From chemistry-request@server.ccl.net Thu Aug 12 05:08:22 1999 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA23203 for ; Thu, 12 Aug 1999 05:08:21 -0400 Message-Id: <199908120908.FAA23203@server.ccl.net> Received: from anti02 (193.6.134.181) by tigris.klte.hu (MX V5.1 Vn6f) with SMTP for ; Thu, 12 Aug 1999 11:01:27 +0200 Comments: Authenticated sender is From: "Tamas Gunda" To: chemistry@ccl.net Date: Thu, 12 Aug 1999 12:05:25 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: CCL:software for preparing input file for large molecul Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) > From: Pradipta Bandyopadhyay > Dear CCL members, > I have a question about the preparation of input file for large molecules. > It is hard to use z-matrix input for a large molecule. So I decided to use > some drawing software to draw the molecule and then extract the coordinates > using 'BABEL'. I have been using ISIS Draw 2.2.1. However, all structures > drawn by me are coming as planar i.e. Z-coordinates are all zero. My > question is > Am I making some mistake or is it intrinsic to ISIS? > and > is there any other software, which can do the things better? > and > what is the standard way of generating input file for a large molecule > (say, has 100 atoms) i.e. my way is correct or not? > Thanks for your help. I will summarize the replies. > Pradipta Dear Pradipta, ISIS Draw is a sketch program, so you can create only "flat" molecules in 2D. You need something to convert them into real 3D molecules. There are a lot of modeling programs for this. As a quick solution, you can download from the ACD LAbs homepage (www.acdlabs.com) a free plug-in for ISIS/Draw, which can make this conversion. You can then export the molecule as a 3D molfile into other programs Hope this helps best regards Tamas Gunda ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666-2479 Research Group of Antibiotics fax : (+36-52) 512914 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 http://dragon.klte.hu/~gundat H-4010 Debrecen Hungary ************************************************************************ From chemistry-request@server.ccl.net Thu Aug 12 05:23:05 1999 Received: from iris.inc.bme.hu (iris.inc.bme.hu [152.66.63.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA23289 for ; Thu, 12 Aug 1999 05:23:04 -0400 Received: from localhost (dino@localhost) by iris.inc.bme.hu (8.9.3/8.9.3) with ESMTP id KAA09734; Thu, 12 Aug 1999 10:19:08 +0100 (BUD) Date: Thu, 12 Aug 1999 10:19:08 +0100 From: Szieberth Denes To: Gary Kedziora cc: chemistry@ccl.net Subject: Re: CCL:Xeon processors In-Reply-To: <199908111419.JAA27164@mercury.chem.nwu.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Has anyone seen a comparison of the performance of a Xeon processor > with a straight Pentium II or III at the same (or nearly the same) > clock speed? I'm interested in performance comparisons using > the usual chemistry applications, good cache-optimized code-- > not implying there is no good cache-optimized chemistry code--or > any other benchmark. > Hi, I was testing a normal pII450 against a pII450 xeon with 1024 kb cache. The application was Gaussian94 compiled with the f2c-gcc combination, the tests jobs were geom. optimizations and freq. calculations on 10-atom molecules with 70-250 basis functions and the results were disappointing: the xeon was only about 5 % faster, despite the bigger and faster cache. dino dino@iris.inc.bme.hu From chemistry-request@server.ccl.net Tue Aug 10 00:03:37 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA06202 for ; Tue, 10 Aug 1999 00:03:37 -0400 Received: from hpdmraaa.compuserve.com (dh-img-rel-1.compuserve.com [149.174.206.132]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id XAA14414 for ; Mon, 9 Aug 1999 23:59:57 -0400 (EDT) Received: (from mailgate@localhost) by hpdmraaa.compuserve.com (8.8.8/8.8.8/HP-REL-1.2) id XAA01959 for chemistry@www.ccl.net; Mon, 9 Aug 1999 23:59:30 -0400 (EDT) Sender: tony@acdlabs.com Received: from noteb-tony.acdlabs.com (mid-qbu-nqf-vty5.as.wcom.net [216.192.98.5]) by hpdmraaa.compuserve.com (8.8.8/8.8.8/HP-REL-1.2) with SMTP id XAA01840; Mon, 9 Aug 1999 23:59:17 -0400 (EDT) Message-Id: <3.0.6.32.19990810000501.00797d10@mail.acdlabs.com> X-Sender: tony@mail.acdlabs.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Tue, 10 Aug 1999 00:05:01 -0700 To: tony@acdlabs.com From: Tony Williams Subject: New FREE Stuff Page from Advanced Chemistry Development Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id AAA06203 TORONTO: August 5th 1999 - ACD announces their NEW Free Stuff Web Page Here at Advanced Chemistry DEvelopment we are proud of the fact that our offer of free software to the chemical community has been welcomed and recently we celebrated over 23,000 downloads of our Chemsketch drawing software. We have continued to expand our list of downloads to include spectroscopy viewers and databases (hyperlinks). We have just unveiled a new web site to allow more intuitive access to these modules and have upgraded the site to include: Updates of FREE software to Version 4.0 Demo movies and presentations, Spectroscopic databases Sample ChemFolder Databases New Chembasic goodies and, by popular request all User's Guides are now available as PDF files. We are always looking for customer feedback to help improve our website so feel free to contact us at the Expanding Universe of Advanced Chemistry Development with your comments (info@acdlabs.com) *********************************************************                   Dr. Antony J. Williams                                U.S. Office                     20 Overland Trail,             West Henrietta, NY-14586                    Tel: 716-321-3528 Cellular: 716-820-0983                         Head Office             Advanced Chemistry Development Inc.       133 Richmond Street West, Suite 605,                Toronto, Ontario, M5H 2L3                                                                            E-mail: tony@acdlabs.com                                     http://www.acdlabs.com                                   Tel:  416-368-3435               Freefone: 1-800-304-3988                    Fax:416-368-5596 ********************************************************* From chemistry-request@server.ccl.net Tue Aug 10 05:07:10 1999 Received: from conserv.orm.mipt.ru (root@conserv.orm.mipt.ru [192.188.189.149]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA07406 for ; Tue, 10 Aug 1999 05:07:03 -0400 Received: from Losev ([192.168.1.43]) by conserv.orm.mipt.ru (8.8.7/8.8.7) with SMTP id NAA00611 for ; Tue, 10 Aug 1999 13:00:51 +0400 Message-ID: <007801bee30f$19971960$2b01a8c0@Losev.conserv.orm.mipt.ru> From: "Andrei Losev" To: Subject: WEB SITE Date: Tue, 10 Aug 1999 13:02:35 +0400 MIME-Version: 1.0 Content-Type: text/plain; charset="windows-1251" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.2106.4 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Dear Colleague, ChemDiv, Inc., combines the expertize in small molecule "historical" compound collections with combinatorial chemistry, custom synthesis and other chemistry development services for drug discovery The complete information regarding our research products and services you can find on our www.chemdiv.com site. We arranged the set of useful links on our site promoting an access of our customers to other useful resources (please, find "Software and Molecular Modeling" section on "Useful Links" page of our site). There we had placed a link to your site. We would appreciate if you could place a link to our site among analogous information on your web site. We hope, that visitors of your site might be interested in our products and services as well. If any terms applied we would very much appreciate sending us the list of such terms. Thank you, Best regards, Andrey Losev Marketing Manager ChemDiv, Inc. 11575 Sorrento Valley Road, Suit 210 San Diego, CA 92121 USA Tell: (619) 794 4860 Fax: (619) 794 4931 Email:maricont@glasnet.ru chemdiv@pacbell.net From chemistry-request@server.ccl.net Tue Aug 10 05:26:37 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA07468 for ; Tue, 10 Aug 1999 05:26:37 -0400 Received: from sun.rhrk.uni-kl.de (sun.rhrk.uni-kl.de [131.246.137.50]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id FAA18494 for ; Tue, 10 Aug 1999 05:22:50 -0400 (EDT) Received: from aix12.rhrk.uni-kl.de ( aix12.rhrk.uni-kl.de [131.246.137.12] ) by sun.rhrk.uni-kl.de id aa12560 ; 10 Aug 1999 11:24 MESZ Received: from aixd1.rhrk.uni-kl.de(really [131.246.137.210]) by aix12.rhrk.uni-kl.de via smtpd with smtp id for ; Tue, 10 Aug 1999 11:22:31 +0200 (MES) (Smail-3.2.0.95 1997-May-7 #6 built 1997-Sep-24) Received: by aixd1.rhrk.uni-kl.de via send-mail with stdio id for gerwalin@rhrk.uni-kl.de; Tue, 10 Aug 1999 11:22:29 +0200 (MES) (Smail-3.2.0.95 1997-May-7 #6 built 1997-Sep-24) Message-Id: Date: Tue, 10 Aug 1999 11:22:29 +0200 (MES) From: Elmar Gerwalin To: chemistry@www.ccl.net Subject: Good experimental Vibration Spectra ? Cc: gerwalin@rhrk.uni-kl.de Hi I'm looking for a source on good exerimental vibrational spectra to use them for comparison to my calculations. Do I have to search for each species separarely or is there a collection of such data available. The old IR/Raman collections (only pictures mostly) from the 70s are not up to date, I think. Of most interest is the knowledge of the fundamentals, the species I'm investigating are "normal" hydrocarbons (CH, CHO-compounds). I'd appreciate any help: links, hints, references Thanks in advance Elmar From chemistry-request@server.ccl.net Wed Aug 11 09:46:49 1999 Received: from hotmail.com (f165.law3.hotmail.com [209.185.241.165]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA18078 for ; Wed, 11 Aug 1999 09:46:49 -0400 Received: (qmail 3960 invoked by uid 0); 11 Aug 1999 13:40:54 -0000 Message-ID: <19990811134054.3959.qmail@hotmail.com> Received: from 158.43.128.105 by www.hotmail.com with HTTP; Wed, 11 Aug 1999 06:40:54 PDT X-Originating-IP: [158.43.128.105] From: "Y Z" To: chemistry@ccl.net Subject: 3D B-spline Interpolation Date: Wed, 11 Aug 1999 09:40:54 EDT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Dear all: Does anyone know any references about the numerical algorithms for the three-dimensional B spline interpolation? Are there any FORTRAN subroutine for this method? Your help will be highly appreciated. Y.Z _______________________________________________________________ Get Free Email and Do More On The Web. Visit http://www.msn.com From chemistry-request@server.ccl.net Wed Aug 11 11:16:07 1999 Received: from fer-net.fcq.unc.edu.ar (root@[200.16.18.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA18452 for ; Wed, 11 Aug 1999 11:15:48 -0400 Received: from fer-net.fcq.unc.edu.ar (IDENT:marcos@localhost [127.0.0.1]) by fer-net.fcq.unc.edu.ar (8.9.3/8.9.3) with SMTP id MAA03392 for ; Wed, 11 Aug 1999 12:05:37 -0400 From: Marcos Villarreal Organization: UNC, Dpto. Qca. Biol.-CIQUIBIC To: chemistry@ccl.net Subject: Parallel CHARMM Date: Wed, 11 Aug 1999 11:36:41 -0400 X-Mailer: KMail [version 1.0.17] Content-Type: text/plain MIME-Version: 1.0 Message-Id: <99081112053700.00628@fer-net.fcq.unc.edu.ar> Content-Transfer-Encoding: 8bit Dear all, For a cuple of weeks I been triying to compile a parralel version of CHARMM 26b1 in my dual PII 266 using Red Hat 6.0 with the 2.2.5smp kernel. I downloaded pvm 3.41, compiled it for smp (with the -DSHMEM key) and run the examples. All seems to work Ok. Then I compiled CHARMM with install.com gnu medium P. No errors but parallel don't work. Then I triyed with a pref.dat with PVM PARALLEL PARAFULL instead the provided with install.com. I don't worked nether. Also I downloaded the LAM 6.3 MPI implementation and acording to the test provided with the distribution it works OK on my machine. Then I compiled with CMPI PARALLEL PARAFULL in pref.dat. Again no errors diring the compilation but parallel dont work. Could anybody please help? Answers (if any) will be summarized. Thanks in advance. ----------------------------------------------- PhD student Marcos Villarreal Departamento de Quimica Biologica Facultad de Ciencias Quimicas Universidad Nacional de Cordoba From chemistry-request@server.ccl.net Wed Aug 11 16:08:52 1999 Received: from merlin.chemse.gatech.edu (merlin.chemse.gatech.edu [130.207.71.251]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA19850 for ; Wed, 11 Aug 1999 16:08:52 -0400 Received: from tedder (tedder.chemse.gatech.edu [130.207.75.15]) by merlin.chemse.gatech.edu (8.9.3/8.9.3) with SMTP id QAA00161 for ; Wed, 11 Aug 1999 16:04:09 -0400 (EDT) Reply-To: From: "Dan Tedder" To: Date: Wed, 11 Aug 1999 16:03:28 -0400 Message-ID: <003001bee434$93c1da60$0f4bcf82@tedder.chemse.gatech.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Is anyone aware of work using fractals to model molecular properties? Please advise and I'll summarize the responses. Dan Tedder School of Chemical Engineering 778 Atlantic Drive Georgia Institute of Technology Atlanta, GA 30332-0100 daniel.tedder@che.gatech.edu 404-894-2856 From chemistry-request@server.ccl.net Thu Aug 12 04:14:05 1999 Received: from ns.apbiotech.com (ns.apbiotech.com [192.36.117.130]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA22996 for ; Thu, 12 Aug 1999 04:14:05 -0400 From: Enrique.Carredano@eu.apbiotech.com Received: from mailgate.se.apbiotech.com (unverified [193.235.253.52]) by ns.apbiotech.com (Rockliffe SMTPRA 3.3.1) with ESMTP id for ; Thu, 12 Aug 1999 10:10:52 +0200 Received: from eunotes.apbiotech.com (unverified [193.180.20.124]) by mailgate.se.apbiotech.com (Rockliffe SMTPRA 3.3.1) with SMTP id for ; Thu, 12 Aug 1999 10:06:53 +0200 Received: by eunotes.apbiotech.com(Lotus SMTP MTA v4.6.3 (778.2 1-4-1999)) id 412567CB.00322196 ; Thu, 12 Aug 1999 10:07:33 +0100 X-Lotus-FromDomain: XYNET To: chemistry@ccl.net Message-ID: <412567CB.00321D9B.00@eunotes.apbiotech.com> Date: Thu, 12 Aug 1999 10:13:14 +0100 Subject: dipole-dipole in protein-protein interactions Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Does anyone know of a good review article about the significance of dipole-dipole interactions in protein-ligand and protein-protein binding? Enrique Carredano, MSc, PhD +46 18 16 50 00 tel Polymer and Surface Chemistry +46 18 16 50 42 direct Amersham Pharmacia Biotech +46 18 16 63 96 fax Bjorkg 30, 751 84 Uppsala Sweden enrique.carredano@eu.apbiotech.com From chemistry-request@server.ccl.net Thu Aug 12 04:15:04 1999 Received: from kasei.materials.ox.ac.uk (kasei.materials.ox.ac.uk [163.1.64.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA23016 for ; Thu, 12 Aug 1999 04:15:02 -0400 Received: from localhost (hfield@localhost) by kasei.materials.ox.ac.uk (8.9.3/8.9.3) with ESMTP id JAA19404 for ; Thu, 12 Aug 1999 09:09:46 +0100 X-Authentication-Warning: kasei.materials.ox.ac.uk: hfield owned process doing -bs Date: Thu, 12 Aug 1999 09:09:46 +0100 (BST) From: Andrew Horsfield X-Sender: hfield@kasei.materials.ox.ac.uk Reply-To: Andrew Horsfield To: Computational Chemistry List Subject: Obtaining lowest 20% of eigenstates Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Together with colleagues at the Unversity of Oxford, I am developing an LCAO DFT code that handles solids as well as molecules. It makes use of numerical orbitals (somewhat akin to DMol3). For a cell containing 64 atoms of silicon with a DZP basis set (sp s*p* d), and using 4 kpoints, 95% of the time is spent on diagonalising the Hamiltonian (lapack is being used). Clearly a scheme that only generates the first few eigenstates (20%) is needed to reduce this time. What would people recommend? Contenders that I have encountered so far are Arpack and Lapack 3. Best regards, Andrew +----------------------------------------------------+ Andrew Horsfield e-mail: horsfield@fecit.co.uk FECIT, 2 Longwalk Road, Stockley Park, Uxbridge, Middlesex UB11 1AB, United Kingdom. phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422 +----------------------------------------------------+ From chemistry-request@server.ccl.net Thu Aug 12 06:45:30 1999 Received: from neon.chem.ucla.edu (neon.chem.ucla.edu [128.97.35.251]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA23603 for ; Thu, 12 Aug 1999 06:45:29 -0400 Received: from localhost (mdb@localhost) by neon.chem.ucla.edu (8.8.0/8.8.0) with SMTP id DAA17319; Thu, 12 Aug 1999 03:48:27 -0700 (PDT) X-Authentication-Warning: neon.chem.ucla.edu: mdb owned process doing -bs Date: Thu, 12 Aug 1999 03:48:27 -0700 (PDT) From: "Michael D. Bartberger" To: Szieberth Denes cc: Gary Kedziora , chemistry@ccl.net Subject: Re: CCL:Xeon processors In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Dino and Gary: Thanks for posting this; these are very valuable numbers to know, especially with the high price of the Xeon processors. Now, this only leaves me to wonder if anyone has been able to get hold of one of an AMD Athlon-based system for some testing.... it would appear that AMD has at last surpassed Intel, at least for now, in raw FPU performance. Some computing magazines and web sites have recieved test boxes and the results are surprising, to say the least! With best regards, -Michael Bartberger UCLA On Thu, 12 Aug 1999, Szieberth Denes wrote: > > > > Has anyone seen a comparison of the performance of a Xeon processor > > with a straight Pentium II or III at the same (or nearly the same) > > clock speed? I'm interested in performance comparisons using > > the usual chemistry applications, good cache-optimized code-- > > not implying there is no good cache-optimized chemistry code--or > > any other benchmark. > > > Hi, > I was testing a normal pII450 against a pII450 xeon with 1024 kb cache. > The application was Gaussian94 compiled with the f2c-gcc combination, the > tests jobs were geom. optimizations and freq. calculations on 10-atom > molecules with 70-250 basis functions and the results were disappointing: > the xeon was only about 5 % faster, despite the bigger and faster cache. > > dino > dino@iris.inc.bme.hu > > > > -= 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 Aug 12 12:09:51 1999 Received: from theo1.theochem.tu-muenchen.de (theo2.theochem.tu-muenchen.de [129.187.191.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA26248 for ; Thu, 12 Aug 1999 12:09:48 -0400 From: kcharoen@theochem.tu-muenchen.de Received: from theo3.theochem.tu-muenchen.de (theo3.theochem.tu-muenchen.de [129.187.157.6]) by theo1.theochem.tu-muenchen.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id SAA11490 for ; Thu, 12 Aug 1999 18:05:33 +0200 Received: by theo3.theochem.tu-muenchen.de (SMI-8.6/SMI-SVR4) id SAA28901; Thu, 12 Aug 1999 18:06:14 +0200 Date: Thu, 12 Aug 1999 18:06:14 +0200 Message-Id: <199908121606.SAA28901@theo3.theochem.tu-muenchen.de> To: chemistry@ccl.net Subject: BSSE should not affect gradient X-Sun-Charset: US-ASCII Dear CCL friends, BSSE accounts for some percents in the interaction energy computed from MO calculation based on supermolecule approach. There are several methods out there to correct the BSSE. I used to have a long debate with friends that if I only want to use the gradient not the energy, my calculation should not suffer from BSSE. I tried to explain to him that the BSSE-corrected potential energy surface (PES) should get along with the uncorrected one smoothly, if not parallely. Yes, the depth may be different but slope should be equal. I have made some calculations to prove my idea and I think it works. However, he may say that this works only for some system. Question is ..... does BSSE affect gradient ? Is there any theory or paper doing on this issue ? I need only the answer but some clever man could take this to make a publication. Thanks and I hope to hear from you. best wishes, Teerakiat ------------------------------------------------------------------------ Teerakiat Kerdcharoen, Ph.D. Profession: University Lecturer Address: Department of Physics, Faculty of Science Mahidol University, Bangkok 10400 THAILAND Office: (66)(2)2461381 FAX (66)(2)2461381 Cellular: (66)(1)9031130 Home: (66)(2)5893099 FAX (66)(2)9547395 E-mail: sctkc@mahidol.ac.th, noy@atc.atccu.chula.ac.th WWW: http://einstein.sc.mahidol.ac.th/simulation Research: Molecular Simulation / Computational Nanotechnology ICQ number: Unusable now, please see again in the future ..... ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Aug 12 13:58:33 1999 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA27146 for ; Thu, 12 Aug 1999 13:58:33 -0400 Received: from tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.20.129]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with ESMTP id NAA16555; Thu, 12 Aug 1999 13:54:20 -0400 Sender: richard@tc.cornell.edu Message-ID: <37B30A4C.A1894E1E@tc.cornell.edu> Date: Thu, 12 Aug 1999 13:54:20 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.2 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Y Z CC: chemistry@ccl.net Subject: Re: CCL:3D B-spline Interpolation References: <19990811134054.3959.qmail@hotmail.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Y Z wrote: > > Dear all: > > Does anyone know any references about the numerical algorithms > for the three-dimensional B spline interpolation? Are there any > FORTRAN subroutine for this method? "A Practical Guide to Splines" by Carl de Boor Applied Mathematical Sciences Vol 27 Springer-Verlag 1985 (QA1.A647) is a classic text that contains Fortran code listings. Perhaps practical to applied mathematicians but I find it impenetrable A much easier book is "The NURBS Book" Les Piegl and Wayne Tiller Chaps 2,3 Springer, New York QA 224 .P54x 1995 It contains short snippets of highly optimized C code that could be translated to Fortran without too much trouble (if you must). Beware: the B-spline formula is easy to apply incorrectly. Make sure your knot vectors and control points are centered on the interval containing the point to be evaluated. You are also welcome to my version of the code (C++). Richard Gillilan Cornell Theory Center ps. May I ask why you are interested? From chemistry-request@server.ccl.net Thu Aug 12 20:19:34 1999 Received: from proxy4.ba.best.com (root@proxy4.ba.best.com [206.184.139.15]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA01273 for ; Thu, 12 Aug 1999 20:19:33 -0400 Received: from acc7 (dynamic31.pm03.san-mateo.best.com [205.149.174.159]) by proxy4.ba.best.com (8.9.3/8.9.2/best.out) with SMTP id RAA11545; Thu, 12 Aug 1999 17:14:09 -0700 (PDT) Message-ID: <00a501bee520$e5aa25c0$9fae95cd@vip.best.com> From: "Nicholas Sobb" To: "Jon Sorenson" Cc: References: Subject: Re: CCL:cLogP calculator Date: Thu, 12 Aug 1999 17:13:27 -0700 Organization: Comgenex 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 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 > > Subj: cLogP calculator > > > Hello, We have an ISIS database for our synthetic compound collection > > (>20,000 cmpds right now). We would like to add a well-validated > > computational package for determining cLogP values. Any suggestions out > > there? Thanks in advance! CompuDrug's PrologP: Predicts partition coefficient of organic compounds in octonal/water system. Combines three different estimation methods based upon the compound fragment/atoms. Available in Windows and UNIX platforms. DLL predictive engine for is available for in-house software developers. Demo available at www.compudrug.com Also available are programs predicting physico-chemical parameters (pKalc, PrologP and PrologD), metabolism pathways (MetabolExpert), toxic effects (HazardExpert) of compounds and assisting in HPLC method development (EluEx). Sincerely, Nicholas Sobb From chemistry-request@server.ccl.net Thu Aug 12 14:12:18 1999 Received: from hotmail.com (f55.law3.hotmail.com [209.185.241.55]) by server.ccl.net (8.8.7/8.8.7) with SMTP id OAA27260 for ; Thu, 12 Aug 1999 14:12:18 -0400 Received: (qmail 82631 invoked by uid 0); 12 Aug 1999 18:06:14 -0000 Message-ID: <19990812180614.82630.qmail@hotmail.com> Received: from 128.205.126.41 by www.hotmail.com with HTTP; Thu, 12 Aug 1999 11:06:13 PDT X-Originating-IP: [128.205.126.41] From: "Y Z" To: tjo@acm.org, yz0@hotmail.com, chemistry@ccl.net Subject: Re: CCL:3D B-spline Interpolation Date: Thu, 12 Aug 1999 14:06:13 EDT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Thank you for your message. I checked that book: "Numerical Recipes in FORTRAN 77" 2nd Edition (Vol1) William H. Press The algorithem is Bicubic Interpolation but not the B-spline interpolation. Can you specify which pages for your algorithm? Thank you for your help. Y.Z. >From: TJ O'Donnell >Reply-To: tjo@acm.org >To: Y Z , chemistry@ccl.net >Subject: Re: CCL:3D B-spline Interpolation >Date: Thu, 12 Aug 1999 10:34:02 -0500 > >There is an algorithm in "Numerical Recipes" >for multi-dimensional B-spline interpolation. >The code is there too, in Fortran or C. Take your pick. > >TJ O'Donnell >tjo@acm.org > >Y Z wrote: > > > > Dear all: > > > > Does anyone know any references about the numerical algorithms > > for the three-dimensional B spline interpolation? Are there any > > FORTRAN subroutine for this method? > > > > Your help will be highly appreciated. > > > > Y.Z > > > > _______________________________________________________________ > > Get Free Email and Do More On The Web. Visit http://www.msn.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 _______________________________________________________________ Get Free Email and Do More On The Web. Visit http://www.msn.com From chemistry-request@server.ccl.net Thu Aug 12 13:39:45 1999 Received: from mail.rdc1.sdca.home.com (imail@ha1.rdc1.sdca.home.com [24.0.3.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA27015 for ; Thu, 12 Aug 1999 13:39:44 -0400 Received: from home.com ([24.5.251.87]) by mail.rdc1.sdca.home.com (InterMail v4.01.01.00 201-229-111) with ESMTP id <19990812173532.PZPS16727.mail.rdc1.sdca.home.com@home.com>; Thu, 12 Aug 1999 10:35:32 -0700 Message-ID: <37B2E96A.5FC69737@home.com> Date: Thu, 12 Aug 1999 10:34:02 -0500 From: "TJ O'Donnell" Reply-To: tjo@acm.org X-Mailer: Mozilla 4.51 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: Y Z , chemistry@ccl.net Subject: Re: CCL:3D B-spline Interpolation References: <19990811134054.3959.qmail@hotmail.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit There is an algorithm in "Numerical Recipes" for multi-dimensional B-spline interpolation. The code is there too, in Fortran or C. Take your pick. TJ O'Donnell tjo@acm.org Y Z wrote: > > Dear all: > > Does anyone know any references about the numerical algorithms > for the three-dimensional B spline interpolation? Are there any > FORTRAN subroutine for this method? > > Your help will be highly appreciated. > > Y.Z > > _______________________________________________________________ > Get Free Email and Do More On The Web. Visit http://www.msn.com > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Aug 12 13:32:15 1999 Received: from relay1.smtp.psi.net (relay1.smtp.psi.net [38.8.14.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA26909 for ; Thu, 12 Aug 1999 13:32:15 -0400 Received: from [206.232.104.11] (helo=gcd.ara.com) by relay1.smtp.psi.net with smtp (Exim 1.90 #1) id 11Eydy-0000mY-00; Thu, 12 Aug 1999 13:28:00 -0400 Received: from POP3 Client by gcd.ara.com (ccMail Link to SMTP R8.20.00.25) id AA934478494; Thu, 12 Aug 1999 12:21:45 -0600 Message-Id: <9908129344.AA934478494@gcd.ara.com> X-Mailer: ccMail Link to SMTP R8.20.00.25 Date: Thu, 12 Aug 1999 03:48:27 -0600 From: "Michael D. Bartberger" To: Cc: , , , Subject: CCL:Xeon processors MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="simple boundary" --simple boundary Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: "cc:Mail Note Part" Dear Dino and Gary: Thanks for posting this; these are very valuable numbers to know, especially with the high price of the Xeon processors. Now, this only leaves me to wonder if anyone has been able to get hold of one of an AMD Athlon-based system for some testing.... it would appear that AMD has at last surpassed Intel, at least for now, in raw FPU performance. Some computing magazines and web sites have recieved test boxes and the results are surprising, to say the least! With best regards, -Michael Bartberger UCLA On Thu, 12 Aug 1999, Szieberth Denes wrote: > > > > Has anyone seen a comparison of the performance of a Xeon processor > > with a straight Pentium II or III at the same (or nearly the same) > > clock speed? I'm interested in performance comparisons using > > the usual chemistry applications, good cache-optimized code-- > > not implying there is no good cache-optimized chemistry code--or > > any other benchmark. > > > Hi, > I was testing a normal pII450 against a pII450 xeon with 1024 kb cache. > The application was Gaussian94 compiled with the f2c-gcc combination, the > tests jobs were geom. optimizations and freq. calculations on 10-atom > molecules with 70-250 basis functions and the results were disappointing: > the xeon was only about 5 % faster, despite the bigger and faster cache. > > dino > dino@iris.inc.bme.hu > > > > > > > > > -= 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 --simple boundary-- From chemistry-request@server.ccl.net Thu Aug 12 15:48:09 1999 Received: from relay1.smtp.psi.net (relay1.smtp.psi.net [38.8.14.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA27845 for ; Thu, 12 Aug 1999 15:48:08 -0400 Received: from [206.232.104.11] (helo=gcd.ara.com) by relay1.smtp.psi.net with smtp (Exim 1.90 #1) id 11F0lW-0000Vv-00; Thu, 12 Aug 1999 15:43:56 -0400 Received: from POP3 Client by gcd.ara.com (ccMail Link to SMTP R8.20.00.25) id AA934486655; Thu, 12 Aug 1999 14:37:41 -0600 Message-Id: <9908129344.AA934486655@gcd.ara.com> X-Mailer: ccMail Link to SMTP R8.20.00.25 Date: Thu, 12 Aug 1999 13:54:20 -0600 From: Richard Gillilan To: Cc: , Subject: CCL:3D B-spline Interpolation MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="simple boundary" --simple boundary Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: "cc:Mail Note Part" Y Z wrote: > > Dear all: > > Does anyone know any references about the numerical algorithms > for the three-dimensional B spline interpolation? Are there any > FORTRAN subroutine for this method? "A Practical Guide to Splines" by Carl de Boor Applied Mathematical Sciences Vol 27 Springer-Verlag 1985 (QA1.A647) is a classic text that contains Fortran code listings. Perhaps practical to applied mathematicians but I find it impenetrable A much easier book is "The NURBS Book" Les Piegl and Wayne Tiller Chaps 2,3 Springer, New York QA 224 .P54x 1995 It contains short snippets of highly optimized C code that could be translated to Fortran without too much trouble (if you must). Beware: the B-spline formula is easy to apply incorrectly. Make sure your knot vectors and control points are centered on the interval containing the point to be evaluated. You are also welcome to my version of the code (C++). Richard Gillilan Cornell Theory Center ps. May I ask why you are interested? -= 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 --simple boundary-- From chemistry-request@server.ccl.net Thu Aug 12 16:14:13 1999 Received: from dqo.fcq.unc.edu.ar (arloa@dqo.fcq.unc.edu.ar [200.16.18.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA28066 for ; Thu, 12 Aug 1999 16:14:06 -0400 Received: from localhost (arloa@localhost) by dqo.fcq.unc.edu.ar (8.8.7/8.8.7) with ESMTP id RAA24906 for ; Thu, 12 Aug 1999 17:15:33 -0300 Date: Thu, 12 Aug 1999 17:15:33 -0300 (ART) From: Marcos Villarreal To: chemistry@ccl.net Subject: Parallel CHARMM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, For a cuple of weeks I been triying to compile a parralel version of CHARMM 26b1 in my dual PII 266 using Red Hat 6.0 with the 2.2.5smp kernel. I downloaded pvm 3.41, compiled it for smp (with the -DSHMEM key) and run the examples. All seems to work Ok. Then I compiled CHARMM with install.com gnu medium P. No errors but parallel don't work. Then I triyed with a pref.dat with PVM PARALLEL PARAFULL instead the provided with install.com. I don't worked nether. Also I downloaded the LAM 6.3 MPI implementation and acording to the test provided with the distribution it works OK on my machine. Then I compiled with CMPI PARALLEL PARAFULL in pref.dat. Again no errors diring the compilation but parallel dont work. Could anybody please help? Answers (if any) will be summarized. Thanks in advance. PhD student Marcos Villarreal Departamento de Quimica Biologica. Facultad de Ciencias Quimicas. Universidad Nacional de Cordoba. Argentina. From chemistry-request@server.ccl.net Thu Aug 12 20:33:18 1999 Received: from relay1.smtp.psi.net (relay1.smtp.psi.net [38.8.14.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA01359 for ; Thu, 12 Aug 1999 20:33:18 -0400 Received: from [206.232.104.11] (helo=gcd.ara.com) by relay1.smtp.psi.net with smtp (Exim 1.90 #1) id 11F5EB-0000tn-00; Thu, 12 Aug 1999 20:29:48 -0400 Received: from POP3 Client by gcd.ara.com (ccMail Link to SMTP R8.20.00.25) id AA934503808; Thu, 12 Aug 1999 19:23:33 -0600 Message-Id: <9908129345.AA934503808@gcd.ara.com> X-Mailer: ccMail Link to SMTP R8.20.00.25 Date: Thu, 12 Aug 1999 17:13:27 -0600 From: "Nicholas Sobb" To: Cc: , Subject: CCL:cLogP calculator MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="simple boundary" --simple boundary Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: "cc:Mail Note Part" > > Subj: cLogP calculator > > > Hello, We have an ISIS database for our synthetic compound collection > > (>20,000 cmpds right now). We would like to add a well-validated > > computational package for determining cLogP values. Any suggestions out > > there? Thanks in advance! CompuDrug's PrologP: Predicts partition coefficient of organic compounds in octonal/water system. Combines three different estimation methods based upon the compound fragment/atoms. Available in Windows and UNIX platforms. DLL predictive engine for is available for in-house software developers. Demo available at www.compudrug.com Also available are programs predicting physico-chemical parameters (pKalc, PrologP and PrologD), metabolism pathways (MetabolExpert), toxic effects (HazardExpert) of compounds and assisting in HPLC method development (EluEx). Sincerely, Nicholas Sobb -= 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 --simple boundary-- From chemistry-request@server.ccl.net Thu Aug 12 23:07:51 1999 Received: from fg702-6.abct.polyu.edu.hk (fg702-6.abct.polyu.edu.hk [158.132.74.201]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA02210 for ; Thu, 12 Aug 1999 23:07:50 -0400 Received: from fg702-6.abct.polyu.edu.hk (dannt.polyu.edu.hk [158.132.31.49]) by fg702-6.abct.polyu.edu.hk (8.8.8/8.8.8) with ESMTP id LAA09662 for ; Fri, 13 Aug 1999 11:07:41 +0900 (HKST) Message-ID: <37B38ADE.23FAB177@fg702-6.abct.polyu.edu.hk> Date: Fri, 13 Aug 1999 11:02:54 +0800 From: Daniel Mok X-Mailer: Mozilla 4.61 [en] (Win95; I) X-Accept-Language: en,zh-TW,zh-CN MIME-Version: 1.0 To: CCL Subject: Computational requiremnet on relativistic method? Content-Type: text/plain; charset=big5 Content-Transfer-Encoding: 7bit Dear Sir, I am a beginner to the field of relativistic MO caln. (Dirac-Fock) I would like to know the computational requirement (CPU time and memory) for doing a geometry optimization. How does it compare to conventional SCF method and other correlated MO techniques? Thanks for any help. Regards, Daniel -- Office: (852)-2766 5629 Fax: (852)-2364 9932 Department of Applied Biology and Chemical Technology The Hong Kong Polytechnic University.