From chemistry-request@www.ccl.net Thu Feb 25 02:15:11 1999 Received: from fen.bilkent.edu.tr (leo.fen.bilkent.edu.tr [139.179.97.92]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id CAA27551 Thu, 25 Feb 1999 02:15:02 -0500 (EST) Received: from gunser.fen.bilkent.edu.tr by fen.bilkent.edu.tr (5.65c/1.4IDA) id AA20347; Thu, 25 Feb 1999 09:17:34 +0300 Received: by gunser.fen.bilkent.edu.tr (SMI-8.6/SMI-SVR4) id JAA27698; Thu, 25 Feb 1999 09:13:01 +0200 Date: Thu, 25 Feb 1999 07:13:00 +0000 (GMT) From: Ulrike Salzner To: "chaudash@aston.ac.uk" Cc: chemistry@www.ccl.net Subject: Re: CCL:Biological relevance of aluminium In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII There was a paper about the involvement of Al3+ in Alzheimer's desease some time ago in Accounts of Chemical Research. I could not find the reference quickly, but I am sure it is no more than 5 years old. Take a look. Uli Salzner =================================================================== Dr. Ulrike Salzner Department of Chemistry Tel.: (312) 290-2122 Bilkent University Fax.: (312) 266-5097 06533 Bilkent, Ankara e-mail: salzner@fen.bilkent.edu.tr Turkey ==================================================================== On Wed, 24 Feb 1999, chaudash@aston.ac.uk wrote: > Hello ccl'ers, > A while back I wrote asking if anyone knew of any biological > role for aluminium. To my knowledge there is no known relevance of > this metal in biological sytems. However I did receive a reply, > where someone mentioned that aluminium plays a part in alcohol > dehydrogenase. I have looked extensively to find out more to no > avail. I would be most grateful for any input. > Many thanks for your time > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: mailhub@aston.ac.uk > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From chemistry-request@www.ccl.net Thu Feb 25 06:03:36 1999 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA28535 Thu, 25 Feb 1999 06:03:36 -0500 (EST) Received: from esi21.ESI.UMontreal.CA (esi21.ESI.UMontreal.CA [132.204.2.91]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id GAA23357 for ; Thu, 25 Feb 1999 06:03:38 -0500 (EST) Received: from localhost (proynov@localhost) by esi21.ESI.UMontreal.CA with SMTP id GAA04707 (8.8.7/IDA-1.6 for ); Thu, 25 Feb 1999 06:03:37 -0500 (EST) X-Authentication-Warning: esi21.ESI.UMontreal.CA: proynov owned process doing -bs Date: Thu, 25 Feb 1999 06:03:37 -0500 (EST) From: Proynov Emil X-Sender: proynov@esi21.ESI.UMontreal.CA To: chemistry@www.ccl.net Subject: CCL: Comment on DFT & Hydrogen bonds Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, On Thu, 28 Jan 1999, Didier MATHIEU wrote: > Hi, > > Many people asked me to summarize the replies to my question concerning > the performance of DFT, and especially early functionals such as > Becke-Perdew86, with regard to the description of the energetic of > H-bonds. > Clearly, everybody agree that hybrid functionals are better than GGA > functionals, the latter being themselves much better than LDA. Recently, > the team by Salahub has developped a LAP functional which performs well. > Somebody also pointed to the need for extended basis sets for > convergence. ---------------- I would like just to add here some references about the LAP functionals mentioned above: I would recommend examining particularly refs. [4-6] enclosed below, from which it can be envisaged that the hybrid methods may not alwas be a panacea as far as intra-molecular hydrogen bonds concern. Moreover, while the hybrid methods seem to be indeed more demanding with respect to basis set convergence (keeping in mind that in Gaussian the basis set optimization is (post) HF-based not DFT-based ), "pure DFT codes" like deMon-KS3, deMol, NUMOL, ADF, DGauss, etc. use basis sets that are specially optimized and adapted to DFT numerics (which leads to less convergence demands and smaller BSSE errors on average). Adamo and Barone have recently found for example that including p,d, and f functions in the Gaussian G6-311 basis set influences substantially the magnitude of the activation barrier for internal proton transfer in malonaldehyde with B3LYP and other hybrid functionals as implemented in Gaussian 98. I double-checked whether a similar basis set sensitivity exists with the PLAP3 functional within the deMon-KS3 code and I did not find a shift larger than 0.1 kcal/mol for this particular case? I also find that the old good GGA BP is not that bad for systems like H2O dimer and HF dimer as far as energetics concern (it just gives a bit shorter O...H and F...H distances). references: [1]. E.I. Proynov and D.R. Salahub, Phys.Rev.B v.49, 7874 (1994) ; Erratum, ibid. v.57, 12616 (1998). [2] E. Proynov, A. Vela and D. R. Salahub, Chem.Phys.Lett. vol.230, 419 (1994); Erratum, ibid., vol 234, 462 (1995). [3] E.I. Proynov, E. Ruiz, A. Vela, and D.R. Salahub, Int. J. Quant. Chem.(Symp.) vol 29, 61 (1995); [4] E. I. Proynov, S. Sirois and D. R. Salahub, Int. J. Quant. Chem.vol.64, 427, (1997). [5] S. Sirois, E. Proynov, D. Nguyen and D.R. Salahub, J.Chem.Phys. v107, 6770 (1997). [6] H. Guo, S. Sirois, E. Proynov, and D.R. Salahub, in: "Density Functional Theory and Its Applications to Hydrogen Bonded Systems" Theoretical treatment of Hydrogen Bondings}, H; Hadzi ed. John Willey (1997). Emil Proynov +-----------------------------+ | Dr Emil Proynov | | proynov@chimie.umontreal.ca | | eproynov@scf.fundp.ac.be | +-----------------------------+ From chemistry-request@www.ccl.net Thu Feb 25 07:37:49 1999 Received: from daisy.imc.cas.cz (daisy.imc.cas.cz [147.231.112.129]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA29007 Thu, 25 Feb 1999 07:37:45 -0500 (EST) Received: from daisy.imc.cas.cz (pepan.imc.cas.cz [147.231.112.146]) by daisy.imc.cas.cz (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id NAA04116 for ; Thu, 25 Feb 1999 13:40:01 +0100 (CET) Sender: saturka@daisy.imc.cas.cz Message-ID: <36D543F2.33A7029B@daisy.imc.cas.cz> Date: Thu, 25 Feb 1999 13:37:07 +0100 From: Martin Saturka Organization: IMC CAS CZ X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX 6.5 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Partial charges & mol2 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, I need some nonexpensive program for computing partial charges for mol2 files. I'm starting from a lot of pdb files and I need it for further processing in docking programm Dock. Thak's a lot. Martin Saturka From chemistry-request@www.ccl.net Thu Feb 25 09:06:31 1999 Received: from earth.ox.ac.uk (darwin.earth.ox.ac.uk [163.1.22.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA29530 Thu, 25 Feb 1999 09:05:44 -0500 (EST) Received: from metropolis.earth.ox.ac.uk (metropolis [163.1.22.59]) by earth.ox.ac.uk (8.9.1a/8.9.1) with SMTP id OAA27517; Thu, 25 Feb 1999 14:05:10 GMT From: Keith Refson MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14037.22677.427440.751227@gargle.gargle.HOWL> Date: Thu, 25 Feb 1999 14:05:09 +0000 (GMT) To: Proynov Emil Cc: chemistry@www.ccl.net Subject: CCL:G:Comment on DFT & Hydrogen bonds In-Reply-To: References: X-Mailer: VM 6.67 under 20.4 "Emerald" XEmacs Lucid Content-Transfer-Encoding: 7bit Proynov Emil writes: > I also find that the old good GGA BP is not that bad for systems like > H2O dimer and HF dimer as far as energetics concern (it just gives a bit > shorter O...H and F...H distances). Is 0.14eV good or bad? The reason I ask will become apparent if you read D. R. Hamman, Phys. Rev. B 55(16) R10157-10160 (1997) In this paper Hamman compares the sublimation energies of Ice with various functionals. (Although his claimed experimental value is a bit suspect at 0.58eV. I thought is was 0.491). Keith Refson -- ------------------------------------------------------------------------------ Email: Keith.Refson@ | Tel: +44 1865 272026 | Dr Keith Refson, | earth.ox.ac.uk | Fax: +44 1865 272072 | Dept of Earth Sciences | | Parks Road, Oxford OX1 3PR, UK| ------------------------------------------------------------------------------ From chemistry-request@www.ccl.net Thu Feb 25 09:36:48 1999 Received: from www.CIRC.gwu.EDU (www.circ.gwu.edu [128.164.127.251]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA01580 Thu, 25 Feb 1999 09:36:47 -0500 (EST) Received: from gwis2.circ.gwu.edu (gwis2 [128.164.127.252]) by www.CIRC.gwu.EDU (8.8.8/8.8.7) with ESMTP id JAA19036; Thu, 25 Feb 1999 09:33:20 -0500 (EST) Received: from localhost (jgauntt@localhost) by gwis2.circ.gwu.edu (8.9.1a/8.9.1) with ESMTP id JAA10086; Thu, 25 Feb 1999 09:39:38 -0500 (EST) Date: Thu, 25 Feb 1999 09:39:38 -0500 (EST) From: Jennifer Michelle Gauntt To: Ulrike Salzner cc: "chaudash@aston.ac.uk" , chemistry@www.ccl.net Subject: Re: CCL:Biological relevance of aluminium In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A more recent article about Al in Alzheimer Disease patients brains can be found in: Anal. Chem. 1998, 70, 1026-1029. This article has many references to others about the same topic. In fact, whether or not elevated levels of Al are found in the brains of AD patients is a rather hot topic in biochem right now. On Thu, 25 Feb 1999, Ulrike Salzner wrote: > There was a paper about the involvement of Al3+ in Alzheimer's desease > some time ago in Accounts of Chemical Research. I could not find the > reference quickly, but I am sure it is no more than 5 years old. Take a look. > Uli Salzner > > =================================================================== > > Dr. Ulrike Salzner > > Department of Chemistry Tel.: (312) 290-2122 > Bilkent University Fax.: (312) 266-5097 > 06533 Bilkent, Ankara e-mail: salzner@fen.bilkent.edu.tr > Turkey > > ==================================================================== > > On Wed, 24 Feb 1999, chaudash@aston.ac.uk wrote: > > > Hello ccl'ers, > > A while back I wrote asking if anyone knew of any biological > > role for aluminium. To my knowledge there is no known relevance of > > this metal in biological sytems. However I did receive a reply, > > where someone mentioned that aluminium plays a part in alcohol > > dehydrogenase. I have looked extensively to find out more to no > > avail. I would be most grateful for any input. > > Many thanks for your time > > > > -------This is added Automatically by the Software-------- > > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > > -- Original Sender From: Address: mailhub@aston.ac.uk > > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > > Web: http://www.ccl.net/chemistry.html > > > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: salzner@gunser.fen.bilkent.edu.tr > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From chemistry-request@www.ccl.net Thu Feb 25 10:05:12 1999 Received: from server.nybc.org (server.nybc.org [192.94.249.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA04715 Thu, 25 Feb 1999 10:05:12 -0500 (EST) Received: from iris.nybc.org ([192.94.249.42]) by server.nybc.org (Netscape Mail Server v2.0) with ESMTP id AAA29777; Thu, 25 Feb 1999 10:06:00 -0400 Received: by iris.nybc.org (980427.SGI.8.8.8/940406.SGI.AUTO) id KAA13346; Thu, 25 Feb 1999 10:11:54 -0500 (EST) From: "Asim Kumar Debnath" Message-Id: <9902251011.ZM13268@iris.nybc.org> Date: Thu, 25 Feb 1999 10:11:52 -0500 In-Reply-To: Martin Saturka "CCL:Partial charges & mol2" (Feb 25, 1:37pm) References: <36D543F2.33A7029B@daisy.imc.cas.cz> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Martin Saturka , chemistry@www.ccl.net Subject: Re: CCL:Partial charges & mol2 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Martin: You can use the program, chunks, which comes with the dock program. It calculates Gasteiger-Marsili charges for mol2 files. In dock3.5 the program is located at /dock3.5/source/database/sdf2mol2/chunks. In Dock4.0, it is located at /dock4.0/dock4/source/databse/chunks. Hope this helps. Good luck. Asim -- ======================================================================= *** *** Asim K. Debnath, Ph.D. **** Assistant Member **** Lindsley F. Kimball Research Institute **** *** The New York Blood Center **** **** 310 E 67 Th Street **** ** **** New York, NY 10021 **** **** **** Tel. (212) 570-3373 **** ** **** Fax. (212) 570-3299 **************** E-mail: adebnath@server.nybc.org ************** ======================================================================== From chemistry-request@www.ccl.net Thu Feb 25 10:35:27 1999 Received: from tracker.excite.com (tracker-rwcmta.excite.com [198.3.99.217]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA06199 Thu, 25 Feb 1999 10:35:26 -0500 (EST) From: t1m1@excite.com Received: from digger.excite.com ([199.172.152.82]) by tracker.excite.com (InterMail v4.00.03.11 201-229-104-111) with ESMTP id <19990225153509.GXXC12274.tracker@digger.excite.com> for ; Thu, 25 Feb 1999 07:35:09 -0800 To: chemistry@www.ccl.net Subject: bond order Message-Id: <919956908.13405.248@excite.com> Date: Thu, 25 Feb 1999 07:35:08 PST X-Mailer: Excite Mail X-Sender-Ip: 134.206.150.8 MIME-Version: 1.0 Content-Type: text/plain Dear Netters I want to know the definition of bond order and their approximatively values for a cyclic molecule between two carbons or carbon-nitrogen. Can i know also if from the values of bond order the delocalisation is detected or not. I've done all the calculations by jaguar and i want to visualize the properties :Homo,Lumo...from spartan,but i don't knowhow to do it. Thank for your advice T.M _______________________________________________________ Get your free, private email at http://mail.excite.com/ From chemistry-request@www.ccl.net Wed Feb 24 12:49:41 1999 Received: from mailgate.rz.uni-karlsruhe.de (exim@nz40.rz.uni-karlsruhe.de [129.13.197.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA21394 Wed, 24 Feb 1999 12:49:35 -0500 (EST) Received: from tchibm3.chemie.uni-karlsruhe.de (dapprich2@tchopin.chemie.uni-karlsruhe.de [129.13.107.204]) by mailgate.rz.uni-karlsruhe.de with esmtp (Exim 2.04 #3) id 10FiQY-0006mP-00; Wed, 24 Feb 1999 18:48:54 +0100 Sender: dapprich2@www.ccl.net Message-ID: <36D43BC5.7947D6FB@tchibm3.chemie.uni-karlsruhe.de> Date: Wed, 24 Feb 1999 18:49:57 +0100 From: Stefan Dapprich Organization: University of Karlsruhe X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.36 i686) X-Accept-Language: de MIME-Version: 1.0 To: Jolanta Grembecka CC: chemistry@www.ccl.net Subject: Re: CCL:G:ONIOM References: <36D41C73.41C6@neon.ch.pwr.wroc.pl> Content-Type: multipart/alternative; boundary="------------AC924B6DEE89046588947DD5" --------------AC924B6DEE89046588947DD5 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Jolanta Grembecka wrote: > Dear CCLers, > I would like to use ONIOM option in G98 for a system which is neutral, > however high layer is negatively charged (-1) while low layer is > positively charged (+1) because each of them include different > molecules. Is it possible to put these information about charges of each > layer in input file? Indeed it is. Just add the charge-multiplicity "couples" to the respective input card in the order high-[medium]-low. In your case: # oniom(... title -1 1 0 1 mol. spec. ... Hope this helps. Stefan -- +----------------------------------------+ Dr. Stefan Dapprich Institut fuer Physikalische Chemie Universitaet Karlsruhe D-76128 Karlsruhe Phone ++49-721-608-7229 Fax ++49-721-608-4856 +----------------------------------------+ From chemistry-request@www.ccl.net Wed Feb 24 12:54:58 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA21432 Wed, 24 Feb 1999 12:54:57 -0500 (EST) Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id MAA18843 for ; Wed, 24 Feb 1999 12:54:43 -0500 (EST) Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id SAA29411; Wed, 24 Feb 1999 18:54:08 +0100 From: Jochen Kuepper Organization: Heinrich-Heine-Universitaet To: Aaron Hu , CCL Subject: Re: CCL:C Program Date: Sun, 3 Apr 2135 01:20:15 +0100 X-Mailer: KMail [version 1.0.17] Content-Type: text/plain References: <19990222133513.23701.rocketmail@send203.yahoomail.com> MIME-Version: 1.0 Message-Id: <99022418540700.24244@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id MAA21433 On Mon, 22 Feb 1999 you wrote: >Could someone tell me how to call a FORTRAN subroutine in a C program >on SGI workstation or PC ? - C and Fortran compiler need to generate same object file format. - You might need to append an "_" to all Fortran names in C, try it out. - All parameters are passed by address ! - arrays are sorted differently, ask again if you need to pass arrays ! Greetings, Jochen ----------------------------------------------------------------------- Jochen Küpper Heinrich-Heine-Universität Düsseldorf jochen@uni-duesseldorf.de Institut für Physikalische Chemie I Universitätsstr. 1, Geb 26.43 Raum 02.29 phone ++49-211-8113681 40225 Düsseldorf fax ++49-211-8115195 Germany http://www-public.rz.uni-duesseldorf.de/~jochen ----------------------------------------------------------------------- From chemistry-request@www.ccl.net Wed Feb 24 16:17:03 1999 Received: from unomail.unomaha.edu (unomail.unomaha.edu [137.48.1.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id QAA24897 Wed, 24 Feb 1999 16:17:02 -0500 (EST) From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.3 (733.2 10-16-1998)) id 86256722.0074CFA9 ; Wed, 24 Feb 1999 15:15:53 -0600 X-Lotus-FromDomain: UNIVERSITY OF NEBRASKA To: William Karney cc: CCL Message-ID: <06256722.0074CED1.00@unomail.unomaha.edu> Date: Wed, 24 Feb 1999 15:15:50 -0600 Subject: Re: CCL:G:memory usage in G94 Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline The default maxium memory usage for a single processor in IRIX is 512 MB To get beyond 512MB one needs to increase the kernel parameter shmmax to the desired level. You then need to re-build the kernel and reboot with this new kernel. There may be some other associated kernel parameters for shared memory which you might want to tweak but this is the main one. From chemistry-request@www.ccl.net Wed Feb 24 18:20:42 1999 Received: from diamin.chem.cinvestav.mx (root@diamin.chem.cinvestav.mx [148.247.11.63]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA25993 Wed, 24 Feb 1999 18:20:40 -0500 (EST) Received: from localhost by diamin.chem.cinvestav.mx via sendmail with smtp id (Debian Smail3.2.0.101) for ; Wed, 24 Feb 1999 17:23:16 -0600 (CST) Date: Wed, 24 Feb 1999 17:23:16 -0600 (CST) From: webmaster RelaQ X-Sender: kaiser@diamin.chem.cinvestav.mx To: "Jerry C.C. Chan" cc: chemistry@www.ccl.net Subject: Re: CCL:Summary: AMD-K6/linux for G98 In-Reply-To: Message-ID: 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 www.ccl.net id SAA25994 On Wed, 24 Feb 1999, Jerry C.C. Chan wrote: > > Sorry for any duplication, it seems the following summary didn't get > posted at the first time. > ------------------------- > > Many thanks for those who responsed to my post. In short, P-II is highly > recommended, DEC Alpha (21164) is a good alternative, Celeron-based > machine MAY be a good choice (see both positive and negative comments > below), AMD-K6 is not at all useful for numerical calculation. The 11th > response from Prof Teppen is very interesting that the performance of his > 4-processor-P-II linux box from Peter Pulay's company (cost $11,000) is > only 15% slower than a Cray T3E-1200 with 4 processors. Please excuse me > for removing some of the signatures in order to shorten this summary. > > Original post: > > We have a plan to get a linux box equipped with AMD-K6 for Gaussian 98 > > calculations. However, it seems that the recommended blas library and > > Portland Fortran compiler are optimized for Intel CPU only (I may be > > mistaken saying so). I would be grateful if anyone could share his/her > > experience concerning the following thoughts > > i. pay more money to buy Intel processor > > ii. go on with our plan (assuming that the performance of Linux/AMDK6-G98 > > won't be very different from Linux/IntelPII-G98) > > iii. keep the AMD but switch to NT/G98W instead of linux/G98 > > ++++++Responses++++++ > 1. From: Drake Diedrich > > BLAS isn't apparently heavily used in Gaussian (only in CI methods), > but... you may still be better off getting an Intel CPU. On heavy floating > point and memory bandwidth I have benchmarked a pentium-166 outperforming an > AMD K6/2-300. Pentiums (and later Intel processors) have pipelined floating > point units while AMD and Cyrix have only a single floating point execution > unit. AMD processors are not competitive with the pentium-II. > You should add the DEC Alpha (21164) to your shortlist of alternatives. > I haven't benchmarked Gaussian on it, but if you search the web you'll find > a hand coded BLAS library for the Alpha that achives 800 MFlops on a 600MHz > chip. The ASCI-Red BLAS library gets only 180 MFlops on our Pentium-II/266. > > -Drake > > 2. From fparnold@balihai.uchicago.edu Tue Feb 23 10:46:42 1999 > > If you follow the links through the Beowulf page (www.beowulf.org) to > their archive for February of 1999 (or possible Jan) there is a comparison > of CHARMm run times on the K6 vs. Celeron. Basically, CHARMm is slow on > the K6, but runs on teh Celeron at the same speed of the PII. So, if > you're not cache limited, this is a cheap option. IF you are, then the K6 > if probably ok. My personal results with GAMESS-US indicates that the > K6-233 is slightly faster than a P200 classic, and roughly 5% faster than > an SGI O2 with an R5000 processor and secondary cache. > > Unfortunately, the real answer therefore is, "buy one, and benchmark it > yourself". If you get good numbers, buy more and make a cluster out of > them. If you don't, you can probably return it and just be out the > shipping fee. > -fred > > 3. From pczyryca@smurf.chem.usu.edu Tue Feb 23 10:46:45 1999 > > K6 is slower than PentiumII (with the same clock). Especially on floating > point operations. This is not OS dependent, so I wouldn't expect better > performance with NT/G98W combination. > Probably it's the best option to spend some more money and buy PentiumII. > Regards, > > * Przemek Czyryca, pczyryca@smurf.chem.usu.edu * > > 4. From gammadas@telis.org Tue Feb 23 10:46:49 1999 > > I had the same questions and similar experiences for g94w/g98w as > mentioned in the message below---I would pay more and get the Intel > PII(PIII will be available in 2 wks!) Also check 2nd message (Jerry: the > next message). Hope it helps! > > 5. From: "Dr.Christian M¸ck-Lichtenfeld" > > I have a small number of PCs at hand, which are run under > Windows NT and Linux. Although the hardware is not exactly > the same, one can come to the overall conclusion that the > AMD processors are about 1.5 - 2 times slower than the > Intel machines. Even a PentiumII with 266 MHz was found to > run a moderate G98W-job in about 60% of the time that an > AMD K6/2 with 300 MHz needed (both with at least 128MB RAM). > A comparison of several Mopac jobs (Mopac93/Linux) on the > AMD K6/2 (300MHz) and on a PentiumII (333MHz) gave the same > result (t(AMD)/t(PII) = 1.5 ... 2). > > I am not a hardware expert but I would suppose that the different > architecture of the CPUs clearly favours Intel over AMD, due to the better > performance in floating point operations. For the aquisition of new > machines I therefore would strongly suggest Intel over AMD. > > I would be very interested to hear from the experiences of other > users, so please forward their answers or summarize if possible. > > Best wishes > > Christian Mueck-Lichtenfeld > > 7. From Steven.Creve@dsm-group.com Tue Feb 23 10:46:52 1999 > > do anything but the last suggestion. WindowsNT is really a *bad* choice for > doing (any kind of) calculations. > I would suggest you contact the people at Gaussian with this problem. > Steven > > 8. From: val > > > i. pay more money to buy Intel processor > > It seems yes, see comments below. > > > ii. go on with our plan (assuming that the performance of Linux/AMDK6-G98 > > won't be very different from Linux/IntelPII-G98) > > Using GAMESS ab-initio program under Linux we found that Intel PII-350 > is significantly faster then AMDK6-350 (in order of 50%) even without > any specific blas libraries. If your budget allows, go to the PII CPU. > > On the other hand, Celeron shows very good performance: Celeron-300A is > close to AMDK6-350, Celeron 333 expected to be a little faster. Both are > really cheap now. > > I have a small collection of GAMESS/ab-initio benchmarks under linux on > my homepage: http://nmr.ioc.ac.ru/Staff/AnanikovVP/ > > > iii. keep the AMD but switch to NT/G98W instead of linux/G98 > > This is very old (and dangerous ;) question, you may look to the CCL > archives, the last discussion finished not long ago. > > For example, a part of the email from Mike Frisch ; > CCL Tue, 5 Jan 1999: > ".. We use the same compiler (Portand) and blas libraries on both Windows/NT > and Linux, and performance is similar. The differences in reported times > are a few percent and probably reflect Linux reporting system time > overhead (as other unix versions do) while this isn't included on a > per-process basis under NT. Elapsed times are sometimes a bit better > under Linux because of better I/O, but the best summary of the situation > is that there isn't a signficant performance diffence for running a > single, stand-alone job under one OS or the other." > > best regards, > Valentin. > > 9. From ivan@lipid.biocomp.unibo.it Tue Feb 23 10:46:57 1999 > > > i. pay more money to buy Intel processor > > That is the way to go. AMD K6 is a great cpu, but NOT for scientific and > technical applications. Its Floating-point unit is VERY slow when compared > to intel one. Get a real PII, the fastest you can afford, don't buy a > Celeron-based machine. > > BTW i tested both CPU with G94. > > > ii. go on with our plan (assuming that the performance of Linux/AMDK6-G98 > > won't be very different from Linux/IntelPII-G98) > > Once more, just to stress it.... > > I don't think the small saving is absolutely worth the the performance > penalty that you have with K6 with scientific and technical programs. > > > > iii. keep the AMD but switch to NT/G98W instead of linux/G98 > > linux is more stable. go for it. > > -- > Dr. Ivan Rossi - CIRB Biocomputing Unit > e-mail: ivan@lipid.biocomp.unibo.it WWW: http://www.biocomp.unibo.it/ivan > > 10. From daniels@kemi.uu.se Tue Feb 23 10:47:00 1999 > > I haven't tried gaussian on the AMD-k6, but from my experiences I would *not* > recommend using the K6 for floating point stuff. I really like the performance > of the K6 for regular stuff like editing, compiling, but the fp perfomance is > simply not good enough. my experience is that the pii is about 50 % faster than > the k6 with the same frequency. the processor is only part of the computer > anyway, you still have to pay the same money for case, monitor, disks etc, so > if the final computer is perhaps 20 % more expensive with the PII, it is still > worth it for fp stuff. What may break down my argument is that in my > calculations, the fp is the bottleneck. In your case it may be the disk, so... > > best regards > Daniel Spångberg > Inorganic Chemistry > Uppsala University > Sweden. > > 11. From teppen@pilot.msu.edu Tue Feb 23 10:47:05 1999 > > If I may propose a fourth option in addition to the three you posted: > > Peter Pulay at the University of Arkansas is a true pioneer of quantum > chemistry - for example, his contributions were cited in Pople's official > Nobel Prize announcement this past fall. He is a former professor of mine > and I like him very much, but I have no other interest in promoting his new > company. > > Pulay has been working on optimized quantum codes since the 1960s and he > just started a company to sell them this past year. He has 5-6 coworkers > including Jon Baker, another master of optimization methods. Several years > ago, Pulay began to parallelize his program for cheap PCs running Linux, > and they now have a system they can sell. Their company is "Parallel > Quantum Solutions" and pulay's e-mail is "pulay@pqs-chem.com". They build > their own PCs and sell a software-hardware bundle. > > I paid $11,000 for a 4-processor (400 MHz Pentium IIs) machine with Linux > and the quantum software installed. I have just got the machine, but > benchmarks indicate that this machine has exceedingly good > performance/price. For pinene using DFT/B3LYP with large basis sets, for > example, the machine i bought for $11,000 was faster than a Cray T3E-600 > with 4 processors and only 15% slower than a Cray T3E-1200 with 4 > processors, both running parallel Gaussian 94. (The G94 calculations were > done by Sosa and Frisch, so were probably pretty well optimized for the > machine, see last July 15 number of J. Comput. Chem. Sosa et al. Vol 19, p. > 1053). I haven't priced those machines but they must be >$100k. If you want > to benchmark against one of your own machines, Pulay would be happy to do > some calculations for you. > > Again, I have no financial interest in telling you this, but it seems like > a great product for working quantum chemists. The graphical interface is > not great, but it is adequate. They put their time into optimizing code. > > Best wishes, > > Brian > > ********************** > Dr. Brian J. Teppen > Assistant Professor > Department of Crop and Soil Sciences > Plant and Soil Science Building, Room 538 > Michigan State University > East Lansing, MI 48824-1325 > > phone: 517-353-5215 > fax: 517-355-0270 > e-mail: teppen@pilot.msu.edu > > 12. From haasj@ubaclu.unibas.ch Tue Feb 23 10:47:08 1999 > > i am a chemistry student in the very last three weeks of studying. I am > using g98 /molden /k6-2-300 and RH 5.2 Linux and 96MB of RAM. I have > encountered that the speed is ok, but not as fast compared to a PII. If i > might I would recon you to buy the K7 (will probably come out this year) > with the EV6 bus protocol of a DEC ALPHA processor 21264. In later times > you would have the opportunity to exchange the proc against an 21264 - > what ever clockspeed... nice option i think. With a PII you are at the > limit of only increasing clockspeed if even possible, although PII are > better in floating point operations. DEC Alpha is for sure a good choice > for later. K6-3 (sharptooth) is also quite nice proc to think of cheaper > than PII but should be equally fast.. (I can only assume that NT system is > equally fast)... > > greetings juergen haas > uni basel > org. chem dep. > > > feel free to contact me again > > 13. From eugene.leitl@lrz.uni-muenchen.de Tue Feb 23 10:47:10 1999 > > AMD K6 ist voll kompatibel zu PPro/P II CPU. Allerdings koennte > Celeron das bessere Preis/Leistungsverhaeltnis bieten. Vielleicht auf > K6-3 oder sogar K7 warten? > > MfG, > Eugen > > 14. From RedAndr@anrb.ru Tue Feb 23 10:47:12 1999 > > It is not good idea buying AMD/K6 CPU for floating point calculations. > Intel processors with same price as AMD have more powerful FPU > performance. In addition all compilers can do optimization only for > Pentium/Pentium Pro unlike AMD or Cyrix. Therefore you have to forget > about using AMD in numerical purposes. You can also buy multiprocessor > station with Intel processors unlike AMD. About Linux and NT. Our > experiments shows that Linux haven't advantage over Windows 95/NT in > numerical calculations. > > > Best regards, > Andrew mailto:RedAndr@anrb.ru > > > 15. From gaussian.com!fox@lorentzian.com Tue Feb 23 10:47:15 1999 > > At this point I cannot vouch for proper operation of G98 on an > AMD processor. We do not have plans for supporting this as a platform. > While most things work on AMD I have at least one site with a problem > trying to run G98W and have several sites that have demonstrated problems > with Cyrix processors which make it impossible to run G98. > > In short I recommend you get Intel. > > Douglas J. Fox > Director of Technical Support > help@gaussian.com > > -----end of summary------ > > > > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > > From chemistry-request@www.ccl.net Thu Feb 25 12:12:07 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA07884 Thu, 25 Feb 1999 12:12:06 -0500 (EST) Received: from poptop.llnl.gov (poptop.llnl.gov [128.115.18.65]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id MAA16832 for ; Thu, 25 Feb 1999 12:12:05 -0500 (EST) Received: from [128.115.55.213] (mac213.llnl.gov [128.115.55.213]) by poptop.llnl.gov (8.8.8/LLNL-3.0.2) with ESMTP id JAA06012 for ; Thu, 25 Feb 1999 09:12:05 -0800 (PST) X-Sender: e001314@popeye.llnl.gov Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 25 Feb 1999 09:15:00 -0800 To: chemistry@ccl.net From: Michelle Francl-Donnay Subject: ACS Computers in Chemistry Division - late ballots Members of COMP - you probably received your ballot after the deadline for its return (2/15). The ballots were mailed late by the commercial concern which handled the mailing. The deadline has been extended to March 5. If you need new ballot materials, please e-mail me and I can provide them. Michelle M Francl COMP secretary 96-98 Michelle M. Francl-Donnay Physicist Lawrence Livermore National Laboratory L-039 PO Box 808 Livermore, CA 94551-0808 925-423-6096 mfrancl@llnl.gov _________ on leave from Department of Chemistry Bryn Mawr College 101 N. Merion Ave. Bryn Mawr, PA 19010 mfrancl@brynmawr.edu From chemistry-request@www.ccl.net Thu Feb 25 16:08:06 1999 Received: from syr.edu (syr.edu [128.230.1.49]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA11050 Thu, 25 Feb 1999 16:08:05 -0500 (EST) Received: from gamera.syr.edu (dgallis@gamera.syr.edu [128.230.18.14]) by syr.edu (8.8.8/8.8.8) with SMTP id QAA21679 for ; Thu, 25 Feb 1999 16:03:35 -0500 (EST) Date: Thu, 25 Feb 1999 16:08:01 -0500 (EST) From: "Damian G. Allis" X-Sender: dgallis@gamera.syr.edu Reply-To: "Damian G. Allis" To: chemistry@www.ccl.net Subject: "*******" in Beta, Gamma Calculations in MOPAC Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings all, When I run (hyper)polarizability calculations in MOPAC97, I get lines of "**************" for certain beta's and gamma's, esp. at higher eV's (.7, 1.0, 1.5, etc.0). Is this a problem with the program, a problem with the molecule I'm running, or just MOPAC's way of noting that some value can't be calculated/is too high to show on the screen? thanks in advance, Damian Allis ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Home Address: | Chemistry Address: 349 Buckingham Ave. | 1-014,2-023,2-016e Center for Sci&Tech Syracuse, NY 13210 | Syracuse University email: dgallis@syr.edu | Syracuse, NY 13244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#8^(= -)*-+-< everything about me: web.syr.edu/~dgallis/ Cornucopia Music: www.cornucopiamusic.com/ From chemistry-request@www.ccl.net Thu Feb 25 16:48:16 1999 Received: from bravais.BRI.NRC.CA (bravais.BRI.NRC.CA [206.167.189.68]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA11972 Thu, 25 Feb 1999 16:48:10 -0500 (EST) Received: from warp.bri.nrc.ca (warp.bri.nrc.ca [206.167.189.119]) by bravais.BRI.NRC.CA (8.8.8/8.8.8) with SMTP id QAA12722 for ; Thu, 25 Feb 1999 16:45:52 -0500 (EST) Received: from localhost by warp.bri.nrc.ca with SMTP id QAA16447; Thu, 25 Feb 1999 16:45:52 -0500 Date: Thu, 25 Feb 1999 16:45:51 -0500 (EST) From: Vladislav Vassiliev To: chemistry@www.ccl.net Subject: General Born Approach & Pairwise Surface Evaluation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL's, I have two simple questions. First. Currently I'm collecting the articles concerning the applications of so-called "generalized Born" based approximation in the molecular mechanics-like simulations. I found a few ones. Maybe I missed some of them. Could you provide me with references you know? Second. I'm looking for the articles dealing with approximate evalution of molecular (SAS, vdw, it does not matter) surface using simple pairwise approximation. Maybe I'll be able collect more with you help? With the best wishes, Vladislav BRI NRC, Montreal, Canada