From chemistry-request@ccl.net Mon Jul 12 23:15:41 2004 Received: from sccrmhc11.comcast.net (sccrmhc11.comcast.net [204.127.202.55]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6D4FeG4017873 for ; Mon, 12 Jul 2004 23:15:40 -0500 Received: from test (pcp05504868pcs.owngsm01.md.comcast.net[69.139.156.84]) by comcast.net (sccrmhc11) with SMTP id <20040713042133011009mc0re>; Tue, 13 Jul 2004 04:21:38 +0000 Message-ID: <002201c46891$7bb1e820$549c8b45@test> From: To: , "Shobe, David" Cc: "CCL computational chemistry list \(E-mail\)" References: <9DD56492790889439F731F5BD6DACA0047FDBD-.at.-srvkyem1.americas.sc-world.com> <5497CBCC-D445-11D8-B2C9-000A95AB5F10-.at.-cnrs-orleans.fr> Subject: CCL:time-dependent and time-independent QM Date: Tue, 13 Jul 2004 00:25:47 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=4.9 required=7.5 tests=FVGT_s_OBFU_Q1,IMPRONONCABLE_1, NO_REAL_NAME,RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net ----- Original Message ----- From: To: "Shobe, David" Cc: "CCL computational chemistry list (E-mail)" Sent: Monday, July 12, 2004 4:52 PM Subject: CCL:time-dependent and time-independent QM > On 12.07.2004, at 22:14, Shobe, David wrote: > > > Where does the part where measuring a property of the system "resets" > > the quantum state of the system come in? That's always been > > mysterious: > > That depends on who you ask, I think that discussion is still > open-ended. The "collapse of the wave function" is part of the original > Copenhagen interpretation of the meaning of the wave function. However, > there are other interpretations. As the term "interpretation" implies, > the choice of one does not change the maths - the equations and wave > functions remain the same. > > The real problem in that discussion is that "measurement" needs to be > defined. In a pure quantum world, there are particles interacting, all > subject to the same laws, and the whole universe is governed by a > single huge wave function. No measurements, no problems. Various > definitions of measurements have been proposed, but none has yet been > found to be without problems. Some say that measuring implies human > consciousness - hence the paradox known as "Schrvdinger's cat". Others > say that measurement is an interaction with a classical object, but > that would imply that quantum mechanics needs to be defined in terms of > its own limiting case, classical mechanics. Perhaps the term "measurement" is already satisfactorily defined in quantum mechanics. The "measurement" of a physical property, which is an operator |p|, e.g. impulse, is a mean value where W is wavefunction of the system. Thus we know how to perform "measurement". The quantum problem, which is associated with the process of "measurement" is related to the fact that those operators, which do not commute, like energy |E| and impulse |p| yield different results depending of their order. Thus, |E*p| operator is different from its |p*E| counterpart and being applied to wavefunction they would yield different results. This leads to the well-known statement that one can not measure energy and impulse at the same time. Commuting operators, like energy and dipole moment do not show such restriction. Supposedly this has little to do with "interpretation" but this is rather a mathematical apparatus of quantum mechanics that can be either confirmed or rejected by experiment. So far we know only confirmations. With kind regards, Victor -- Victor Anisimov School of Pharmacy University of Maryland From chemistry-request@ccl.net Tue Jul 13 09:44:55 2004 Received: from ismss-2.biu.ac.il (ismss-2.biu.ac.il [132.70.46.151]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6DEirFA015542 for ; Tue, 13 Jul 2004 09:44:54 -0500 Received: from gefen.os.biu.ac.il ([132.70.60.26]) by ismss-2.biu.ac.il with InterScan Messaging Security Suite; Tue, 13 Jul 2004 17:52:03 +0300 Received: from localhost (aped@localhost) by gefen.os.biu.ac.il (AIX5.2/8.11.6p2/8.11.0/BIU.1.0) with ESMTP id i6DEovp753882 for ; Tue, 13 Jul 2004 17:50:57 +0300 Date: Tue, 13 Jul 2004 17:50:56 +0300 (IDT) From: Pinchas Aped To: chemistry_at_ccl.net Subject: CCL: using SCF=QC in G03 on Linux system Message-ID: X-Complaints-To: abuse_at_mail.biu.ac.il Organization: "Bar-Ilan University, Ramat-Gan, Israel " MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-imss-version: 2.5 X-imss-result: Passed X-imss-scores: Clean:95.45783 C:22 M:2 S:5 R:5 X-imss-settings: Baseline:1 C:1 M:1 S:1 R:1 (0.0000 0.0000) X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear All: We have recently installed Gaussian 03 on an Intel-based system with Linux (RedHat 9.0). Most job types ran successfully, but when we tried to use SCF=QC the job aborted after a few seconds without any error message. has anyone experienced such problems with Gaussian on Linux systems? (the same job ran to completion on AIX and IRIX systems). Thanks in advance Pinchas Aped ------------------------------------------------------------------------ Dr. Pinchas Aped Tel.: (+972-3) 531-7683 Department of Chemistry FAX : (+972-3) 535-1250 Bar-Ilan University E-Mail: aped_at_mail.biu.ac.il 52900 Ramat-Gan, ISRAEL WWW: http://www.biu.ac.il/~aped ------------------------------------------------------------------------ From chemistry-request@ccl.net Tue Jul 13 11:16:50 2004 Received: from mx5.net.nih.gov (mailfwd.nih.gov [165.112.130.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6DGGnFA019669 for ; Tue, 13 Jul 2004 11:16:49 -0500 Received: from mx5.net.nih.gov (localhost [127.0.0.1]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i6DGMsMK014643 for ; Tue, 13 Jul 2004 12:22:54 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i6DGMo61014580; Tue, 13 Jul 2004 12:22:50 -0400 Date: Tue, 13 Jul 2004 12:19:41 -0400 From: Rick Venable To: Anil Korkut cc: chemistry!at!ccl.net Subject: Re: CCL:normal modes problem/CHARMM In-Reply-To: Message-ID: References: ReplyTo: Rick_Venable!at!nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net There's a forum at www.charmm.org which adresses Minimization and Normal Modes, etc. The asterisks indicate a formatting problem, not a 'blank' normal mode, but they should be near zero in any event. I strongly suggest checking the output logs of your minimization and normal mode calc for warning and error messages; there is a problem. I'd use a lot less SD min, maybe just 100-200 steps to relieve bad contacts. Also, try a smaller and simpler test case. On Mon, 12 Jul 2004, Anil Korkut wrote: > I am doing an NMA calculation for a protein with 3000 atoms using > charmm simulation package. > > I minimized my structure to a gradient of 1e-6 with 2000 steps of sttepest > descent followed by about 8000 steps of ABNR. > > I know that the first six normal modes should have zero frequency. > > However, I got no frequency values for the first two normal modes!!!! > > The translational and rotational modes start at mode 3 and the vibrational > modes start at mode 9 instead of 7. > > The frequency values are > VIBRAN> PRINT NORM MODE 1 THRU 16 DIPO > > NORMAL MODES > > 1********** 2********** 3 -0.01 4 -0.01 5 0.00 > 6 0.00 7 0.00 8 0.01 9 1.51 10 1.76 > 11 2.40 12 3.03 13 3.40 14 3.76 15 4.05 > 16 4.29 > > > I have done the same calculation with a different force field (opls-ua) > using TINKER and results were as expected (i.e. no blank modes, no > negative > eigenvalues) > > The nomal mode 7 from tinker has very similar freq. value to normal mode 9 > > from charmm. > > I also used BPTI as a sample protein and the same problem exists. > > Does anyone have any idea what is going wrong here? > > I can post my script, if anyone is interested. > > Thanks > > ______________________________________________________________ > Anil Korkut > Dept of Biochemistry and Mol. Biophysics > Columbia University, > 630 West 168th St, BB204 > New York, NY 10032 > office ph (212) 305 1846 > ______________________________________________________________ > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY!at!ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST!at!ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow!at!nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable!at!nih.gov ALT email: rvenable!at!speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@ccl.net Tue Jul 13 07:33:29 2004 Received: from host20 (host20.lctn.uhp-nancy.fr [193.50.239.24]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6DCXRFA008631 for ; Tue, 13 Jul 2004 07:33:28 -0500 Received: from ptxav (pt-xav.lctn.uhp-nancy.fr [193.50.239.125]) by host20 (AIX4.3/8.9.3/8.9.3) with SMTP id OAA17432; Tue, 13 Jul 2004 14:40:50 +0200 From: "Xavier ASSFELD" To: , , "Shobe, David" Cc: "CCL computational chemistry list \(E-mail\)" Subject: RE: time-dependent and time-independent QM Date: Tue, 13 Jul 2004 14:36:42 +0200 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) In-Reply-To: <002201c46891$7bb1e820$549c8b45@test> X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 Importance: Normal X-Spam-Status: No, hits=0.3 required=7.5 tests=FVGT_s_OBFU_Q1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net X> -----Message d'origine----- X> De : Computational Chemistry List [mailto:chemistry-request|at|ccl.net]De X> la part de victor_anisimov|at|comcast.net X> Envoyi : mar. 13 juillet 2004 06:26 X> @ : hinsen|at|cnrs-orleans.fr; Shobe, David X> Cc : CCL computational chemistry list (E-mail) X> Objet : CCL:time-dependent and time-independent QM X> X> Perhaps the term "measurement" is already satisfactorily defined X> in quantum X> mechanics. The "measurement" of a physical property, which is an X> operator |p|, X> e.g. impulse, is a mean value where W is wavefunction of the X> system. Thus we know how to perform "measurement". The quantum problem, X> which is associated with the process of "measurement" is X> related to the fact that X> those operators, which do not commute, like energy |E| and X> impulse |p| yield different X> results depending of their order. Thus, |E*p| operator is X> different from its |p*E| X> counterpart and being applied to wavefunction they would yield X> different results. This X> leads to the well-known statement that one can not measure X> energy and impulse at X> the same time. Commuting operators, like energy and dipole X> moment do not show X> such restriction. X> Just my 2 eurocents, I think that the problem of measuring something of a quantum system is related to the superposition state. A quantum system can be in a superposition of eigenstate, e.g. a hydrigen atom can be in state Y = c1*1s +c2*2s. When you measure in which state the hydrogen atom is, you will find c1*c1 times the energy of the 1s state and c2*c2 times the energy of the 2s state. You'll never find c1*c1*E1+c2*c2*E2 value! When you measure the energy the wavefunction is "reduced" to only one eigenstate. Hope that I throw oil on fire... Yours X> Supposedly this has little to do with "interpretation" but this X> is rather a mathematical X> apparatus of quantum mechanics that can be either confirmed or X> rejected by X> experiment. So far we know only confirmations. X> X> With kind regards, X> Victor X> X> -- X> Victor Anisimov X> School of Pharmacy X> University of Maryland X> X> X> X> -= This is automatically added to each message by the mailing script =- X> To send e-mail to subscribers of CCL put the string CCL: on your X> Subject: line X> and send your message to: CHEMISTRY|at|ccl.net X> X> Send your subscription/unsubscription requests to: X> CHEMISTRY-REQUEST|at|ccl.net X> HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs X> X> If your mail is bouncing from CCL.NET domain send it to the maintainer: X> Jan Labanowski, jlabanow|at|nd.edu (read about it on CCL Home Page) X> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ X> X> X> X> X> ...Xav Pr. Xavier Assfeld Xavier.Assfeld|at|lctn.uhp-nancy.fr Laboratoire de Chimie thiorique (T) 33 3 83 68 43 82 Universiti Henri Poincari (F) 33 3 83 68 43 71 F-54506 Nancy B.P. 239 http://www.lctn.uhp-nancy.fr From chemistry-request@ccl.net Tue Jul 13 02:13:10 2004 Received: from postfix4-1.free.fr (postfix4-1.free.fr [213.228.0.62]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6D7D9FA026776 for ; Tue, 13 Jul 2004 02:13:09 -0500 Received: from [213.228.59.246] (nas-cbv-3-213-228-59-246.dial.proxad.net [213.228.59.246]) by postfix4-1.free.fr (Postfix) with ESMTP id 63F4715FA1A for ; Tue, 13 Jul 2004 09:19:12 +0200 (CEST) Mime-Version: 1.0 (Apple Message framework v618) In-Reply-To: <002201c46891$7bb1e820$549c8b45@test> References: <9DD56492790889439F731F5BD6DACA0047FDBD|at|srvkyem1.americas.sc-world.com> <5497CBCC-D445-11D8-B2C9-000A95AB5F10|at|cnrs-orleans.fr> <002201c46891$7bb1e820$549c8b45@test> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <08DF5535-D49D-11D8-B2C9-000A95AB5F10|at|cnrs-orleans.fr> Content-Transfer-Encoding: 7bit From: hinsen|at|cnrs-orleans.fr Subject: Re: CCL:time-dependent and time-independent QM Date: Tue, 13 Jul 2004 09:19:53 +0200 To: CCL computational chemistry list (E-mail) X-Mailer: Apple Mail (2.618) X-Spam-Status: No, hits=1.3 required=7.5 tests=FVGT_s_OBFU_Q1,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On 13.07.2004, at 06:25, wrote: > Perhaps the term "measurement" is already satisfactorily defined in > quantum > mechanics. The "measurement" of a physical property, which is an > operator |p|, > e.g. impulse, is a mean value where W is wavefunction of the > system. Thus we know how to perform "measurement". The quantum Then what is the physical procedure to obtain the mean value? Measurement is a physical operation, not a mathematical one. > Supposedly this has little to do with "interpretation" but this is > rather a mathematical > apparatus of quantum mechanics that can be either confirmed or > rejected by experiment. So far we know only confirmations. It is true that quantum mechanics is largely confirmed by experiment, but that doesn't resolve the question of the definition of measurement. The different interpretations that have been proposed for the wave function make no difference for the experiments that have been devised so far, otherwise the issue might have been settled by now. I suspect that ultimately the problem is an artificial one, that "measurement" is an unnecessary idealization that doesn't fit the quantum world. Any experimental setup can be described by quantum mechanics, even though the maths may be too complicated to do the computations explicitly. An apparatus suitable for "measurement" is simply one whose states are sufficiently distinct to permit observation by human sensory organs. ------------------------------------------------------------------------ ------- Konrad Hinsen Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: hinsen|at|llb.saclay.cea.fr ------------------------------------------------------------------------ ------- From chemistry-request@ccl.net Tue Jul 13 06:29:28 2004 Received: from relay.uni-heidelberg.de (relay.uni-heidelberg.de [129.206.100.212]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6DBTQFA005877 for ; Tue, 13 Jul 2004 06:29:27 -0500 Received: from mail.iwr.uni-heidelberg.de (mail.iwr.uni-heidelberg.de [129.206.104.30]) by relay.uni-heidelberg.de (8.12.10/8.12.10) with ESMTP id i6DBZTIY029441 for ; Tue, 13 Jul 2004 13:35:29 +0200 (MET DST) Received: from kenzo.iwr.uni-heidelberg.de (IDENT:YEA8esnkSOnHI8nCCf3/e/FSmPCB+ZFg_at_kenzo.iwr.uni-heidelberg.de [129.206.120.29]) by mail.iwr.uni-heidelberg.de (8.12.10/8.12.9) with ESMTP id i6DBZTPF029267 for ; Tue, 13 Jul 2004 13:35:29 +0200 (MET DST) Received: from jasmin.iwr.uni-heidelberg.de (jasmin.iwr.uni-heidelberg.de [129.206.120.31]) by kenzo.iwr.uni-heidelberg.de (8.12.8/8.12.8) with ESMTP id i6DBZTCL007762 for ; Tue, 13 Jul 2004 13:35:29 +0200 Received: from jasmin.iwr.uni-heidelberg.de (localhost.localdomain [127.0.0.1]) by jasmin.iwr.uni-heidelberg.de (8.12.10/8.12.10) with ESMTP id i6DBZT8X010326 for ; Tue, 13 Jul 2004 13:35:29 +0200 Received: from localhost (becker@localhost) by jasmin.iwr.uni-heidelberg.de (8.12.10/8.12.10/Submit) with ESMTP id i6DBZSBe010322 for ; Tue, 13 Jul 2004 13:35:29 +0200 Date: Tue, 13 Jul 2004 13:35:28 +0200 (CEST) From: Torsten Becker To: chemistry_at_ccl.net Subject: Re: CCL:time-dependent and time-independent QM In-Reply-To: <002201c46891$7bb1e820$549c8b45@test> Message-ID: References: <9DD56492790889439F731F5BD6DACA0047FDBD_at_srvkyem1.americas.sc-world.com> <5497CBCC-D445-11D8-B2C9-000A95AB5F10_at_cnrs-orleans.fr> <002201c46891$7bb1e820$549c8b45@test> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.2 required=7.5 tests=FVGT_s_OBFU_Q1,MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Tue, 13 Jul 2004 victor_anisimov_at_comcast.net wrote: > > Perhaps the term "measurement" is already satisfactorily defined in quantum > mechanics. The "measurement" of a physical property, which is an operator |p|, > e.g. impulse, is a mean value where W is wavefunction of the > system. Thus we know how to perform "measurement". What you describe here is not a measurement. Given a measurable quantity represented by an Operator P, the outcome of a measurement will be one of the Eigenvalues p_i of P, not the mean value . If |W_i> is an Eigenvector of P with Eigenvalue p_i, then gives you the probability that your measurement yields p_i. Only after plenty of single measurements you can access the mean value. The 'measurement problem' in the Copenhagen Interpretation, as Konrad Hinsen wrote already, means that the measuring apparatus is not included in the system describtion given by the wavefunction |W>. In the Copenhageninterpretation the measuring apparatus is described in the framework of classical physics and measuring a system leads to a collaps of its wavefunction. 'Collapse of the wavefunction` means that after a measurement that yielded p_i, the system is no longer in the state |W> but it 'collapsed' into the state |W_i>. > The quantum problem, > which is associated with the process of "measurement" is related to the fact that > those operators, which do not commute, like energy |E| and impulse |p| yield different > results depending of their order. Energy and momentum usually do commute. They have to, otherwise energy and momentum would not both be conserved in physical processes. So the operator P usually commutes with the Hamiltonian H. There are of course non-commuting operators like position and momentum and indeed that's the jist of QM. But it is not related to the measurement problem. ************************************************************************ Torsten Becker Computational Molecular Biophysics IWR, Universitaet Heidelberg +49-6221-54-8808 (office) Im Neuenheimer Feld 368 +49-0177-7273406 (mobile) D-69120 Heidelberg; Germany torsten.becker_at_iwr.uni-heidelberg.de *********************************** From chemistry-request@ccl.net Tue Jul 13 11:42:52 2004 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6DGgmFA021079 for ; Tue, 13 Jul 2004 11:42:50 -0500 Received: by CELEBRIS04 with Internet Mail Service (5.5.2655.55) id <36FNMSWD>; Tue, 13 Jul 2004 13:48:18 -0300 Message-ID: <4DB0991764FED5119A2A000475B057CA1C57BD@CELEBRIS04> From: Ian Hovell To: "'chemistry'" Subject: CCL:Summary Choice of computer for G03 Date: Tue, 13 Jul 2004 13:48:17 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2655.55) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net As promised here is a summary to the following question >I'm looking for the ideal computer for running G03. I was wondering what >people on the list, when buying a new computer dedicated to Gaussian03, >would go fo? Would people go for cpu speed, cache memory, RAM or hard disk. >Where would the emphasise be? And what OS would you opt for. I'm sure these >questions have been asked for before so if any body can point me to a URL >they know, okay. >Thanks for your help and time. The answers; I don't believe you will get definite answers to your question. I've seen people on this list using computers of all kinds, single or multi processors, Linux, Windows, Mac, etc... running Gaussian. Maybe the most important question is what kind of simulations do you want to do on this computer? Of course, I'd go for the best computer possible, ant that means best CPU, with large cache, maximum RAM and a large HD. Especially, if you plan on doing ab-initio calculations on large molecules, you will need lots of HD space, and maybe consider a 62 bit processor. As for OS, I'd definetely go for Linux, unless you choose a multi-processor computer for which Linux isn't available. HTH, Gustavo Seabra. Ian, I have grown fond of Mac's again, since OS X is the only operating system where I can do both professional development in C and Python alongside Word - all without an emulator and/or dual booting. The prices for dual processors are comparable to what Dell has, if not a little cheaper (list prices, YMMV). Whatever you get, there are a number of things to consider: 1) People forget that there are things like memory bandwidth and disk/IO bandwidth. Thus, they purchase the fastest processor(s) they can, and wonder why their jobs don't run as fast as they'd expected. I'd plan for 1 job per 1 or 2 processors for maximum efficiency. If you have to use integral files, I'd investigate fast disks, SCSI, etc. 2) Compilers make a HUGE difference. gcc/g77 are way slower than machine-specific compilers (Intel/PC or IBM/Mac). While it costs a little $$, getting 20-50% faster run-time is a cheap upgrade. Some compilers also have difficulties with some parallel libraries, or don't offer them - check with Gaussian if there's any good or bad purchases. 3) The safe recommendation is that one should get as much memory and disk as possible. See (1) for kinds and/or speeds of disk. Regarding cache, I don't know how particular portions of Gaussian relate to cache hits/misses - they should know this. Of course, running more than a single job on the box is quite a bit worse re: cache than differences with a single job. And I think people now feel that machines should NEVER page (some turn off the option in Linux), so lots and lots of RAM is required. 4) Do you want to be your own system manager? Do you have access to one who is competent? If not, maybe Linux will be a bother - nothing's real good out of the box as I understand things. I run off-the-shell OS X to success. 5) Do you need any kind of compatibility with PC/Mac/Linux/...? Does the machine have to have a graphics head or is it merely a server - the latter is WAY easier to configure and maintain. I'm not sure how PC's communicate with Mac/Linux/Unix, but the latter three seem to talk to each other well. Hope this helps... Joe I've used various versions of Gaussian on various machines at supercomputing centers for many years (at least 18 years). My current favorite machine is SGI's itantuim/altix machine. It is shared memory so gaussian speed-up is nearly linear (at least up to 8 processors, as many as I have tried), and the 64 bit system makes file size limitations no longer an issue. I have been able to optimizations/frequency calculations on molecules with nearly 150 atoms, including Re atoms, using good quality DFT methods, as well as MP2 calculations that choked other machines I have used. Steve Williams I hope that helps Ian Hovell From chemistry-request@ccl.net Tue Jul 13 06:04:01 2004 Received: from sys11.mail.msu.edu (sys11.mail.msu.edu [35.9.75.111]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6DB41FA004951 for ; Tue, 13 Jul 2004 06:04:01 -0500 Received: from pm794-22.dialip.mich.net ([35.12.21.124]) by sys11.mail.msu.edu with asmtp (Exim 4.32 #22) (TLSv1:RC4-SHA:128) id 1BkLAj-0006Gk-4k for CHEMISTRY/at/ccl.net; Tue, 13 Jul 2004 07:10:05 -0400 Mime-Version: 1.0 X-Sender: chieny/at/mail.msu.edu Message-Id: Date: Tue, 13 Jul 2004 07:10:02 -0400 To: CHEMISTRY/at/ccl.net From: Yao-Ying Chien Subject: CCL: your favorite threads? Content-Type: text/plain; charset="us-ascii" X-Virus: None found by Clam AV X-Spam-Status: No, hits=5.6 required=7.5 tests=NO_RDNS2,RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, I ran into an old CCL "a bit more on molecular computational chemistry", http://www.ccl.net/cgi-bin/ccl/message.cgi?2002+11+11+002 Another one was, "CCL:orbitals" http://server.ccl.net/cgi-bin/ccl/message.cgi?2003+05+28+022 They are interesting. Wonder what are your favorite thread(s)? Has this SUMMARY been done before? -- Regards, Yao-Ying Chien Department of Crop and Soil Sciences Michigan State University Plant and Soil Sciences Building, Rm A526 East Lansing, MI 48824-1325 Office: (517)355-0271x249 SGI lab: (517)355-0271x253 Fax: (517)355-0270 email: chieny/at/msu.edu From chemistry-request@ccl.net Tue Jul 13 15:25:39 2004 Received: from mxout4.cac.washington.edu (mxout4.cac.washington.edu [140.142.33.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i6DKPcFA029168 for ; Tue, 13 Jul 2004 15:25:38 -0500 Received: from homer11.u.washington.edu (homer11.u.washington.edu [140.142.15.115]) by mxout4.cac.washington.edu (8.12.11+UW04.02/8.12.11+UW04.03) with ESMTP id i6DKVX9i016552 for ; Tue, 13 Jul 2004 13:31:38 -0700 Received: from localhost (ohucke@localhost) by homer11.u.washington.edu (8.12.11+UW04.02/8.12.11+UW04.05) with ESMTP id i6DKVXYx047210 for ; Tue, 13 Jul 2004 13:31:33 -0700 Date: Tue, 13 Jul 2004 13:31:33 -0700 (PDT) From: "O. Hucke" To: chemistry$at$ccl.net Subject: SAR database software Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, we are looking for a (ideally free, of course) database software for the storage and the work with SAR data. Ideally the program should be able to o store 3D structures of inhibitors o perform substructure searches o provide a web interface for online access (?) Any hints are highly appreciated. Thanks, Oliver _________________________ Oliver Hucke, Dr. University of Washington Dept. of Biochemistry Seattle, WA 98195 _________________________ From chemistry-request@ccl.net Tue Jul 13 21:43:26 2004 Received: from web15408.mail.cnb.yahoo.com (web15408.mail.cnb.yahoo.com [202.43.216.211]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i6E2hOFA010460 for ; Tue, 13 Jul 2004 21:43:25 -0500 Message-ID: <20040714024930.81476.qmail_at_web15408.mail.cnb.yahoo.com> Received: from [61.178.59.179] by web15408.mail.cnb.yahoo.com via HTTP; Wed, 14 Jul 2004 10:49:30 CST Date: Wed, 14 Jul 2004 10:49:30 +0800 (CST) From: =?gb2312?q?Jinsong=20Zhao?= Subject: CCL: Orient molecule in GRID To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=3.5 required=7.5 tests=DATE_IN_PAST_12_24, IMPRONONCABLE_2,MK_YAHOO_REDIR_01,WLS_URI_OPT_150 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, I have a set of molecule, I hope to do molecular interaction field (MIF) analysis using GRID21 (Molecular Discovery Ltd.). I hope to do a CoMFA like analysis, i.e., performing PLS analysis on the MIF data, thus molecular orientation or molecular alignment is very important in such situation. However, I don't know how to control the molecular orientation in GRID21 and give a reasonable box arround the molecule. Any suggestions will be really appreciated. Thanks in advance. Regards, Jinsong ===== (Mr.) Jinsong Zhao Ph.D. Candidate School of the Environment Nanjing University No.22 Hankou Road, Najing 210093 P.R. China E-mail: zh_jinsong_at_yahoo.com.cn _________________________________________________________ Do You Yahoo!? C_at_E.CwPGS&SP>!SP#,"R;KQ"KQ1iC@M