From jkl@ccl.net Sun Jul 26 16:03:55 1998 Return-Path: X-Sender: arichon@208.140.99.1 (Unverified) Message-Id: Date: Sun, 26 Jul 1998 16:03:04 +0100 To: jkl@ccl.net From: netsci@awod.com (Network Science) Subject: Bioinformatics YellowPages Book CD Cc: netsci@awod.com Network Science Corporation is compiling information for The Bioinformatics YellowPages to made available later this year in CD-ROM and pdf format from the NetSci web site. If your company or institution provides software, hardware, databases, laboratory reagents, or services, please contact us at netsci@awod.com for information inclusion in the book. Company information will be listed at no charge. Network Science netsci@awod.com From 9702029k@lv.levels.unisa.edu.au Wed Jul 29 01:51:50 1998 Received: from LV.Levels.UniSA.Edu.Au (SYSTEM@LV.levels.unisa.edu.au [130.220.16.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id BAA09062 Wed, 29 Jul 1998 01:51:48 -0400 (EDT) Received: from xiy205359.unisa.edu.au ("port 2536"@XIY205359.Levels.UniSA.Edu.Au) by Levels.UniSA.Edu.Au (PMDF V5.1-10 #27872) with SMTP id <01IZZ78XW9OA8WXBJI@Levels.UniSA.Edu.Au> for chemistry@www.ccl.net; Wed, 29 Jul 1998 15:21:46 +0930 Received: by xiy205359.unisa.edu.au with Microsoft Mail id <01BDBB06.1EE899C0@xiy205359.unisa.edu.au>; Wed, 29 Jul 1998 15:32:39 +0930 Date: Wed, 29 Jul 1998 15:32:36 +0930 From: Josh Bowden <9702029k@lv.levels.unisa.edu.au> Subject: RAID 0 on NT (striped sets in software)? To: "'chemistry@www.ccl.net'" Message-id: <01BDBB06.1EE899C0@xiy205359.unisa.edu.au> MIME-version: 1.0 Content-type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id BAA09062 Hello everyone, I should have included this in my last message, but - Has anyone tried the RAID 0 setup on NT (striped sets) (ie software controled RAID) and does it make any difference to disk access times/computational speed? Thankyou Josh Josh Bowden University of South Australia Ian Wark Research Institute 9702029k@lv.levels.unisa.edu.au From huesser@physik.unizh.ch Wed Jul 29 04:23:56 1998 Received: from caprice.physik.unizh.ch (caprice.physik.unizh.ch [130.60.164.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAB10251 Wed, 29 Jul 1998 04:23:55 -0400 (EDT) Received: by caprice.physik.unizh.ch (8.7.3cf2.18) id KAA24477; Wed, 29 Jul 1998 10:23:50 +0200 From: Peter Huesser Message-Id: <199807290823.KAA24477@caprice.physik.unizh.ch> Subject: exchange and correlatio To: CHEMISTRY@www.ccl.net Date: Wed, 29 Jul 1998 10:23:50 +0200 (MEST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hello Does somebody knows a summary of the exchange and correlation energy terms and the ideas behind the approximations. I am also interested in a summary of basis sets. Thank's in advance Peter Huesser Email: huesser@physik.unizh.ch From glendening.cd@pg.com Wed Jul 29 09:03:39 1998 Received: from bbhm.na.pg.com (bbhm.na.pg.com [137.179.109.61]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA11014 Wed, 29 Jul 1998 09:03:38 -0400 (EDT) From: glendening.cd@pg.com Received: from bbhm.na.pg.com (bbhm.na.pg.com [137.179.109.61]) by bbhm.na.pg.com (8.8.8/8.8.8) with ESMTP id JAA07459 for ; Wed, 29 Jul 1998 09:01:52 -0400 (EDT) Received: (from x400@localhost) by bbhm.na.pg.com (8.7.6/8.7.3) id JAA07454 for chemistry@www.ccl.net; Wed, 29 Jul 1998 09:01:51 -0400 (EDT) Received: from MCI; Wed, 29 Jul 1998 8:59:00 -0400 Date: Wed, 29 Jul 1998 8:59:00 -0400 Subject: Position Available To: chemistry@www.ccl.net Message-Id: X-Mailer: Worldtalk (4.1)/STREAM Procter & Gamble currently has an opening in the Human & Environmental Safety Division for a BS/MS candidate. The position involves building biological databases that are searchable by chemical structure. The application is housed in ORACLE and uses client server technology (ODBC) and an MS Access front-end. Expertise is necessary in organic chemistry and computer science, specifically chemical drawing packages, Windows 95, programming skills, and database development. Reply directly to glendening.cd@pg.com. Cheryl Glendening The Procter & Gamble Co. Miami Valley Laboratories 11810 E. Miami River Rd. Ross, OH 45061 glendening.cd@pg.com From bittner@UH.EDU Wed Jul 29 11:59:27 1998 Received: from Post-Office.UH.EDU (pmdf@Post-Office.UH.EDU [129.7.1.20]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA12578 Wed, 29 Jul 1998 11:59:27 -0400 (EDT) Received: from Denali (Denali.Chem.UH.EDU) by Post-Office.UH.EDU (PMDF V5.1-10 #U2811) with SMTP id <0EWV002KP5R382@Post-Office.UH.EDU> for chemistry@www.ccl.net; Wed, 29 Jul 1998 10:59:28 -0500 (CDT) Date: Wed, 29 Jul 1998 10:57:03 -0500 From: "Eric R. Bittner" Subject: gradients of overlap integrals Sender: bittner@Post-Office.UH.EDU To: chemistry@www.ccl.net Message-id: <35BF464F.15FB@uh.edu> Organization: university of houston MIME-version: 1.0 X-Mailer: Mozilla 3.04GoldC-SGI (X11; I; IRIX 6.3 IP32) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Greatings CCL'ers We need to calculate the gradient of an overlap integral between tight-binding basis functions. i.e. we need d/dx I believe these are called "Pulay forces" but I have not been able to dig up a reference to that effect. Is there a standard reference or technique for computing these? Thanks, ERB -- Eric R. Bittner bittner@uh.edu Dept. of Chemistry ph: 713-743-2775 University of Houston fax: 713-743-2709 Houston TX 77204 http://k2.chem.uh.edu/bittner/ "confutatis maledictis, flammis acribus addictis..." From anina01@mail.cryst.bbk.ac.uk Tue Jul 28 09:27:57 1998 Received: from pandora.cryst.bbk.ac.uk (pandora.cryst.bbk.ac.uk [192.84.212.49]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA27251 Tue, 28 Jul 1998 09:27:56 -0400 (EDT) Received: from localhost (anina01@localhost) by pandora.cryst.bbk.ac.uk (8.8.7/8.8.7) with SMTP id OAA06836; Tue, 28 Jul 1998 14:33:25 +0100 X-Authentication-Warning: pandora.cryst.bbk.ac.uk: anina01 owned process doing -bs Date: Tue, 28 Jul 1998 14:33:25 +0100 (BST) From: Alex Ninaber X-Sender: anina01@pandora.cryst.bbk.ac.uk Reply-To: Alex Ninaber To: chemistry@www.ccl.net Subject: Re: CCL:Hardware for modeling In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, To give you another alternative: in the UK DEC 533 computers are currently sold for 1500 pounds (~1000 dollar). I think you have to buy a cheap PC monitor with that and some extra ram. It uses Linux as operating system, so a lot of software should work. If you want DEC Unix it will cost you an extra 1000 or so (not really worth it, it seems). I think the DEC will beat the PII233 at least 3-4 times if it comes to number crunching. The reason why it is so cheap is that Samsung apparently is making very cheap clone motherboards for the DEC chip. Compusys (or sis?) is selling them and Annex as well, if you ask for it. Tomorrow we will get our test machine, if everything is ok, we will buy 8 more and start a farm. Another thing: I am not sure how well the multiprocessor part is implemented in Linux. I read the kernel mail digest often, and some problems seem to occur with it (not always). Also, remember that software is usually not optimized for a multiprocessor Linux environment, so you probably end up running two programs, one on each processor (maybe you can solve that with running MPI on top of it, depending on the program). Alex On Tue, 28 Jul 1998, Marcos Villarreal wrote: > > Hi CCLers. > > I am starting my PhD in Chemistry. I will study Lipid-Protein > interaccion whit empiricals force fields. We have few > computer resourses, so we are going to by one computer. > We have aronud $ 3000 and the way I see, we have two alternatives: > a) one single procesor Pentium 2 of 400 whit one disk of 9 Gb. > b) two procesor Pentium 2 of 266 whit two disks of 4 Gb. > Both whit 128 Mb RAM and RED HAT Linux. I will be the only one > using this machine. > Which one is the best for MM/MD. > Thank you very much in advance. > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: arloa@dqo.fcq.unc.edu.ar > -- Original Sender From: Address: arloa@dqo.fcq.unc.edu.ar > 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 lavelle@mbi.ucla.edu Tue Jul 28 14:38:54 1998 Received: from theta1.ben2.ucla.edu (theta1.ben2.ucla.edu [164.67.131.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA29907 Tue, 28 Jul 1998 14:38:53 -0400 (EDT) Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by theta1.ben2.ucla.edu (8.8.8/8.8.8) with SMTP id LAA20982; Tue, 28 Jul 1998 11:38:53 -0700 Received: from pc-ll.chem.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA02013; Tue, 28 Jul 1998 11:38:50 -0700 Message-Id: <9807281838.AA02013@ewald.mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0 Date: Tue, 28 Jul 1998 11:40:47 -0700 To: chemistry@www.ccl.net From: Laurence Lavelle Subject: Re: CCL:Hardware for modeling In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi Marcos, If you have a multithread application then dual pentium (new motherboards should take up to dual PII 450 which leaves room for CPU upgrade when prices drop). If you do not have a multithread application but will use the machine at same time for other applications then MD application will have one CPU and the other CPU will take care of system overhead (esp. SCSI) and handle any other application. Or you can run two MD jobs at same time (each will have about 90% CPU time (although this depends on HD activity)) if RAM is not a problem. Depends on your run. If your doing only MM/MD then 128MB RAM should be ok. If you plan on any ab initio don't get any motherboard that takes less than 512MB. DRAM is now very cheap and you will want to add more. If you do not have a multithread application and heavy MD runs then go with PII 400. You want max cache and 100MHz motherboard. It is difficult to compare systems without details but my guess is that the dual 266 is older while PII 400 is newer. That means newer chipset etc., better performance all round. Laurence At 09:25 AM 7/28/98 -0300, Marcos Villarreal wrote: > >Hi CCLers. > >I am starting my PhD in Chemistry. I will study Lipid-Protein >interaccion whit empiricals force fields. We have few >computer resourses, so we are going to by one computer. >We have aronud $ 3000 and the way I see, we have two alternatives: >a) one single procesor Pentium 2 of 400 whit one disk of 9 Gb. >b) two procesor Pentium 2 of 266 whit two disks of 4 Gb. >Both whit 128 Mb RAM and RED HAT Linux. I will be the only one >using this machine. >Which one is the best for MM/MD. > Thank you very much in advance. > > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: arloa@dqo.fcq.unc.edu.ar >-- Original Sender From: Address: arloa@dqo.fcq.unc.edu.ar >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 tsonchev+@pitt.edu Wed Jul 29 13:06:23 1998 Received: from post-ofc05.srv.cis.pitt.edu (root@post-ofc05.srv.cis.pitt.edu [136.142.185.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA13612 Wed, 29 Jul 1998 13:06:22 -0400 (EDT) Received: from unixs1.cis.pitt.edu (tsonchev@unixs1.cis.pitt.edu [136.142.185.31]) by post-ofc05.srv.cis.pitt.edu with SMTP (8.8.8/8.8.8/cispo-7.2.2.2) ID for ; Wed, 29 Jul 1998 13:06:22 -0400 (EDT) Date: Wed, 29 Jul 1998 13:06:22 -0400 (EDT) From: Stefan Tsonchev X-Sender: tsonchev@unixs1.cis.pitt.edu To: chemistry@www.ccl.net Subject: Lanczos Algorithm request Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello: I need a program to solve the eigenvalue problem for a very large (tens of thousands of lines) sparse matrix. It should use the Lanczos methos for finding the lowest eigenvalues (which is what I need). All the programs that I have seen seem to require the matrix as an input. However, the advantage of the problem that I am dealing with is that I do not need to generate the matrix. I have a simple rule for generating its elements, only a small number of which are non-zero. I wonder if someone could refer me to a program that does solve this kind of problem without generating the matrix, but only needs to be given the rule for creating its elements? I will appreciate your help. Stefan Tsonchev, tsonchev+@pitt.edu From mchalla@ice.lanl.gov Wed Jul 29 13:34:36 1998 Received: from ice.lanl.gov (ice.lanl.gov [128.165.22.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA13938 Wed, 29 Jul 1998 13:34:35 -0400 (EDT) Received: from localhost (mchalla@localhost) by ice.lanl.gov (8.8.7/8.8.7) with SMTP id LAA28468; Wed, 29 Jul 1998 11:31:01 -0600 Date: Wed, 29 Jul 1998 11:31:01 -0600 (MDT) From: Matt Challacombe T-12 To: Stefan Tsonchev cc: chemistry@www.ccl.net Subject: Re: CCL:Lanczos Algorithm request In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Stefan, Try ARPACK, available from netlib. Cheers, Matt +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ Matt Challacombe Los Alamos National Laboratory http://www.t12.lanl.gov/~mchalla/ Theoretical Division email: mchalla@t12.lanl.gov Group T-12, Mail Stop B268 phone: (505) 665-5905 Los Alamos, New Mexico 87545 fax: (505) 665-3909 +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ On Wed, 29 Jul 1998, Stefan Tsonchev wrote: > > Hello: > > I need a program to solve the eigenvalue problem for a very large (tens > of thousands of lines) sparse matrix. It should use the Lanczos methos > for finding the lowest eigenvalues (which is what I need). All the > programs that I have seen seem to require the matrix as an input. > However, the advantage of the problem that I am dealing with is that I > do not need to generate the matrix. I have a simple rule for generating > its elements, only a small number of which are non-zero. > > I wonder if someone could refer me to a program that does solve this > kind of problem without generating the matrix, but only needs to be > given the rule for creating its elements? I will appreciate your help. > > Stefan Tsonchev, > tsonchev+@pitt.edu > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: tsonchev+@pitt.edu > -- Original Sender From: Address: tsonchev+@pitt.edu > 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 srk@engc.bu.edu Wed Jul 29 14:52:10 1998 Received: from engc.bu.edu (3v6wgAoh8nbtOyrU27Wh8eNZPzltw8Og@ENGC.BU.EDU [128.197.185.241]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA14529 Wed, 29 Jul 1998 14:52:09 -0400 (EDT) Received: (from srk@localhost) by engc.bu.edu ((8.8.8.buoit.b4)/8.8.8/(BU-W-06/24/98-b7)) id OAA27648; Wed, 29 Jul 1998 14:52:10 -0400 (EDT) From: "S. Roy Kimura" Message-Id: <199807291852.OAA27648@engc.bu.edu> Subject: TINKER vs CHARMm To: chemistry@www.ccl.net Date: Wed, 29 Jul 1998 14:52:10 -0400 (EDT) Cc: srk@engc.bu.edu X-Mailer: ELM [version 2.4ME+ PL19 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCLers, Recently, I have been thinking about using the TINKER package (by Jay Ponder) rather than CHARMm since TINKER's source looks much easier to modify. As a check, I decided to calculate the internal energy of a 9 residue peptide in vaccuum using both the CHARMm and TINKER programs. However, I have been getting rather different energies even though I used the same parameter sets and identical coordinates (for TINKER, I used the charmm.prm file supplied with the TINKER distribution which is supposed to be equivalent to CHARMm22 parameters). Does anyone have any idea what the problem might be? Roy ----- S. Roy Kimura Molecular Engineering Research Laboratory Department of Biomedical Engineering Boston University email: srk@bu.edu phone: (617)353-4697 From smb@smb.chem.niu.edu Wed Jul 29 17:14:57 1998 Received: from cz2.chem.niu.edu (cz2.chem.niu.edu [131.156.9.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id RAA15322 Wed, 29 Jul 1998 17:14:57 -0400 (EDT) Received: from cz.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/920502.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA22387; Wed, 29 Jul 98 15:24:31 -0500 Received: from smb.chem.niu.edu by cz.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA18443; Wed, 29 Jul 98 16:24:33 -0500 Received: from smb by smb.chem.niu.edu via SMTP (940816.SGI.8.6.9/940406.SGI) for id QAA01097; Wed, 29 Jul 1998 16:12:48 -0500 Sender: smb@smb.chem.niu.edu Message-Id: <35BF904F.3F54@smb.chem.niu.edu> Date: Wed, 29 Jul 1998 16:12:47 -0500 From: Steven Bachrach X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP12) Mime-Version: 1.0 To: computational chemistry list Subject: ECCC-5 Full Announcement Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The Fifth Electronic Computational Chemistry Conference (ECCC-5) will be held November 2-30, 1998 entirely on the world-wide web. All areas of computational chemistry are covered by this conference, from QSAR to ab intio to MD to use of computers in education. There is NO REGISTRATION FEE for ECCC5. Therefore, we strongly encourage all computational chemists to participate! All contributions are web-based articles that will be mounted either on the conference server or on an author's local werver. Articles may be either "papers" - those that will be submitted to the official proceedings for publication in the Internet Journal of Chemistry (www.ijc.com) - or "posters" - which will be posted only for the duration of the conference. Discussions of these contributions will be enabled through a web-based form system. Each participant can read and respond to any comment on any article. Complete details on registration, abstract submission, article creation, etc. can be found at the ECCC-5 web site http://hackberry.chem.niu.edu/ECCC5/ IMPORTANT DATES: September 25, 1998 - Abstracts of Papers due October 5, 1998 - Registration Opens October 23, 1998 - Final Papers and Posters due November 2, 1998 - Conference Begins November 30, 1998 - Conference Ends On behalf of the ECCC-5 Scientific Organizing Committee: Steven M. Bachrach, Northern Illinois University Tom Cundari, University of Memphis David Deerfield, Pitssburgh Supercomputer Scenter Herbert Homeier, Universitaet Regensburg Anne McCoy, Ohio State University Charles Reynolds, Rohm and Haas -- Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802