance ? Athlon has > better choice choosing > > > M/B and Cache. So DDRAM, which performs two r or wr functions per clock, > could serve well > > > increasing the total performance too. > > I think CPU is the most important, memory and bus clock are second. Right? There is a balance between them. -- ============================================================ Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ From chemistry-request@server.ccl.net Thu Mar 15 16:57:54 2001 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FLvrD21158 for ; Thu, 15 Mar 2001 16:57:53 -0500 Received: from [129.187.43.64] by mailout.lrz-muenchen.de with ESMTP; Thu, 15 Mar 2001 22:57:52 +0100 Sender: Eugene.Leitl@lrz.uni-muenchen.de Message-Id: <3AB13A67.B9476D32@lrz.uni-muenchen.de> Date: Thu, 15 Mar 2001 22:55:51 +0100 From: Eugene.Leitl@lrz.uni-muenchen.de X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.17-21mdksecure i586) X-Accept-Language: en, de-DE, ru MIME-Version: 1.0 To: "Phillip D. Matz" CC: "art'" , Yubo Fan , Familia Esguerra Neira , chemistry@ccl.net Subject: Re: CCL:Short Budget References: <006501c0ad7e$404a0050$b4297986@chem.wsu.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit "Phillip D. Matz" wrote: > Not to start a flamer here or anything, but this thread has a very specific > application in mind - Gaussian98. All of this discussion (at least what Oh, we're still talking about Gaussian98? Sorry, I thought the thread sidetracked. Of course in this case the problem is not underdefined. > I've seen thus far) is all related to the hardware factors that affect G98 > computation efficiency. So your post is correct in that it doesn't say > anything that is incorrect, but at the same time give us credit for knowing > what the topic is for what we are still talking about. Athlons seem to not be able to make much use from DDR SDRAM's higher bandwidth, but Gaussian98 might be different in this case. It will be interesting to compare it with Gaussian98 benchmarks on dual-Athlong DDR systems (a well-known Beowulfer is currently running a few benchmarks, hopefully it will include Gaussian98). From chemistry-request@server.ccl.net Thu Mar 15 15:08:37 2001 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FK8bD20233 for ; Thu, 15 Mar 2001 15:08:37 -0500 Received: from cornell.edu ([132.236.170.133]) by cornell.edu (8.9.3/8.9.3) with ESMTP id PAA21405 for ; Thu, 15 Mar 2001 15:08:38 -0500 (EST) Message-ID: <3AB12069.9091FDB5@cornell.edu> Date: Thu, 15 Mar 2001 15:04:57 -0500 From: "J. D. Gans" X-Mailer: Mozilla 4.76 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Qmol: Molecular viewer for Windows Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Qmol is a OpenGL based program for viewing molecular structures and animating molecular trajectories. It runs under Windows 95/98/NT/00 and supports the following features: (*) Generate AVI movies from a molecular trajectory. (*) Print to any Windows supported printer (at the resolution of the printer!) and copy images to the Windows clip board. (*) Display wire frame, stick figure, ball and stick, point and space-filling molecular structures from a PDB file. (*) Animate molecular trajectories stored in the DCD file format (both big- and little-endian). (*) Kabsch rotate all structures in a trajectory against the initial structure. (*) Interactively measure bond lengths, bond angles and torsion angles. (*) Dynamically adjust user selected torsion angles. (*) Display atom labels. (*) Display coordinate axis. (*) Dynamic modification of the color scheme (including color-by-element, color-by-atom-number, color-by-temperature and color-by-occupancy). (*) Dynamic lighting. (*) Adjust atomic radii (including radii-by-temperature and radii-by-occupancy). The source code and binary executable are freely available from http://lancelot.bio.cornell.edu/jason/qmol.html Jason Gans Shalloway Lab Department of Molecular Biology & Genetics Cornell University From chemistry-request@server.ccl.net Thu Mar 15 17:42:10 2001 Received: from cougar.it.wsu.edu (root@[134.121.1.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2FMgAD21700 for ; Thu, 15 Mar 2001 17:42:10 -0500 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cougar.it.wsu.edu (8.9.3/8.9.3) with SMTP id OAA23247; Thu, 15 Mar 2001 14:41:57 -0800 (PST) Message-ID: <001701c0ada1$1f6b00a0$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: Cc: "art'" , "Yubo Fan" , "Familia Esguerra Neira" , References: <006501c0ad7e$404a0050$b4297986@chem.wsu.edu> <3AB13A67.B9476D32@lrz.uni-muenchen.de> Subject: Re: CCL:Short Budget Date: Thu, 15 Mar 2001 14:41:49 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 > bandwidth, but Gaussian98 might be different in this case. It will be Yeah, I'm really curious how well G98 takes advantage of the extra bandwidth of DDR SDRAM. My own tests regarding the Athlon with PC100 and PC133 (CAS2 and 3) indicated that G98 was indifferent to the CAS latency but really benefited by the increase in effective bandwidth in going from PC100 to PC133 (ie by changing the memory FSB asynchronously with the KT133 chipset). > systems (a well-known Beowulfer is currently running a few benchmarks, I doubt Dr. Brown will be benchmarking G98 on the dual-athlon rig but it would be nice (I don't think he has a license but I may be wrong here). Of course I should be asking him rather than lamenting about it here on the CCL I suppose. At any rate it would be nice to have some numbers on a P4 system with the dual-channel rambus just to see if the extra bandwidth really boosts the effective IPC for G98 code (although I doubt it will lower the price/performance enough to justify the cost) simply as a matter of curiosity. ----- Original Message ----- From: To: "Phillip D. Matz" Cc: "art'" ; "Yubo Fan" ; "Familia Esguerra Neira" ; Sent: Thursday, March 15, 2001 1:55 PM Subject: Re: CCL:Short Budget > "Phillip D. Matz" wrote: > > > Not to start a flamer here or anything, but this thread has a very specific > > application in mind - Gaussian98. All of this discussion (at least what > > Oh, we're still talking about Gaussian98? Sorry, I thought the thread > sidetracked. Of course in this case the problem is not underdefined. > > > I've seen thus far) is all related to the hardware factors that affect G98 > > computation efficiency. So your post is correct in that it doesn't say > > anything that is incorrect, but at the same time give us credit for knowing > > what the topic is for what we are still talking about. > > Athlons seem to not be able to make much use from DDR SDRAM's higher > bandwidth, but Gaussian98 might be different in this case. It will be > interesting to compare it with Gaussian98 benchmarks on dual-Athlong DDR > systems (a well-known Beowulfer is currently running a few benchmarks, > hopefully it will include Gaussian98). >