From chemistry-request@server.ccl.net Tue Oct 2 04:30:38 2001 Received: from mail.uni-kl.de ([131.246.137.52]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f928Ub529280 for ; Tue, 2 Oct 2001 04:30:37 -0400 Received: from aixs1.rhrk.uni-kl.de (exim@aixs1.rhrk.uni-kl.de [131.246.137.3]) by mail.uni-kl.de (8.11.5/8.11.5) with ESMTP id f928UYR27475; Tue, 2 Oct 2001 10:30:34 +0200 (MET DST) Received: from aixd1.rhrk.uni-kl.de ([131.246.137.210] ident=exim) by aixs1.rhrk.uni-kl.de with esmtp (Exim 3.33 #2) id 15oKwk-000B1c-00; Tue, 02 Oct 2001 10:30:34 +0200 Received: from gerwalin (helo=localhost) by aixd1.rhrk.uni-kl.de with local-esmtp (Exim 3.03 #5) id 15oKwj-000ihU-00; Tue, 02 Oct 2001 10:30:33 +0200 Date: Tue, 2 Oct 2001 10:30:33 +0200 (MES) From: Elmar Gerwalin To: Borislav Kovacevic cc: chemistry@ccl.net Subject: Re: CCL:file size limits In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi ! On Mon, 1 Oct 2001, Borislav Kovacevic wrote: > > My question is: why are total size of temporary files in Gaussian (rwf) and in Molpro limited to max. 16 GB under the Linux operating system. I had a similar question and Gaussian answerded: ------- Rev. A.9 on Tru64 Unix uses 64 bit integers for most everything except it does use a 32 bit hash table. So in principle you need not split files but there is a limit, now lifted in Rev. A.10 because we have implemented a 64 bit hash table, of about 20GB. The 16GB limit you refer to is for machines like Linux where g98 is a 32 bit application. You should be able to do this calculation if you specify MaxDisk=20GB but if you have the disk partitioned you will need to name the RWF as a set of files with fixed sizes so that they stay below the size of the partition. The SCR file is less used since we have gotten the capability to split the RWF. By using only one file we can better utilize the available disk up to the limit. If you do use both the SCR and the RWF file you are still limited and if the SCR file hits 20GB it is done but the disk space cannot be as easily recovered and re-used as when all of it is allocated out of the RWF. If splitting the RWF and specifying MaxDisk=20GB does not get things going send the last 50 lines of the output and the first 5 lines, through the route, of the input. Douglas J. Fox Technical Support Gaussian, Inc. help@gaussian.com ------ Maybe that helps a bit. Bye Elmar ============================================================== Elmar Gerwalin , University of Kaiserslautern, Germany gerwalin@rhrk.uni-kl.de (soon: ) http://www.rhrk.uni-kl.de/~gerwalin ============================================================== From chemistry-request@server.ccl.net Tue Oct 2 06:13:32 2001 Received: from wn1.sci.kun.nl ([131.174.8.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f92ADW532084 for ; Tue, 2 Oct 2001 06:13:32 -0400 Received: from studs3.sci.kun.nl by wn1.sci.kun.nl via studs3.sci.kun.nl [131.174.124.4] with ESMTP id f92ADTD12806 (8.11.3/3.19); Tue, 2 Oct 2001 12:13:29 +0200 (MET DST) From: "E.L. Willighagen" Received: by studs3.sci.kun.nl via egonw@localhost id f92ADSr12388 (8.11.3/3.7); Tue, 2 Oct 2001 12:13:28 +0200 (MET DST) Date: Tue, 2 Oct 2001 12:13:28 +0200 (MET DST) Message-Id: <200110021013.f92ADSr12388@studs3.sci.kun.nl> To: chemistry@ccl.net, egonw@sci.kun.nl Subject: Sequence assembly/reconstruction in chemistry Hi all, i am writing a literature review on sequence assembly/reconstruction in (bio)chemistry. I am familiar with the DNA/RNA reconstruction from digests, bu i was wondering if there are other sequence assembly problems in (biochemistry). I am looking for: 1. a good review/tutorial on DNA/RNA reconstruction (recent techniques for dealing with DNA repetition, performance of algorithms etc) 2. pointers to articles/book to other sequence assembly/reconstruction problems in (bio)chemistry. kind regards, Egon Willighagen From chemistry-request@server.ccl.net Tue Oct 2 03:32:11 2001 Received: from hotmail.com ([64.4.19.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f927WB527309 for ; Tue, 2 Oct 2001 03:32:11 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 2 Oct 2001 00:32:06 -0700 Received: from 150.244.85.38 by lw12fd.law12.hotmail.msn.com with HTTP; Tue, 02 Oct 2001 07:32:05 GMT X-Originating-IP: [150.244.85.38] From: "Viviane du Lac" To: chemistry@ccl.net Subject: Help. Cluster or multiprocessor PC? Date: Tue, 02 Oct 2001 07:32:05 +0000 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1; format=flowed Message-ID: X-OriginalArrivalTime: 02 Oct 2001 07:32:06.0003 (UTC) FILETIME=[5628D430:01C14B14] Hello, In our lab, we are trying to start some theoretical calculations about reactivity (mainly the location of transition states) of organic and organometallic molecules. We intend to use programs as Gaussian and/or GAMESS, and only two or three people are going to submit their jobs to the machine. The problem we face is what kind of machine to buy. Whith a budget of about 1000 USD we were thinking about a four processor PC, but some told us that maybe a small cluster would be better. I would really thank any piece of advice on the subject. Thank you, Olalla Nieto viviane_du_lac@hotmail.com _________________________________________________________________ Descargue GRATUITAMENTE MSN Explorer en http://explorer.msn.es/intl.asp From chemistry-request@server.ccl.net Mon Oct 1 12:55:36 2001 Received: from mail.ncifcrf.gov ([129.43.100.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f91Gta502757 for ; Mon, 1 Oct 2001 12:55:36 -0400 Received: from 661301 ([129.43.27.150]) by mail.ncifcrf.gov (8.11.3/8.11.3) with SMTP id f91GtaJ08686 for ; Mon, 1 Oct 2001 12:55:36 -0400 (EDT) Message-ID: <00c301c14a9a$22699b90$961b2b81@661301> From: "Yun Tang" To: Subject: Ask for a dock program Date: Mon, 1 Oct 2001 12:57:20 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00C0_01C14A78.9B429ED0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_00C0_01C14A78.9B429ED0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable BlankDear CCLers, I am very interested in docking a small molecule into the active site of = a protein-DNA complex. The active site is supposed to be made up of part = of protein, part of DNA, and Mg2+ ions. I have tried to use DOCK, = AutoDock and FlexX to do it. Unfortunately, it seems that all these = programs have not considered DNA and Mg2+ ions as parts of the active = site or receptor yet. I am just wondering if anybody has similar experience or knows any = program to handle such docking problem. Any suggestion or advice would = be highly appreciated! Best regards, Yun ******************************************************************* * Yun TANG, Ph.D. * * Laboratory of Medicinal Chemistry Tel: 301-846-5974 (O) * * Center for Cancer Research 301-668-8935 (H) * * National Cancer Institute, NIH * * 376 Boyles Street Fax: 301-846-6033 * * Frederick, MD 21702 E-Mail: yuntang@helix.nih.gov * ******************************************************************* ------=_NextPart_000_00C0_01C14A78.9B429ED0 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Blank
Dear CCLers,
 
I am very interested in docking = a small=20 molecule into the active site of a protein-DNA complex. The active site = is=20 supposed to be made up of part of protein, part of DNA, and Mg2+ ions. I = have=20 tried to use DOCK, AutoDock and FlexX to do it. Unfortunately, it seems = that all=20 these programs have not considered DNA and Mg2+ ions as parts of the = active site=20 or receptor yet.
 
I am just wondering if anybody = has similar=20 experience or knows any program to handle such docking problem. Any = suggestion=20 or advice would be highly appreciated!
 
Best regards,
 
Yun
****************************************************************= ***
*=20 Yun TANG,=20 Ph.D.           &n= bsp;           &nb= sp;           &nbs= p;            = ;=20 *
* Laboratory of Medicinal Chemistry    Tel: = 301-846-5974=20 (O)      *
* Center for Cancer=20 Research           = ;    =20 301-668-8935 (H)      *
* National Cancer = Institute,=20 NIH           &nbs= p;            = ;         =20 *
* 376 Boyles=20 Street           &= nbsp;       =20 Fax: 301-846-6033          = *
*=20 Frederick, MD=20 21702           &n= bsp;  =20 E-Mail: yuntang@helix.nih.gov=20 *
*******************************************************************<= /FONT>
------=_NextPart_000_00C0_01C14A78.9B429ED0-- From chemistry-request@server.ccl.net Mon Oct 1 14:02:03 2001 Received: from Lucy.UCIS.Dal.Ca ([129.173.1.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f91I23503725 for ; Mon, 1 Oct 2001 14:02:03 -0400 Received: from chem1.chem.dal.ca (CHEM1.Chem.Dal.Ca [129.173.17.47]) by Lucy.UCIS.Dal.Ca (8.11.5/8.11.5) with ESMTP id f91I20s26750 for ; Mon, 1 Oct 2001 15:02:01 -0300 (ADT) Message-Id: <200110011802.f91I20s26750@Lucy.UCIS.Dal.Ca> Received: from CHEM1/SpoolDir by chem1.chem.dal.ca (Mercury 1.40); 1 Oct 101 15:02:01 -0400 Received: from SpoolDir by CHEM1 (Mercury 1.40); 1 Oct 101 15:01:34 -0400 From: "BAN FUQUIANG" Organization: Chemistry, Dalhousie University To: CHEMISTRY@ccl.net Date: Mon, 1 Oct 2001 15:01:30 AST MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: escaped charge effects of PCM model Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01b) Dear all: I am trying to understand the escaped charge effects of the DPCM (polarizable dielectric model) solvation model. I have two questions: (1) How the escaped charge effects are defined. (2) How can I analyze the escaped charge effects of a DPCM calculation using Gaussian 98 program. Thanks From chemistry-request@server.ccl.net Mon Oct 1 14:15:40 2001 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f91IFc503849 for ; Mon, 1 Oct 2001 14:15:39 -0400 Received: (from osman@localhost) by sd.accelrys.com (8.11.0/8.11.0) id f91IJBG19069 for chemistry@server.ccl.net; Mon, 1 Oct 2001 11:19:11 -0700 Received: from OGUNER-LAP.accelrys.com (dhcp388.sd.accelrys.com [172.30.201.134]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id f91IJAk19061; Mon, 1 Oct 2001 11:19:10 -0700 Message-Id: <5.1.0.14.2.20010927085501.022b1308@sparky2.sd.accelrys.com> X-Sender: osman@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 01 Oct 2001 11:15:41 -0700 To: chemistry@server.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, qsar_society@accelrys.com From: "Osman F. Guner" Subject: Call for papers: ADME/Tox Informatics Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_16200344==_.ALT" --=====================_16200344==_.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable ADME/TOX INFORMATICS At Spring ACS meeting in Orlando (April 7-11, 2002) Sponsored by the Chemical Information Division (CINF) Co-sponsored by Division of Medicinal Chemistry (MEDI), Division of Chemical Toxicology (TOXI), and Division of Computers in Chemistry (COMP) The symposium will be on the informatics challenges faced with the=20 increasing contribution of ADME/Tox studies in the early drug=20 discovery. If you are working on predictive ADME/Tox in lead discovery,=20 lead optimization, or combinatorial library design and analysis, you may=20 want to share your views and results with the scientific community by=20 contributing to this symposium. How are you managing the information=20 flow? How is information captured and made available to scientists in a=20 multi-disciplinary set up? Are there examples of increased quality of=20 candidates through use of predictive ADME/Tox in early discovery? Please use the OASys to submit your abstract. You can access the CINF=20 symposia at OASys via http://oasys.acs.org/oasys.htm. The deadline for=20 submitting abstracts is November 1st. Thx...osman --- Osman F. G=FCner, Ph.D. Director, Lead Identification & Optimization Accelrys Inc. (858) 799-5341 osman@accelrys.com http://www.accelrys.com --=====================_16200344==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable ADME/TOX INFORMATICS

At Spring ACS meeting in Orlando (April 7-11, 2002)

Sponsored by the Chemical Information Division (CINF)
Co-sponsored by Division of Medicinal Chemistry (MEDI),
Division of Chemical Toxicology (TOXI),
and Division of Computers in Chemistry (COMP)

The symposium will be on the informatics challenges faced with the increasing contribution of ADME/Tox  studies in the early drug discovery.  If you are working on predictive ADME/Tox in lead discovery, lead optimization, or combinatorial library design and analysis, you may want to share your views and results with the scientific community by contributing to this symposium.  How are you managing the information flow?  How is information captured and made available to scientists in a multi-disciplinary set up? Are there examples of increased quality of candidates through use of predictive ADME/Tox in early discovery?

Please use the OASys to submit your abstract. You can access the CINF symposia at OASys via http://oasys.acs.org/oasys.htm. The deadline for submitting abstracts is November 1st.

Thx...osman

---
Osman F. G=FCner, Ph.D.
Director,  Lead Identification & Optimization
Accelrys Inc.   (858) 799-5341
osman@accelrys.com        http://www.accelrys.= com --=====================_16200344==_.ALT-- From chemistry-request@server.ccl.net Mon Oct 1 14:30:29 2001 Received: from hotmail.com ([64.4.9.193]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f91IUO504029 for ; Mon, 1 Oct 2001 14:30:25 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 1 Oct 2001 11:30:20 -0700 Received: from 63.50.231.105 by lw9fd.law9.hotmail.msn.com with HTTP; Mon, 01 Oct 2001 18:30:20 GMT X-Originating-IP: [63.50.231.105] From: "Fernando De La Vega" To: chemistry@ccl.net Subject: Using Hyperchem for visualizing Gaussian98 or Jaguar generated Orbitals Date: Mon, 01 Oct 2001 11:30:20 -0700 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 01 Oct 2001 18:30:20.0299 (UTC) FILETIME=[202E65B0:01C14AA7] Hi to All, I have noticed that Hyperchem has an import/export facility that allows the retrieval and saving of orbital information in a text file with the extension .ext. I think that it should be possible then to use Hyperchem as a front end to visualize orbitals from other packages (Gaussian, Jaguar, etc.). I would like to know if anyone knows whether this is indeed possible and how to do it. Are there any conversion utilities out there that would take a Gaussian/Jaguar file and convert it into a .ext file? Does anyone knows what the structure of this .ext file is? I have searched on the web for this topic and also on the Hyperchem website but there is no mention on the subject. Thanks. Fernando De La Vega Fernando_DeLa_Vega@hotmail.com _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp From chemistry-request@server.ccl.net Mon Oct 1 15:28:09 2001 Received: from sirius.chem.vt.edu (IDENT:root@[128.173.181.42]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f91JS9504702 for ; Mon, 1 Oct 2001 15:28:09 -0400 Received: from localhost (crawdad@localhost) by sirius.chem.vt.edu (8.11.0/8.11.0) with ESMTP id f91JS9k22120 for ; Mon, 1 Oct 2001 15:28:09 -0400 X-Authentication-Warning: sirius.chem.vt.edu: crawdad owned process doing -bs Date: Mon, 1 Oct 2001 15:28:09 -0400 (EDT) From: "T. Daniel Crawford" X-Sender: To: Subject: Linux file size limits In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 1 Oct 2001, Borislav Kovacevic wrote: > > Hi CCLers, > My question is: why are total size of temporary files in Gussian (rwf) and > in Molpro limited to max. 16 Gb under the Linux operating sistem. > I know that in 32 bit operating system maximum file size is 2GB. > In Gaussian I can split rwf files but 8 (16GB) is maximum number of > them. Why? > In new version of Linux (kernel 2.4) this 2 Gb problem is solved, i.e. I > can have a file larger than 2 Gb. I tried with Molpro and sucessfully > wrote file larger than 2 Gb, but it seems that there is a 16 Gb limit > anyway. > Why this limit exists and is there any way to change it? > > Thanks very much! > I cannot help with the MolPro limits as I'm not familiar enough with the details of that code. However, I can try to clarify a few points regarding filesize limits under Linux on 32-bit systems (e.g, ix86, athlon, etc.). This doesn't directly address your question, but does deal with this general topic and other questions recently posted to this list. (1) The 2.4.X Linux kernels support filesizes > 2 GB, including under the ext2 filesystem. (2) For C-language programs, even with a 2.4.X kernel, one must use the correct -D flags to make use of large-file support. These are: -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE They must be added for any codes which call low-level I/O routines such as open(), read(), write(), close(), etc. This will work for both GNU and Portland compilers, by the way. (3) For Fortran programs, if one is using the Portland Group compilers, PGI has provided large-file support through their I/O library: http://www.pgroup.com/faq.htm#execute1k If, instead, one if using the GNU Fortran compiler g77, it is still possible to obtain code capable of reading/writing large files, but a bit more problematic. If anyone cares to do this, let me know and I'll explain how. If there's sufficient interest on this list, I'll post it. -Daniel -- T. Daniel Crawford Department of Chemistry crawdad@vt.edu Virginia Tech www.chem.vt.edu/chem-dept/crawford -------------------- PGP Public Key at: http://www.chem.vt.edu/chem-dept/crawford/publickey.txt From chemistry-request@server.ccl.net Mon Oct 1 16:25:24 2001 Received: from amtulsmtp01.bp.com ([65.198.138.94]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f91KPJ505477 for ; Mon, 1 Oct 2001 16:25:20 -0400 Received: from amchiav002.nap.am.bp.com (inetgate3.bp.com [192.195.167.53]) by amtulsmtp01.bp.com (Switch-2.1.0/Switch-2.1.0) with SMTP id f91KQQb10129 for ; Mon, 1 Oct 2001 15:26:27 -0500 (CDT) Received: from 149.178.200.224 by amchiav002.nap.am.bp.com (InterScan E-Mail VirusWall NT); Mon, 01 Oct 2001 15:23:24 -0500 Received: by AMNAPX4 with Internet Mail Service (5.5.2653.19) id <4BDHRVTS>; Mon, 1 Oct 2001 15:23:24 -0500 Message-ID: From: "Golab, Joseph T" To: "'chemistry@ccl.net'" Subject: 2002 Spring National ACS Meeting -- PHYS Division Date: Mon, 1 Oct 2001 15:23:23 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" !!! CALL FOR PAPERS 2002 Spring National ACS Meeting (April 7-11) !!! "Molecular Modeling and Simulation of Reaction Mechanisms, Kinetics, and Catalysis" (PHYS) >>>>> SUBMISSION DEADLINE November 1, 2001 <<<<< As part of the 2002 Spring National ACS Meeting (April 7-11, 2002) in Orlando, a PHYS symposium will be held on "Molecular Modeling and Simulation of Reaction Mechanisms, Kinetics, and Catalysis". Molecular modeling and simulation methodologies have reached levels of sophistication and accuracy that make them increasingly useful for reaction mechanisms, kinetics, and catalysis. In addition, an impressive array of modeling software exists that when properly applied by chemists and chemical engineers lead to significant enhancements in the design, pilot, and production stages of chemical processes. Even so, the capabilities and limitations of the technology are often not well-known while the demand for new computational methods continues to rise. For example, if a mechanistic reaction pathway is modeled well, it is still hard to predict the impact of promoters or poisons. Zeolite catalyzed reaction mechanisms are not well understood and tools that predict elementary thermal reaction rate constants > from first principles still cannot be used by chemical engineers for process design. Even so, a substantial acceleration of research and development efforts can be achieved through the proper integration of experimental, engineering, and chemistry modeling applications. The purpose of the symposium is to foster the continued, efficient dialogue between practitioners in both experimental and computational kinetics and catalysis that leads to real links exploitable to industry, government, and academia. The goal of the session is to educate potential, novice, and expert modelers by emphasizing how methods and successes have helped (or have the potential to help) the fields of kinetics and catalysis. Contributed papers should focus on applications and new developments that highlight overlap with and support of other areas of kinetics and catalysis. Feel free to identify how modeling is implemented in your organization, share achievements, and philosophize on future challenges or rewards. It is anticipated that the audience will consist of those who need to understand possible uses and results and those who simply want to learn about the area. We are seeking papers on the following topics: Homogeneous, Heterogeneous, and Enzymatic Catalysis; Gas, Solution, Condensed Phase, Surface, and Elementary Kinetics; Potential Energy Surfaces; Process Screening; and Tools. We strongly encourage you to submit a suitable paper for this session using the on-line abstract submission system. The OASys web address is http://oasys.acs.org/. Once at the OASys page, click on the Physical division acronym (PHYS) which will lead you to a listing of the Orlando symposia. PLEASE NOTE THAT THE SUBMISSION DEADLINE IS NOVEMBER 1, 2002. Please distribute this information to other researchers in industry, academia, and national labs. Thank you for your consideration. Professor Thanh N. Truong Dr. Joseph T. Golab Department of Chemistry BP Chemicals 315 S 1400 E, Rm 2020 MAIL CODE C-7 University of Utah 150 West Warrenville Road Salt Lake City, UT 84112 Naperville, Illinois 60563 Tel: (801) 581-4301 Tel: (630) 961-7878 Fax: (801) 581-4353 Fax: (630) 420-4382 Email: truong@chemistry.utah.edu Email: GolabJT@BP.com From chemistry-request@server.ccl.net Mon Oct 1 16:35:11 2001 Received: from mail.chem.tamu.edu (IDENT:root@[165.91.176.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f91KZB505702 for ; Mon, 1 Oct 2001 16:35:11 -0400 Received: from [165.91.176.63] (account shen HELO mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro SMTP 3.5b3) with ESMTP id 460418 for chemistry@ccl.net; Mon, 01 Oct 2001 15:29:43 -0500 Sender: jshen@ccl.net Message-ID: <3BB8D2E3.FB73E187@mail.chem.tamu.edu> Date: Mon, 01 Oct 2001 15:32:35 -0500 From: Jingyi Shen Organization: TAMU X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: DFT and rare earth system Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CClers, I have been trying to do some DFT single point energy calculation on a periodic structure of gadlinium clusters. I use the Dmol3 software in MSI cerius 4.2 and I have encountered convergence problem assiciated with the 4f7 electrons. I heard that it is possible to include the f electrons with large core basis set in Gaussian, but I did not find any equivalent option in the Dmol3 software. I am wondering if fixing spin density on the rare earth atoms will solve the convergence problem and if so how? What other measures could be taken? Could anybody reccommend to me some references on the calculations of rare earth system? Thank you very much for the help! Jingyi Shen From chemistry-request@server.ccl.net Tue Oct 2 10:20:01 2001 Received: from lancelot.imb-jena.de ([192.124.248.76]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f92EK0505118 for ; Tue, 2 Oct 2001 10:20:00 -0400 Received: (from pineda@localhost) by lancelot.imb-jena.de (SGI-8.9.3/8.8.8) id QAA83915 for chemistry@ccl.net; Tue, 2 Oct 2001 16:20:00 +0200 (CEST) From: pineda@imb-jena.de (Felipe Pineda) Message-Id: <10110021620.ZM181796@lancelot.imb-jena.de> Date: Tue, 2 Oct 2001 16:19:59 +0000 In-Reply-To: Gao Ying "CCL:protein interfaces" (Sep 27, 9:26am) References: X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@ccl.net Subject: linux cluster vs intranet Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers! I shall be very grateful if someone of you would share with me his/her experiences in building a linux cluster based on 2 or more dual athlon 760MP boxes. The main points of interest are networking devices (ethernet adapter/s on each node, switch, etc.) requirements and the possibility of disk space sharing in such a system (one or several "centralized" HDs on e.g. the frontend node vs "distributed" on each node). Is the difference between running an intranet consisting of such independent linux boxes and a true beowulf cluster only a (clustering) software question, or are the hardware requirements different? Many thanks in advance for your attention and kind feedback. Best regards felipe -- ********************************************************************** * Felipe Pineda,PhD * * Institut fuer Molekulare Biotechnologie * * AG Theoretische Biophysik * * Beutenbergstrasse 11, Jena Vox: +49-3641-65-6491 * * Postfach 100 813, D-07708 Jena, Germany Fax: -6495 * * web: www.imb-jena.de/~pineda * ********************************************************************** ********************************************************************** * DISCLAIMER: Unless indicated otherwise, everything in this note is * * my personal opinion, not an official statement of my employer * ********************************************************************** From chemistry-request@server.ccl.net Tue Oct 2 10:52:34 2001 Received: from ap.stmarys.ca ([140.184.21.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f92EqY505681 for ; Tue, 2 Oct 2001 10:52:34 -0400 Received: from localhost (cpye@localhost) by ap.stmarys.ca (8.11.1/8.11.1) with ESMTP id f92EqUh08705; Tue, 2 Oct 2001 11:52:30 -0300 (ADT) Date: Tue, 2 Oct 2001 11:52:30 -0300 (ADT) From: Cory Pye X-Sender: cpye@ap To: BAN FUQUIANG cc: CHEMISTRY@ccl.net Subject: Re: CCL:escaped charge effects of PCM model In-Reply-To: <200110011802.f91I20s26750@Lucy.UCIS.Dal.Ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 1 Oct 2001, BAN FUQUIANG wrote: > Dear all: > > I am trying to understand the escaped charge effects of the DPCM > (polarizable dielectric model) solvation model. I have two questions: > (1) How the escaped charge effects are defined. > From Gauss's Law, the sum of the surface charges should be equal and opposite to the charge inside the cavity. The sum of the surface charges and the true charge as specified in the Gaussian input is the escaped (or outlying) charge. It is due to the fact that some of the electron density resides outside the cavity. You can avoid a good chunk of the escaped charge effects by the COSMO model CPCM. I coded a similar solvation model in the ADF package while post-doc'ing in Calgary. The original genius behind the model was Klamt (now at COSMOlogic). > (2) How can I analyze the escaped charge effects of a DPCM > calculation using Gaussian 98 program. > > Thanks > ************* ! Dr. Cory C. Pye ***************** ! Assistant Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye@crux.stmarys.ca http://apwww.stmarys.ca/cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From chemistry-request@server.ccl.net Tue Oct 2 11:22:43 2001 Received: from mail.gmd.de ([129.26.8.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f92FMg506064 for ; Tue, 2 Oct 2001 11:22:43 -0400 Received: from cartan.gmd.de (cartan [129.26.8.171]) by mail.gmd.de (8.9.3/8.9.3) with ESMTP id RAA18455; Tue, 2 Oct 2001 17:22:40 +0200 (MET DST) Received: from escher (escher [129.26.8.103]) by cartan.gmd.de (8.10.2+Sun/8.10.2) with SMTP id f92FLWh14260; Tue, 2 Oct 2001 17:21:32 +0200 (MEST) Message-Id: <200110021521.f92FLWh14260@cartan.gmd.de> Date: Tue, 2 Oct 2001 17:22:40 +0200 (MEST) From: Christian Buning Reply-To: Christian Buning Subject: Re: Ask for a dock program To: chemistry@ccl.net Cc: yuntang@ncifcrf.gov MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: A0Kkx5pQLyv2nvEz76NImw== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.4.2 SunOS 5.8 sun4u sparc Dear Yun, I would like to correct the info you gave in your request. FlexX is in fact able to consider both metal ions and DNA as part of the active site, so it might be a good choice for your problem. Christian > >BlankDear CCLers, > >I am very interested in docking a small molecule into the active site of a protein-DNA complex. The active site is supposed to be made up of part of protein, part of DNA, and Mg2+ ions. I have tried to use DOCK, AutoDock and FlexX to do it. Unfortunately, it seems that all these programs have not considered DNA and Mg2+ ions as parts of the active site or receptor yet. > >I am just wondering if anybody has similar experience or knows any program to handle such docking problem. Any suggestion or advice would be highly appreciated! > >Best regards, > >Yun >******************************************************************* >* Yun TANG, Ph.D. * >* Laboratory of Medicinal Chemistry Tel: 301-846-5974 (O) * >* Center for Cancer Research 301-668-8935 (H) * >* National Cancer Institute, NIH * >* 376 Boyles Street Fax: 301-846-6033 * >* Frederick, MD 21702 E-Mail: yuntang@helix.nih.gov * >******************************************************************* ------------------------------------------------------------------------ Dr. Christian Buning Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI) Schloss Birlinghoven D-53754 Sankt Augustin Tel: +49 - 2241 - 14 - 2997 Fax: +49 - 2241 - 14 - 2656 E-mail: Christian.Buning@scai.fraunhofer.de Internet: http://www.scai.fraunhofer.de ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Tue Oct 2 12:12:30 2001 Received: from sun2.ruf.uni-freiburg.de ([132.230.1.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f92GCT506942 for ; Tue, 2 Oct 2001 12:12:29 -0400 Received: from uni-freiburg.de (PC2-IR4.physchem.uni-freiburg.de [132.230.171.109]) by sun2.ruf.uni-freiburg.de (8.9.3+Sun/8.9.1) with ESMTP id SAA12576; Tue, 2 Oct 2001 18:12:28 +0200 (MET DST) Message-ID: <3BB9E858.E326821C@uni-freiburg.de> Date: Tue, 02 Oct 2001 18:16:24 +0200 From: Oliver Hucke X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, yuntang@ncifcrf.gov Subject: Re: Ask for a dock program References: <00c301c14a9a$22699b90$961b2b81@661301> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Yun, we use FlexX for ligand docking calculations. With this program, you can include non protein structures as part of the receptor. I have done so with Chlorophylls and Pheophytines and it should be possible with DNA as well, if you include it as hetero-file in the rdf file (you have to convert your dna to the mol2 format for this purpose - this is documented in the manual in the section about the receptor description file). We also had the problem with the inclusion of mg. It could be solved by the inclusion of the following lines in the amino.dat file (~/flex/static_data/ dircectory): @template _mg atom mg iact mg - - - metal metal_sp The MG in our pdb file was named MG2, so that we had to add the following line to the @templates section of our receptor description file: MG2 * * _mg Hope this helps. Let me know if you have further questions. Kind regards, Oliver ______________________________________ Oliver Hucke Inst. fuer Physikalische Chemie II Universitaet Freiburg Albertstr. 23a D-79104 Freiburg Tel. : +49-761-203-5130 (/-6179) Fax. : +49-761-203-6189 email: hucke@uni-freiburg.de ______________________________________ From chemistry-request@server.ccl.net Tue Oct 2 12:07:46 2001 Received: from mailhub1.shef.ac.uk ([143.167.1.9]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f92G7k506887 for ; Tue, 2 Oct 2001 12:07:46 -0400 Received: from ramsley.shef.ac.uk ([143.167.103.254]) by mailhub1.shef.ac.uk with esmtp (Exim 3.22 #4) id 15oS5B-000694-00; Tue, 02 Oct 2001 17:07:45 +0100 Received: from RAMSLEY/SpoolDir by ramsley.shef.ac.uk (Mercury 1.48); 2 Oct 01 17:16:03 +0100 Received: from SpoolDir by RAMSLEY (Mercury 1.48); 2 Oct 01 17:16:00 +0100 From: "Nick Rhodes" To: CHEMISTRY@ccl.net Date: Tue, 2 Oct 2001 17:15:53 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:Sequence assembly/reconstruction in chemistry CC: egonw@sci.kun.nl Priority: normal In-reply-to: <200110021013.f92ADSr12388@studs3.sci.kun.nl> X-mailer: Pegasus Mail for Win32 (v3.12a) Message-Id: > i am writing a literature review on sequence assembly/reconstruction in > (bio)chemistry. I am familiar with the DNA/RNA reconstruction from digests, > bu i was wondering if there are other sequence assembly problems in > (biochemistry). > > I am looking for: > 1. a good review/tutorial on DNA/RNA reconstruction > (recent techniques for dealing with DNA repetition, performance of > algorithms etc) Have a look at "Algorithms on strings, trees and sequences - computer science and computational biology" by Dan Gusfield, Cambridge University Press, 1997. Could you please post a summary of the responses that you get? Good luck, Nick ***************************************************************** Nick Rhodes, Computational Information Systems Research Group, Department of Information Studies, University of Sheffield, Regent Court, 211 Portobello Street, Sheffield, South Yorkshire, S1 4DP, United Kingdom. From chemistry-request@server.ccl.net Tue Oct 2 09:23:31 2001 Received: from france.chem.duke.edu ([152.3.169.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f92DNV503268 for ; Tue, 2 Oct 2001 09:23:31 -0400 Received: from mole.chem.duke.edu (mole.chem.duke.edu [152.3.169.102]) by france.chem.duke.edu (8.9.3/8.9.3) with ESMTP id JAA05706 for ; Tue, 2 Oct 2001 09:23:30 -0400 (EDT) Received: from localhost (andres@localhost) by mole.chem.duke.edu (8.9.3+Sun/8.9.1) with ESMTP id JAA22075 for ; Tue, 2 Oct 2001 09:23:30 -0400 (EDT) X-Authentication-Warning: mole.chem.duke.edu: andres owned process doing -bs Date: Tue, 2 Oct 2001 09:23:29 -0400 (EDT) From: Gerardo Andres Cisneros To: chemistry@ccl.net Subject: parallel g98 on AMD? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello I've managed to compile and run g98 on an AMD platform using the blas libraries for intel (recomended by gaussian). However this machine is dual processor but every time I try to run the same job in parallel I get the following error message: %g98 tim0_2pAMD shmget failed.: Invalid argument I have no problem running this job using a single processor. I haven't installed Linda on this machine but since it's dual processor I don't see the need for it, or should I?. Thanks in advance, Andres -- G. Andres Cisneros Department of Chemistry Duke University andres@chem.duke.edu From chemistry-request@server.ccl.net Tue Oct 2 14:28:34 2001 Received: from cranc02.cra.canon.com ([146.184.1.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f92ISX508898 for ; Tue, 2 Oct 2001 14:28:33 -0400 Received: by cranc02.cra.canon.com with Internet Mail Service (5.5.2653.19) id ; Tue, 2 Oct 2001 11:28:33 -0700 Message-ID: <3FD2BCBD9153D41192B100C04F1FD832728433@cranc02.cra.canon.com> From: "Thoms, Travis" To: "Computational Chemistry List (E-mail)" Subject: What is a reasonable length of time for a DFT geometry optimizati on? Date: Tue, 2 Oct 2001 11:28:29 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Greetings! I am currently running a DFT geometry optimization for the molecule Ir(phenylpyridine)3 (Gamess US, 750MHz Duron). It is currently on its third week of calculation, and it is still not finished. Can anyone tell me how to develop a sense for how long these things take,and maybe some clues on how to shorten the run? Thanks, Travis Thoms Research Associate Canon R&D Center Americas. inc. Telephone: 1-408-468-2864 Facsimile:1-408-468-2810 tthoms@cra.canon.com From chemistry-request@server.ccl.net Tue Oct 2 15:18:57 2001 Received: from mr.usu.edu ([129.123.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f92JIv509861 for ; Tue, 2 Oct 2001 15:18:57 -0400 Received: from tapaskar (tapaskar.chem.usu.edu [129.123.3.37]) by mr.usu.edu (Postfix) with SMTP id 3466D1D2C0 for ; Tue, 2 Oct 2001 13:18:56 -0600 (MDT) Message-ID: <008901c14b76$dbb4fc20$25037b81@tapaskar> From: "Tapas Kar" To: "CCL" Subject: HAl-NH, H2Al-NH2 references Date: Tue, 2 Oct 2001 13:17:20 -0600 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Hi, I am looking for theo & Expt references for the following molecules or their derivatives. HAl-NH, H2Al-NH2 and H3Al-NH3 Thanks, Tapas ------------------------------------------------------------------ "We owe a lot to the Indians, who taught us how to count, without which no worthwhile scientific discovery could have been made." - Albert Einstein - ------------------------------------------------------------------ Tapas Kar, Ph. D Department of Chemistry & Biochemistry Utah State University Logan, UT 84322-0300 Tel: 435-797-7230 Fax: 435-797-3390 Email: tapaskar@cc.usu.edu tapas@risky3.chem.usu.edu From chemistry-request@server.ccl.net Tue Oct 2 15:51:33 2001 Received: from phm.utoronto.ca ([128.100.70.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f92JpW510506 for ; Tue, 2 Oct 2001 15:51:33 -0400 Received: from phm.utoronto.ca (lpk04.phm.utoronto.ca [128.100.70.180]) by phm.utoronto.ca (8.9.3+Sun/8.9.3) with ESMTP id PAA05279 for ; Tue, 2 Oct 2001 15:45:17 -0400 (EDT) Sender: william@phm.utoronto.ca Message-ID: <3BBA1A4D.134247AE@phm.utoronto.ca> Date: Tue, 02 Oct 2001 15:49:33 -0400 From: William Wei Reply-To: william@phm.utoronto.ca Organization: Faculty of Pharmacy, U of T X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Help for ssh! Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Dear CClers, I want a free software of ssh server code for IRIX6.5 in SGI octane workstation. I have download openssh and ossh, but they all can not be compiled successfully in my machine. Any help is appreciated. Thanks. William. From chemistry-request@server.ccl.net Tue Oct 2 13:39:27 2001 Received: from atom.chem.utk.edu (IDENT:qmailr@[160.36.200.55]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f92HdQ508406 for ; Tue, 2 Oct 2001 13:39:27 -0400 Received: (qmail 29785 invoked by uid 1012); 2 Oct 2001 18:04:52 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 2 Oct 2001 18:04:52 -0000 Date: Tue, 2 Oct 2001 14:04:52 -0400 (EDT) From: To: chemistry@ccl.net Subject: GAMESS: how to perform very large CISD calcs using GUGA Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear fellow GAMESS users: I am trying to perform a CISD calculation on H2 using a very large atomic basis set (250 to 350 one-electron basis functions). I'm running GAMESS version 6 SEP 2001 (R2) and using CITYP=GUGA to exploit the high point group symmetry of H2. Once I go past 200 one-electron basis functions I get a message from subroutine DRTSYM: NEXT IS TOO LARGE Any ideas on how to work around this limit using CITYP=GUGA? Thanks in advance, RJH -- Robert J. Hinde Department of Chemistry University of Tennessee Knoxville, TN 37996-1600 865-974-4840 voice 865-974-3454 fax rhinde@utk.edu // preferred attachment formats: PDF, RTF, text my schedule is at http://proton.chem.utk.edu/~hinde/schedule.html From chemistry-request@server.ccl.net Tue Oct 2 13:49:59 2001 Received: from c001.snv.cp.net ([209.228.32.118]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f92Hnx508546 for ; Tue, 2 Oct 2001 13:49:59 -0400 Received: (cpmta 5279 invoked from network); 2 Oct 2001 10:49:53 -0700 Date: 2 Oct 2001 10:49:53 -0700 Message-ID: <20011002174953.5278.cpmta@c001.snv.cp.net> X-Sent: 2 Oct 2001 17:49:53 GMT Received: from [199.98.21.13] by mail.roberttopper.com with HTTP; 02 Oct 2001 10:49:53 PDT Content-Type: text/plain Content-Disposition: inline Mime-Version: 1.0 To: CHEMISTRY@ccl.net From: Robert Topper Cc: roberttopper@roberttopper.com X-Mailer: Web Mail 3.9.3.5 Subject: ECCC8 Preliminary Announcement X-Sent-From: roberttopper@roberttopper.com Dear colleagues, We are pleased to notify you that the Eighth Electronic Computational Chemistry Conference (ECCC8) will be held during the month of March 2002, entirely on the Internet, at http://eccc8.cooper.edu . As in previous years, the conference is multidisciplinary and covers all aspects of computational and theoretical chemistry, as well as computational molecular biology and computational and theoretical molecular and atomic physics. Participants will be able to view the presentations and discuss them entirely through a web browser. As with the previous seven ECCCs, ECCC8 has NO registration fee and is a completely virtual, online conference. Abstracts for all contributions to ECCC8 will be reviewed by the Scientific Organizing Committee (SOC) to insure novelty, scientific value, and appopriateness for inclusion in the conference. The members of the SOC will be announced soon. Nominations for the SOC (including self-nominations) are hereby solicited. Contributions should be presented in HTML format, and ideally will take full advantage of the interactive nature of the World-Wide Web to present their findings and conclusions. In addition to completed work, work in progress is also acceptable for an ECCC8 presentation. Authors may choose to either serve their contributions from their own local web site, or upload them to the ECCC8 server. Uploaded contributions will be removed from the server at the end of ECCC8. All authors are additionally encouraged to submit their work for peer review and subsequent publication in the ECCC8 Proceedings. Current plans call for the proceedings to be published in Theoretical Chemistry Accounts. This peer review will be separate from, and in addition to, the review of abstracts for the presentations. More information on how authors may prepare their contribution for possible inclusion in the proceedings will follow soon. Detailed general information on Theoretical Chemistry Accounts can be found at http://link.springer.de/link/service/journals/00214/index.htm As in ECCC7, a single weeklong "interactive" session will be part of the conference. This session will be held via asynchronous postings of questions to the conference site, which authors can choose to receive either at the site, at their personal email account, or both. All authors must commit to having at least one co-author available (i.e. checking the discussion board at least daily) during the "interactive" session to provide timely responses (within approximately 24 hours) to any questions that conferees may have about their online presentation. Failure to participate in the interactive session may result in the "poster" or "paper" being withdrawn from the conference. Important dates for ECCC8 are: January 18, 2002 - Abstracts of "posters" due February 11, 2002 - Registration opens February 27, 2002 - Final "posters" due March 4, 2002 - Conference begins March 18, 2002 - Interactive Session begins March 24, 2002 - Interactive Session ends April 1, 2002 - ECCC8 ends May 27, 2002 - All papers due for TCA Proceedings Please note that the deadline for receipt of an abstract for the conference is January 18, 2002. Please also note that "posters" which are not completely ready by the beginning of the conference may be considered to be withdrawn. Complete details on how the conference will operate, abstract submission, and conference registration will be found at http://eccc8.cooper.edu This site is not yet open but will be online in the near future. We invite all interested parties to contribute to ECCC8 and participate! Please share this announcement with your colleagues and post it wherever appropriate so that ECCC can continue to thrive and be a vital meeting for the computational chemistry community. Also, please feel free to email us with your questions or comments. Robert Topper, Department of Chemistry (topper@cooper.edu) ECCC8 Principal Organizer and Co-Chair, ECCC8 Web Team Chris Lent and Bob Hopkins, Cooper Union Computer Center Co-Chairs, ECCC8 Web Team School of Engineering The Cooper Union for the Advancement of Science and Art 51 Astor Place New York, NY 10003 From chemistry-request@server.ccl.net Tue Oct 2 12:47:11 2001 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f92GlA507567 for ; Tue, 2 Oct 2001 12:47:11 -0400 Received: from sun5.lrz-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP; Tue, 2 Oct 2001 18:47:09 +0200 Received: from localhost (ui22204@localhost) by sun5.lrz-muenchen.de (8.8.8+Sun/8.8.8) with ESMTP id SAA05776; Tue, 2 Oct 2001 18:47:08 +0200 (MET DST) X-Authentication-Warning: sun5.lrz-muenchen.de: ui22204 owned process doing -bs Date: Tue, 2 Oct 2001 18:47:08 +0200 (MET DST) From: Eugene Leitl X-X-Sender: To: Felipe Pineda cc: Subject: Re: CCL:linux cluster vs intranet In-Reply-To: <10110021620.ZM181796@lancelot.imb-jena.de> Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Since I'm getting tired of forwarding these queries to the Beowulf list http://www.beowulf.org/pipermail/beowulf/ I'm pointing out this resource once again. On Tue, 2 Oct 2001, Felipe Pineda wrote: > Dear CCLers! > > I shall be very grateful if someone of you would share with me his/her > experiences in building a linux cluster based on 2 or more dual athlon 760MP > boxes. The main points of interest are networking devices (ethernet adapter/s > on each node, switch, etc.) requirements and the possibility of disk space > sharing in such a system (one or several "centralized" HDs on e.g. the frontend > node vs "distributed" on each node). Is the difference between running an > intranet consisting of such independent linux boxes and a true beowulf cluster > only a (clustering) software question, or are the hardware requirements > different? > > Many thanks in advance for your attention and kind feedback.