From chemistry-request@server.ccl.net Wed Jan 5 23:10:42 2000 Received: from sundown.cs.cornell.edu (SUNDOWN.CS.CORNELL.EDU [128.84.96.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA21324 for ; Wed, 5 Jan 2000 23:10:42 -0500 Received: from FAFE.CS.CORNELL.EDU (IDENT:avijit@FAFE.CS.CORNELL.EDU [128.84.211.80]) by sundown.cs.cornell.edu (8.9.3/8.9.3/R-3.0) with ESMTP id WAA04409 for ; Wed, 5 Jan 2000 22:01:45 -0500 (EST) Date: Wed, 5 Jan 2000 22:01:41 -0500 (EST) From: Avijit Ghosh To: chemistry@ccl.net Subject: Building one's own cluster and 4 gig MB's In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL Members, We are currently considering buying a cluster of machines for || MPI work, as well as a four gig box using the ungodly expensive AMI Megaplex mother board. My question in particular is how are people's experiences using the AMI motherboard w/ both solaris and/or linux (w/ the current set of patches) at 4 gigs. Are there are any obvious incompatibilities that we should be concerned with. (I've been assured that there are stable bigmem patches floating around somewhere). Also, in a fit of madness we are somewhat hesitantly considering getting dual celeron (500mhz) boxes rather than dual PIII's (The celerons would be sitting on the same mb and would have 100 mhz ram etc (allegedly). The tradeoff would be only perhaps then the 128k full speed cache v 512k 1/2 speed cache and the specfp ratings of the celeron v pIII doesn't look so bad. Needless to say, most people don't build clusters w/ celeron boxes but the pricing ($1100 v $1400 w/ 256 megs) seems good enough to at least consider before chalking it off as a bit of delirium caused by too much alcohol. In any case, any bits of wisdom, advice and such would be very much appreciated. -Thanks much, Dr. Avi Ghosh From chemistry-request@server.ccl.net Thu Jan 6 08:50:24 2000 Received: from denebola.ceti.etat-ge.ch (denebola.ceti.etat-ge.ch [160.53.239.115]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA24387 for ; Thu, 6 Jan 2000 08:50:23 -0500 Received: by denebola.etat-ge.ch with Internet Mail Service (5.5.2448.0) id ; Thu, 6 Jan 2000 13:39:20 +0100 Message-ID: From: "De Vito David (DIP)" To: "'chemistry@ccl.net'" Subject: Relativistic potentials with Gaussian 98 Date: Thu, 6 Jan 2000 13:39:19 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" I'd like to do some optimisation with relativistic potentials on hexaaqua complexes of rhodium (III) and iridium (III) with Gaussian 98. I have found some good potentials at the Stuttgart University, but I'd like to find some good publications or receive some advices from people that has good knowledges about this delicate subject. Thank you very much for all the help that the scientific community could me give. Best regards from Switzerland, D. De Vito. (reply address: david.devito@chiphy.unige.ch). **************************************************************** D. De Vito Department of Physical Chemistry Group of Prof. Weber (Computational Chemistry) University of Geneva Office 106 - Sciences II 30, Quai Ernest-Ansermet 1211 Geneva 4 / Switzerland +4122 / 702.65.35 (Office) +4122 / 328.92.16 (Home) +4176 / 532.47.40 (Mobile) http://lcta.unige.ch/~devito (Personal Page) http://www.unige.ch/sciences/chimie (Web Master) **************************************************************** From chemistry-request@server.ccl.net Thu Jan 6 00:22:12 2000 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA21646 for ; Thu, 6 Jan 2000 00:22:12 -0500 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id XAA11337 for ; Wed, 5 Jan 2000 23:13:15 -0500 (EST) Sender: desingh@mailbox.syr.edu Message-ID: <3874177C.8EDF4069@syr.edu> Date: Wed, 05 Jan 2000 23:18:04 -0500 From: Deepak Singh Organization: Birge Group, Dept. Of Chemistry, Syracuse Univ. X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: speed up G98 job Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi folks, I am running 2-3 DFT jobs on systems ranging from 25-35 heavy atoms using a route section like this #T B3LYP/6-31G** Opt Test Pop=Reg. I have MAXDISK set to 15GB on my SGI Octane (1.8GB RAM). I think that my jobs are taking longer than they should .. And they are not using up the memory as efficiently as I'd like. I guess what I am looking for is the kind of insight missing in the G98 manual. Thanks Deepak -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Thu Jan 6 02:08:40 2000 Received: from lrz.uni-muenchen.de (eugene.leitl@lsajca1-204-033.dsl.gtei.net [4.3.204.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA22014 for ; Thu, 6 Jan 2000 02:08:39 -0500 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id WAA03289 for ; Wed, 5 Jan 2000 22:56:45 -0800 Resent-From: Eugene Leitl Resent-Message-ID: <14452.15533.282720.223789@lrz.uni-muenchen.de> Resent-Date: Wed, 5 Jan 2000 22:56:45 -0800 (PST) Resent-To: References: Mime-Version: 1.0 (generated by tm-edit 7.106) Content-Type: text/plain; charset=US-ASCII In-Reply-To: Emil Briggs's message of "Tue, 21 Dec 1999 23:28:04 -0500 (EST)" Message-Id: <547lhonouv.fsf@intech19.enhanced.com> Lines: 79 X-Mailer: Gnus v5.5/Emacs 20.3 Precedence: bulk From: To: Emil Briggs Cc: beowulf@beowulf.gsfc.nasa.gov, rgb@phy.duke.edu Subject: Re: BLAS recommendations Date: 05 Jan 2000 17:19:20 -0500 From: Camm Maguire Emil Briggs writes: > 3. For the Level 3 BLAS the ATLAS package is a good solution under > Linux. R. Clint Whaley and Antoine Petitet have released version > 3.0BETA of ATLAS which also has some support for generating > optimized Level 1 and Level 2 BLAS libs. (You can grab it > at http://www.netlib.org/atlas/) > Thanks for the tip about 3.0 beta. It looks good! It is my intention to ship this version with the upcoming Debian release. > The license seems fairly liberal even though it's not GPL. I havn't > benchmarked the new release yet but from looking at the source > I suspect that the Level1 and Level2 performance is not particularly > good yet. The problem is that ATLAS uses GCC which does not take > advantage of the new prefetch instructions supported by the PIII > and the Athlon. For the Level1 and Level2 BLAS libs the use of > these instructions is very important in order to hide main-memory latency. > Preliminary results on our PII 350 machines indicate a speedup (over the reference blas) of 2.5-4x on the level2 routines. While this is significantly below the level3 performance, it is, IMHO, still quite good, and handily outperforms my own hand-tuned gcc level2 code (which also outperformed the netlib reference implementation). In fact, using this lib shaves a nice 30% off the running time of our production code when executed on a single machine. (Of course, to see significant benefits on a cluster, the array sizes have to be quite large when using level2, larger than we use in production currently.) What's even better is the mechanism they've provided for supplying your own level2 primatives, in case you know quite a bit about your hardware, to time against all the others and incorporate into the library if they prove faster. In principle, you could quite simply supply an assemly routine using 'prefetch', and insert it into ATLAS. So my question is: do PII CPU's understand the 'prefetch' instruction? What type of performance gains do you expect when employing this instruction? Any suggestions as to other non-gcc invoked assembler calls which could make a big difference? > The stuff I wrote was assembly language versions of the Level1 BLAS > for the Athlon which use the new prefetch instructions. They're GPL > and could probably be adapted for the PIII fairly easily. (I don't > have a PIII so I havn't done this). You can get these at > > http://nemo.physics.ncsu.edu/~briggs/blas_src_v0.11_tar.gz > > Presumably at some point in the future GCC will be able to generate > better code that uses the new instructions and the assembly language > won't be necessary but for now thats not the case. > Thanks for these examples! Can they be adapted to the PII as well? > For recommendations I would say that ATLAS is a great choice for the > Level3 stuff. If you've got an Athlon then my libs are OK > for the Level1. No recommendations for Level2 (Our codes don't > require much Level2 stuff so it hasn't been a high priority for me). > > > Regards > Emil > > ------------------------------------------------------------------- > To unsubscribe send a message body containing "unsubscribe" > to beowulf-request@beowulf.org Take care, -- Camm Maguire camm@enhanced.com ========================================================================== "The earth is but one country, and mankind its citizens." -- Baha'u'llah ------------------------------------------------------------------- To unsubscribe send a message body containing "unsubscribe" to beowulf-request@beowulf.org From chemistry-request@server.ccl.net Thu Jan 6 03:33:26 2000 Received: from mrelay.inscc.utah.edu (mrelay.inscc.utah.edu [155.101.3.60]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA22311 for ; Thu, 6 Jan 2000 03:33:26 -0500 Received: from mail.inscc.utah.edu (mail.inscc.utah.edu [155.101.3.59]) by mrelay.inscc.utah.edu (8.9.2/8.9.2) with ESMTP id AAA01323; Thu, 6 Jan 2000 00:25:26 -0700 (MST) Received: from localhost.localdomain (loki.chpc.utah.edu [155.101.16.46]) by mail.inscc.utah.edu with ESMTP id AAA25661; Thu, 6 Jan 2000 00:21:04 -0700 (MST) Date: Thu, 6 Jan 2000 00:24:22 -0700 (MST) From: "Brian D. Haymore" To: eugene.leitl@lrz.uni-muenchen.de cc: chemistry@ccl.net Subject: Re: CCL:Building one's own cluster and 4 gig MB's In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would shy away from quad processor boxes due to the limited memory bandwidth in current SMP intel systems. Any use of this type of system that requires memory bandwidth will pay a high penalty. If your specific needs do not, then by all means go for it. A PIII 600 sees around 400MB/s average memory bandwidth with PC-100 memory based on the "streams" tests. Now if you have a quad processor you get 1/4 of 400 per proc which is pathetic. Celerons do an ok job, but our testings have shown that in caculations like Gaussian the cache does kill the performance in comparison to PII/PIII systems. Note, I've not tested with the new coppermine PIII processors that have 256K of full speed cache. Pluss if you use current compilers, probably comercial, you can see some speed benifit of the new SSE instruction set of the PIII that isn't to be hand in the current celeron processor. To step away from that whole idea I'd propose the AMD K7/Athlon processor. Whe have found in our tests it to performe 20-80% faster then the same Mhz Intel processor. That said you can now dedicate a single memory bus to each processor and in many cases get near dual intel processor performance with a single processor. You might want to check with your hardware vendor of choice to see if you can "Demo" hardware that you might like to buy before buying it to test it accourding to your needs. It was in doing just thist that I did my first tests on the Athlon processor. Since then we have been quite exclusive in buying Athlons due to there performance and stability. -- Brian D. Haymore University of Utah Center for High Performance Computing 155 South 1452 East RM 405 Salt Lake City, Ut 84112-0190 Email: brian@chpc.utah.edu - Phone: (801) 585-1755 - Fax: (801) 585-5366 On Wed, 5 Jan 2000 eugene.leitl@lrz.uni-muenchen.de wrote: > > Please reply directly to the original author: > > From: Avijit Ghosh > > Dear CCL Members, > > We are currently considering buying a cluster of machines > for || MPI work, as well as a four gig box using the ungodly expensive AMI > Megaplex mother board. My question in particular is how are people's > experiences using the AMI motherboard w/ both solaris and/or linux (w/ the > current set of patches) at 4 gigs. Are there are any obvious > incompatibilities that we should be concerned with. (I've been assured > that there are stable bigmem patches floating around somewhere). > > Also, in a fit of madness we are somewhat hesitantly considering > getting dual celeron (500mhz) boxes rather than dual PIII's (The celerons > would be sitting on the same mb and would have 100 mhz ram etc > (allegedly). The tradeoff would be only perhaps then the 128k full speed > cache v 512k 1/2 speed cache and the specfp ratings of the celeron v > pIII doesn't look so bad. Needless to say, most people don't build > clusters w/ celeron boxes but the pricing ($1100 v $1400 w/ 256 megs) > seems good enough to at least consider before chalking it off as a bit of > delirium caused by too much alcohol. In any case, any bits of wisdom, > advice and such would be very much appreciated. > > -Thanks much, > Dr. Avi Ghosh > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > ------------------------------------------------------------------- > To unsubscribe send a message body containing "unsubscribe" > to beowulf-request@beowulf.org > From chemistry-request@server.ccl.net Thu Jan 6 12:44:59 2000 Received: from theo1.theochem.tu-muenchen.de ([129.187.191.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA25624 for ; Thu, 6 Jan 2000 12:44:58 -0500 From: kcharoen@theochem.tu-muenchen.de Received: from theo3.theochem.tu-muenchen.de (theo3.theochem.tu-muenchen.de [129.187.157.6]) by theo1.theochem.tu-muenchen.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id RAA19183 for ; Thu, 6 Jan 2000 17:35:10 +0100 Received: by theo3.theochem.tu-muenchen.de (SMI-8.6/SMI-SVR4) id RAA04100; Thu, 6 Jan 2000 17:36:04 +0100 Date: Thu, 6 Jan 2000 17:36:04 +0100 Message-Id: <200001061636.RAA04100@theo3.theochem.tu-muenchen.de> To: chemistry@ccl.net Subject: MM3 Parameters Cc: kcharoen@theo3.theochem.tu-muenchen.de X-Sun-Charset: US-ASCII Dear CCL fellows, I am doing MM3 calculations of organic compounds that contains functional groups using TINKER. Unfortunately, TINKER does not contains parameters required for carboxylic, esters and thiol. I have added carboxylic and esters into the parameter file but I don't have parameters for thiol (-SH and -S-) since our library does not provide the literature. It would be very grateful to you, if somebody could provide me the parameter sets for thiol and sulfide that were published in J. Phys. Org. Chem. 4 (1991) p. 647-658 and J. Phys. Org. Chem. (1991) p. 659-666. Parameters in form of TINKER format is appreciated but not necessary. If I could get such parameters, I am willing to post the whole TINKER MM3 file that are updated with lot of functional groups to the WEB or e-mail. Many thanks in advance. take care, Teerakiat ------------------------------------------------------------------------ Teerakiat Kerdcharoen, Ph.D. Profession: University Lecturer Address: Department of Physics, Mahidol University, Bangkok 10400 Phone: (66)(2)2461381 FAX (66)(2)2461381 Cellular: (66)(1)9547395 E-mail: teerakiat@hotmail.com Homepage: http://einstein.sc.mahidol.ac.th/simulation Research: Computer Simulation / Computational Nanotechnology ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Jan 6 13:06:48 2000 Received: from hydra.chem.rug.nl (hydra.chem.rug.nl [129.125.35.229]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA25766 for ; Thu, 6 Jan 2000 13:06:48 -0500 Received: from [129.125.7.13] (theochem1.chem.rug.nl [129.125.7.13]) by hydra.chem.rug.nl (AIX4.2/UCB 8.7/8.7) with ESMTP id RAA26000 for ; Thu, 6 Jan 2000 17:57:34 +0100 (MET) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: swart@hydra.chem.rug.nl Message-Id: In-Reply-To: <000d01bf503e$ac1c6640$a731c281@unige.ch> Date: Thu, 6 Jan 2000 18:00:36 +0100 To: CHEMISTRY@ccl.net From: Marcel Swart Subject: Re: CCL:Normal modes with ADF99 >Good Morning and best wishes to all the Scientist Community ! > >I have some problems with frequencies calculations with ADF 99. I obtain a >lot of imaginary modes even if the structure seems to be optimized (I have >already successfully performed the jobs at HF level). Could someone help me, >giving some advices about displacements to use (cartesian vs z-mat), >symmetry or numerical precision ? First of all. ADF 99 is a DENSITY FUNCTIONAL program (i.e. the Amsterdam Density Functional program). Everyone knows that DFT gives better geometries than HF, and the geometries from DFT are generally different >from HF ones. Simply because HF lacks electron correlation which IS present in DFT. The fact that you get imaginary frequencies indicates indeed that you do NOT have an optimized geometry. So, I suggest that you first optimize the geometry with ADF99 (CONVERGE grad=1.0e-5), which should not be too difficult, because ADF99 is a fast, accurate and parallel program. Secondly, in the frequencies run, you should use an integration accuracy of at least 6.0, but I personally prefer even higher values. After you have done this, and still get imaginary frequencies, come back for more advice. >The second question is is there any programm that allows me to visualize the >normal modes ? We are using the Cerius 2 package, but the new TAPE21 files >aren't compatible with our version of Cerius 2. Check the ADF homepage (http://www.scm.com) because they include some support for Cerius. Best regards, Marcel Swart ========================================= drs. Marcel Swart Theoretical Chemistry (MSC) Molecular Dynamics (GBB) Rijksuniversiteit Groningen Chemistry Department Nijenborgh 4 9747 AG Groningen The Netherlands tel : +31 - (0)50 - 3634377 fax : +31 - (0)50 - 3634441 E-mail : m.swart@chem.rug.nl WWW: http://hydra.chem.rug.nl/~swart/ ========================================= From chemistry-request@server.ccl.net Thu Jan 6 13:35:30 2000 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA25940 for ; Thu, 6 Jan 2000 13:35:27 -0500 Received: from localhost (noronha@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id PAA38639 for ; Thu, 6 Jan 2000 15:26:10 -0200 Date: Thu, 6 Jan 2000 15:26:10 -0200 (BDB) From: antonio luiz oliveira de noronha To: chemistry@ccl.net Subject: MOPAC2000 - Using CCl4 as a solvent in MST Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Happy 2000 CCl friends. I really need a help. How may I especify the CCl4 instead of water for calculations using the continuum model in MOPAC2000. Best Regards. ___________________________________________________________________ | | |Antonio Luiz Oliveira de Noronha - noronha@dedalus.lcc.ufmg.br | |Medicinal Chemistry of Organotin Compounds | |NEQUIM - Medicinal Chemistry Group | |Chemistry Departament - DQ | |UFMG - Federal University of Minas Gerais - Brazil | |Av. Antonio Carlos, 6627 - Campus Pampulha | |CEP 31270-901 - Belo Horizonte - MG - Brazil | |VOICE +55 31 499 5765 - FAX +55 31 499 5700 | |___________________________________________________________________| From chemistry-request@server.ccl.net Thu Jan 6 10:36:25 2000 Received: from mail4.nycap.rr.com (mail4-1.nyroc.rr.com [24.92.33.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA25039 for ; Thu, 6 Jan 2000 10:36:23 -0500 Received: from claessen.nycap.rr.com ([24.29.72.223]) by mail4.nycap.rr.com (Post.Office MTA v3.5.3 release 223 ID# 0-59787U250000L250000S0V35) with SMTP id com; Thu, 6 Jan 2000 09:29:23 -0500 Reply-To: From: "Rolf Claessen" To: "Carlos Robles V. " , "=?iso-8859-1?Q?Lista_de_Qu=EDmica?=" Subject: RE: I'm looking for a translator Date: Thu, 6 Jan 2000 09:23:49 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3612.1700 In-Reply-To: <200001051551.MAA04805@mail1.manquehue.net> Importance: Normal Hi Carlos, I have made a list of quite a few programs that generate 3D structures from 2D input such as structure drawing programs or smiles. Have a look at http://www.claessen.net/chemistry/soft_mod_en.html 3D Viewer might be the best for your purposes. I also collected addresses of online programs at http://www.claessen.net/chemistry/soft_www_en.html Try ComSpec3D, CyberMol or the VRML File Creator. Good luck, Rolf > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > Behalf Of Carlos Robles V. > Sent: Wednesday, January 05, 2000 1:49 PM > To: Lista de Química > Subject: CCL:I'm looking for a translator > > > Hi, everybody: > > I have files which list topology of the molecule as a list of > atoms (given as elements) and a list of bonds between them > for example: > > atoms 8 > atom C1 0.000 0.000 0.000 > atom C2 0.000 0.000 0.000 > atom H3 0.000 0.000 0.000 > atom H4 0.000 0.000 0.000 > atom H5 0.000 0.000 0.000 > atom H6 0.000 0.000 0.000 > atom H7 0.000 0.000 0.000 > atom H8 0.000 0.000 0.000 > > bonds 7 > bond C1 C2 simple > bond C1 H3 simple > bond C1 H4 simple > bond C1 H5 simple > bond C2 C1 simple > bond C1 H6 simple > bond C1 H7 simple > bond C1 H8 simple > bond H3 C1 simple > bond H4 C1 simple > bond H5 C1 simple > > As can you see, the coordinates values zero, so I need to translate my > input file into a file with the real (or approximate) spacial coordinates > for that molecule. I don't need a program that display the structure (I'll > do by myself after). I know that there is a program called CONCORD > > http://www.tripos.com/software/concord.html > > which takes SMILEs and creates an approximate 3D structure. But i see that > is a commercial program, and I need a freeware or shareware program (under > LINUX), cause it's for educational and research purposes. > > Thanks a lot . > > Carlos Robles V. > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: > gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Jan 6 13:17:33 2000 Received: from mrelay.inscc.utah.edu (mrelay.inscc.utah.edu [155.101.3.60]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA26256 for ; Thu, 6 Jan 2000 13:17:33 -0500 Received: from mail.inscc.utah.edu (mail.inscc.utah.edu [155.101.3.59]) by mrelay.inscc.utah.edu (8.9.2/8.9.2) with ESMTP id LAA03882; Thu, 6 Jan 2000 11:18:01 -0700 (MST) Received: from chpc.utah.edu (loki.chpc.utah.edu [155.101.16.46]) by mail.inscc.utah.edu with ESMTP id LAA29542; Thu, 6 Jan 2000 11:13:37 -0700 (MST) Sender: brian@chpc.utah.edu Message-ID: <3874DC19.30F714F7@chpc.utah.edu> Date: Thu, 06 Jan 2000 11:16:57 -0700 From: "Brian D. Haymore" X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en MIME-Version: 1.0 To: eugene.leitl@lrz.uni-muenchen.de CC: chemistry@ccl.net Subject: Re: CCL:Software for a PC Cluster References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit eugene.leitl@lrz.uni-muenchen.de wrote: > > From: "James G. Macmillan" > > CCL, > > Could someone give me some advice on software that runs under linux on a PC > Parallel Cluster? My experience is with SPARTAN under UNIX and NT. > > Several people in Math, Physics, and Computer Science are planning a PC > Cluster and I have been asked what software I might what to use on the > system. Since SPARTAN does not compile under linux I will need to find a > software package. > > You may want to send your replies directly to me as I am not sure this is of > general interest. > > Jim Macmillan > > ********************************************** > James G. Macmillan, Ph.D. > Department of Chemistry > University of Northern Iowa > Cedar Falls, IA 50614-0423 > > Ph: (319) 273-2476 FAX: (319) 273-7127 > E-mail: macmillan@uni.edu > ICQ: 10405682 > ******************************************** > Wine improves with age. The older I get, the better I like it. - Anonymous > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > ------------------------------------------------------------------- > To unsubscribe send a message body containing "unsubscribe" > to beowulf-request@beowulf.org http://www.beowulf-underground.org http://sal.kachinatech.com/ These are two great sites that list a lot of applications that can run on a beowulf cluster. You might also want to search the boewulf/extreme linux mailing list archives as many announcements of applications have been made over both. -- Brian D. Haymore University of Utah Center for High Performance Computing 155 South 1452 East RM 405 Salt Lake City, Ut 84112-0190 Email: brian@chpc.utah.edu - Phone: (801) 585-1755 - Fax: (801) 585-5366 From chemistry-request@server.ccl.net Thu Jan 6 16:56:06 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA27349 for ; Thu, 6 Jan 2000 16:56:05 -0500 Received: from el1 ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with SMTP id <01JKE3SQZLSU00028F@trentu.ca> for chemistry@ccl.net; Thu, 6 Jan 2000 16:55:26 EST Date: Thu, 06 Jan 2000 16:59:00 -0500 From: Errol Lewars Subject: Y2K (diytterbium potassium) To: chemistry@ccl.net Message-id: <38751024.FBF@trentu.ca> Organization: Trent University MIME-version: 1.0 X-Mailer: Mozilla 3.01Gold (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit 2000 01 06 Hello, I hope CCLers will excuse me for mentioning, just before it ceases to be topical, the molecule Y2K (diytterbium potassium). See _Science_, 17 December 1999, p. 2281. The authors conclude that its preparation is "unlikely to [represent an] explosive event" but that it "could be the material of the millenium." E. Lewars =========== From chemistry-request@server.ccl.net Thu Jan 6 17:30:37 2000 Received: from sirocco.cc.mcgill.ca (sirocco.CC.McGill.CA [132.206.27.12]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA27569 for ; Thu, 6 Jan 2000 17:30:37 -0500 Received: from lansend.cc.mcgill.ca (lansend.CC.McGill.CA [132.206.37.4]) by sirocco.cc.mcgill.ca (8.9.1/8.9.1) with SMTP id RAA25054 for ; Thu, 6 Jan 2000 17:29:59 -0500 (EST) Message-Id: <200001062229.RAA25054@sirocco.cc.mcgill.ca> Received: by MicroMailer 3.72 (.Lan.McGill.CA) on Thu, 06 Jan 2000 17:29:33 -0500 From: "Balakrishnan Viswanathan" Organization: Chemistry Dept., McGill University To: CHEMISTRY@ccl.net Date: Thu, 6 Jan 2000 17:29:35 -0500 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: (Fwd) CCL:Y2K (diytterbium potassium) Reply-to: viswana@chemistry.mcgill.ca X-Confirm-Reading-To: viswana@chemistry.mcgill.ca X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01d) Dear CCLers, I believe the author of the original post is suffering from Y2K problems himself as Y is Yttrium and Ytterbium is Yb. Just a friendly reminder. Balakrishnan ------- Forwarded Message Follows ------- Date sent: Thu, 06 Jan 2000 16:59:00 -0500 From: Errol Lewars Subject: CCL:Y2K (diytterbium potassium) To: chemistry@ccl.net Organization: Trent University 2000 01 06 Hello, I hope CCLers will excuse me for mentioning, just before it ceases to be topical, the molecule Y2K (diytterbium potassium). See _Science_, 17 December 1999, p. 2281. The authors conclude that its preparation is "unlikely to [represent an] explosive event" but that it "could be the material of the millenium." E. Lewars =========== -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY- REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net Balakrishnan Viswanathan viswana@chemistry.mcgill.ca Lab: (514) 398-6920 Fax: (514) 398-2382 From chemistry-request@server.ccl.net Thu Jan 6 18:06:25 2000 Received: from socrates.cgl.ucsf.edu (socrates.cgl.ucsf.edu [128.218.27.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA27957 for ; Thu, 6 Jan 2000 18:06:24 -0500 Received: (from ross@localhost) by socrates.cgl.ucsf.edu (8.9.3/8.9.3/GSC1.6) id PAA16544 for chemistry@ccl.net; Thu, 6 Jan 2000 15:05:46 -0800 (PST) Date: Thu, 6 Jan 2000 15:05:46 -0800 (PST) From: Bill Ross Message-Id: <200001062305.PAA16544@socrates.cgl.ucsf.edu> To: chemistry@ccl.net Subject: Re: AMBER 6 announcement A reference at the end of our announcement of AMBER 6 omitted an author. The amended final paragraph reads: In addition to the capabilities in AMBER 6, a major effort is going on to broaden the applicability of the force field to more functional groups of organic molecules, such that one has an accurate representation of both the conformational and non-bonded interactions of any organic molecule. A paper in this area has been submitted to J. Comp. Chem. (Junmei Wang, Piotr Cieplak, and Peter Kollman, submitted) and Wang is further developing the program ANTECHAMBER to enable efficient handling of many molecules at a time. Our apologies for the error. Bill Ross From chemistry-request@server.ccl.net Thu Jan 6 21:00:43 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA28785 for ; Thu, 6 Jan 2000 21:00:43 -0500 Received: from el1 ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with SMTP id <01JKECCZU6UW00038P@trentu.ca> for chemistry@ccl.net; Thu, 6 Jan 2000 21:00:02 EST Date: Thu, 06 Jan 2000 21:03:37 -0500 From: Errol Lewars Subject: Y2K molecule--correction To: chemistry@ccl.net Message-id: <38754979.5406@trentu.ca> Organization: Trent University MIME-version: 1.0 X-Mailer: Mozilla 3.01Gold (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit 2000 01 06 Re my message: -------- 2000 01 06 >Hello, >I hope CCLers will excuse me for mentioning, just before it ceases >to be >topical, the molecule Y2K (diytterbium potassium). See _Science_, >17 >December 1999, p. 2281. The authors conclude that its preparation >is >"unlikely to [represent an] explosive event" but that it "could be the >material of the millenium." > E. Lewars >=========== Sorry, Y is Yttrium, not Ytterbium (which is Yb). _My_ fault. Or maybe my computer had a Y2k problem. E. Lewars ======= From chemistry-request@server.ccl.net Thu Jan 6 17:15:26 2000 Received: from mtiwmhc03.worldnet.att.net (mtiwmhc03.worldnet.att.net [204.127.131.38]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA27491 for ; Thu, 6 Jan 2000 17:15:25 -0500 Received: from nt ([12.67.17.111]) by mtiwmhc03.worldnet.att.net (InterMail v03.02.07.07 118-134) with SMTP id <20000106221246.NMUX2478@nt> for ; Thu, 6 Jan 2000 22:12:46 +0000 Message-Id: <3.0.32.20000106151705.008fc390@postoffice.worldnet.att.net> X-Sender: mrmopac@postoffice.worldnet.att.net X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Thu, 06 Jan 2000 15:18:38 -0700 To: CHEMISTRY@ccl.net From: "James J. P. Stewart" Subject: MOPAC2000 - Using CCl4 as a solvent in MST Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" >I really need a help. >How may I especify the CCl4 instead of water for calculations using the >continuum model in MOPAC2000. > To specify CCl4 as a solvent, use keyword "CCL4", see http://home.att.net/~mopacmanual/node330.html Jimmy Stewart