From chemistry-request@ccl.net Wed Feb 2 01:27:41 2005 Received: from smtp4.dti.ne.jp (smtp4.dti.ne.jp [202.216.228.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j126Rbra025735 for ; Wed, 2 Feb 2005 01:27:38 -0500 Received: from oemcomputer (PPP79.fukuoka-ip.dti.ne.jp [211.132.92.79]) by smtp4.dti.ne.jp (3.10s) with SMTP id j126RZKT009474 for ; Wed, 2 Feb 2005 15:27:35 +0900 (JST) Message-ID: <002a01c508ef$c9117e60$4f5c84d3@oemcomputer> From: "Telkuni Tsuru" To: Subject: Movement unit for geometry optimization Date: Wed, 2 Feb 2005 15:24:00 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Spam-Status: No, hits=3.6 required=7.5 tests=IMPRONONCABLE_1, 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 Hello, CCLers. I like to ask the movement unit for geometry optimization. The books which I have describe the optimization method as follows: ... when one can't find optimized structure, one should calculate force constant of atoms as the differentiation of energy, and move each atoms obeying the force direction. ... Exactly, there are many MO calculating softwares: Gaussian, Mopac, ... and so on. I wonder what units they use. 0.1[A], 0.05[A] or 0.01[A] ? * [A] is angstrom. If you know the information which concerns with this question, please let me know. When I receive replies, I will summarize them. Sincerely yours, ---------------------------------------------------- Telkuni Tsuru telkuni #%# venus.dti.ne.jp From chemistry-request@ccl.net Wed Feb 2 02:38:01 2005 Received: from web54410.mail.yahoo.com (web54410.mail.yahoo.com [68.142.225.166]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j127c0ra028182 for ; Wed, 2 Feb 2005 02:38:00 -0500 Received: (qmail 499 invoked by uid 60001); 2 Feb 2005 06:37:58 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=jrH6urNiQUEi/VbBamTqQ8I2wLk6uOq9okcOkzT0/er6GmWUGSB14pmK2/XuhNoLeFlY4r/LmOdQNDt++A+CQTMEV52rL1VGorHqF8n9m+7LGeFztY9ddcORu5x8Yf9ngNmdk4bMPl9eBNnmp9UNJCXXvPjbRlaxC7Lfmh9jBwU= ; Message-ID: <20050202063758.497.qmail_at_web54410.mail.yahoo.com> Received: from [80.191.213.6] by web54410.mail.yahoo.com via HTTP; Tue, 01 Feb 2005 22:37:58 PST Date: Tue, 1 Feb 2005 22:37:58 -0800 (PST) From: talia mah Subject: help me To: chemistry_at_ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1028815011-1107326278=:287" X-Spam-Status: No, hits=5.1 required=7.5 tests=FROM_ENDS_IN_NUMS, FROM_HAS_ULINE_NUMS,HTML_MESSAGE,MK_BAD_HTML_04,RCVD_IN_DSBL, RCVD_IN_NJABL,RCVD_IN_NJABL_PROXY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-1028815011-1107326278=:287 Content-Type: text/plain; charset=us-ascii Dear: I want run opt=z-matrix freq scf=(tight,direct) by method mp2/6-311g** for moleculs cycloheptanone ,cyclooctanone, Indanone,3,4-dihydro-2H-naphthalene-1-one ,banzocycloheptanone,banzocyclooctane for my project with gaussian 98 A.7 I run this method by in put: %mem=256mb %nosave %rwf=rwf1,245mw,rwf2,245mw,rwf3,245mw,rwf4,245mw %CHK=E:\2MP2\CYC7 maxdisk=1960mw but I can not accept correct answer Please write me how I can run and show me a way for this run and write me correct ratio between memory and N-basis and maxdisk and how I can recognize correct memory and maxdisk? thanks __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-1028815011-1107326278=:287 Content-Type: text/html; charset=us-ascii
Dear:
 I want run opt=z-matrix freq scf=(tight,direct)
 by method mp2/6-311g** for moleculs cycloheptanone
 ,cyclooctanone, Indanone,3,4-dihydro-2H-naphthalene-1-one
,banzocycloheptanone,banzocyclooctane for my project with
 gaussian 98 A.7 I run this method by in put:
 %mem=256mb
  %nosave
  %rwf=rwf1,245mw,rwf2,245mw,rwf3,245mw,rwf4,245mw
  %CHK=E:\2MP2\CYC7 maxdisk=1960mw
 but I can not accept correct answer

 Please write me how I can run and show me a way for this run
and write me correct ratio between memory and N-basis and maxdisk
and how I can recognize correct memory and maxdisk?
 thanks

__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com --0-1028815011-1107326278=:287-- From chemistry-request@ccl.net Wed Feb 2 06:13:16 2005 Received: from avas.unife.it (avas.unife.it [192.167.219.15]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j12BDEmK003092 for ; Wed, 2 Feb 2005 06:13:15 -0500 Received: from localhost (unknown [127.0.0.1]) by avas.unife.it (Postfix) with ESMTP id A1AB765930 for ; Wed, 2 Feb 2005 11:11:00 +0100 (CET) Received: from dns.unife.it (dns.unife.it [192.167.219.2]) by avas.unife.it (Postfix) with ESMTP id BC58265A6E for ; Wed, 2 Feb 2005 11:10:58 +0100 (CET) Received: from [192.167.212.243] (chim243.unife.it [192.167.212.243]) by dns.unife.it (Postfix) with ESMTP id 79E6872F01 for ; Wed, 2 Feb 2005 11:10:58 +0100 (CET) User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2106 Date: Wed, 02 Feb 2005 11:09:08 +0200 Subject: dft question on sugar From: Nicola Catozzi To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="ISO-8859-1" X-Virus-Scanned: Cineca AppOs 0.83 at avas.unife.it X-Spam-Status: No, hits=3.7 required=7.5 tests=IMPRONONCABLE_1,NO_RDNS, RM_fl_ConsWord6s autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j12BDGmK003097 Hi I want to know if there are someone expert in DFT calculation methods on carbohydrates? My question is: which is or which are the best functionals for dft that describe correctly hydrogen bond and weak interaction like van der walls etc in sugar moieties? Now I9m using b3lyp but it under estimate that kind of forces in my experiments...while hf overestimate these effects. thanks By Nicola ====================================================== * Dott. Nicola Catozzi * * Department of Chemistry - University of Ferrara * * Via Borsari, 46 - 44100 Ferrara (Italy) * * Tel. +39.0532291177; Fax +39.0532291167 * * E-mail ctzncl /a\ unife.it * ====================================================== From chemistry-request@ccl.net Wed Feb 2 06:24:31 2005 Received: from mar.qf.ub.es (mar.qf.ub.es [161.116.73.101]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j12BOUmK003607 for ; Wed, 2 Feb 2005 06:24:30 -0500 Received: from [127.0.0.1] (stefan.qf.ub.es [161.116.73.181]) by mar.qf.ub.es (Postfix) with ESMTP id 11135FA7EA for ; Wed, 2 Feb 2005 10:24:18 +0100 (CET) Message-ID: <42009B73.9040906/at/qf.ub.es> Date: Wed, 02 Feb 2005 10:20:51 +0100 From: Stefan Bromley User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.7.3) Gecko/20040910 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry/at/ccl.net Subject: Re: orbital and reality Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit 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 all, I have been following the evolution of the discussion on the reality of orbitals with interest. I think it is important, however, to be careful to distinguish claims about the possible physical reality of the orbital model and the possible physical reality of actual wavefunctions. Malcolm Davis for example writes: "Folks have tried to show that there is some "normal" reality underlying QM that we just cannot measure. Such "Hidden Variable" theories have been ruled out by "Bell's Inequality" and the "Aspect" experiments. So, wave functions are as real as it gets". This is a very common misconception and is one I hope that does not pervade throughout the whole of the CCL community. Bell's inequality and the Aspect experiments rule out only *local* hidden variable theories. Based on the work of de Broglie, David Bohm in the 1950s developed an example of a theory not ruled out by the Bell inequality (A suggested interpretation of the quantum theory in terms of "hidden" variables. I & II. D. Bohm, Phys. Rev. 85, 166-193, 1952). In fact Bell's inequality came about largely through contemplation of Bohm's work - in particular its non-local aspect. Importantly, Bohm's theory, by the necessity of its construction, it is exacty equivalent in its predictions to standard quantum mechanics. The extra given by such a theory is many-fold in terms of physical insight but arguably little in terms of present day measurement. You can find a large resource of literature on the theory (see e.g. The Quantum Theory of Motion: An account of the de Broglie-Bohm Causal Interpretation of Quantum Mechanics by Peter Holland, Cambridge University Press 1995). In this theory (or interpretation) the wavefunction is a real field which gives rise to a quantum potential acting on a real particle (e.g. an electron) which follows a *non-classical* trajectory in real space. I do not wish to go into the merits or physical validity of such an interpretation but just to note that it is perfectly possible to have a quantum theory where wavefunctions and electrons do have "an underlying" physical reality. It is, perhaps, of further note that Bohm's causal interpretation of quantum mechanics based on the wavefunction as a guiding field to particles has lead to some recent advances in the modelling/interpretation of scattering and tunnelling processes and Quantum Field theory (see e.g. O. V. Prezhdo et al. Phys.Rev. Lett. 86, 3521, 2001, C. L. Lopreore et al. Phys. Rev. Lett. 82, 5190, 1999, A. S. Sanz et al. Phys. Rev. B 69, 11513, 2004, Phys. Rev. Lett. 93, 090402, 2004) Best regards, Stefan Bromley From chemistry-request@ccl.net Wed Feb 2 11:37:44 2005 Received: from century.fen.bilkent.edu.tr (century.fen.bilkent.edu.tr [139.179.97.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j12GbcmK017296 for ; Wed, 2 Feb 2005 11:37:41 -0500 Received: from fen.bilkent.edu.tr (fenII-124.fen.bilkent.edu.tr [139.179.97.239]) by century.fen.bilkent.edu.tr (8.12.8/8.12.8) with ESMTP id j12EbfR4026817 for ; Wed, 2 Feb 2005 16:37:42 +0200 (EET) Message-ID: <4200E86C.6080508 -()- fen.bilkent.edu.tr> Date: Wed, 02 Feb 2005 16:49:16 +0200 From: Ulrike Salzner Organization: Bilkent University User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry -()- ccl.net Subject: Xeon vs. PIV Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit 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 Hello, I have money for a couple of PCs and there is a choice between dual CPU Intel server mainboards with two 2.8 GHz Xeon processors and a single CPU mainboard with one 3.2 GHz Pentium IV processor. The Server with two CPUs would coast a bit more than twice as much ($1960) than the a machine with one CPU ($875). I could just buy twice as many single CPUs machines to get the same number of processors. What would give me a better throughput for calculations mainly with G03? Is the Xeon processor worth the cost for this purpose or would I waste money? Thanks for advice, Ulrike Salzner salzner -()- bilkent.edu.tr Associate Professor Department of Chemistry Bilkent University From chemistry-request@ccl.net Wed Feb 2 16:48:50 2005 Message-ID: <1107380928.42014ac0be7cd _(a)_ webmail.nd.edu> Date: Wed, 2 Feb 2005 16:48:48 -0500 From: Jan K Labanowski To: chemistry _(a)_ ccl.net Subject: Call for Papers - Large Scale Molecular Dynamics, Nanoscale, and Mesoscale Modeling and Simulation: Bridging the Gap ----- Forwarded message from rbross _(a)_ mmm.com ----- Date: Wed, 2 Feb 2005 14:15:21 -0600 From: rbross _(a)_ mmm.com Reply-To: rbross _(a)_ mmm.com Subject: Call for Papers - Large Scale Molecular Dynamics, Nanoscale, and Mesoscale Modeling and Simulation: Bridging the Gap To: jlabanow _(a)_ nd.edu CALL FOR PAPERS Large Scale Molecular Dynamics, Nanoscale, and Mesoscale Modeling and Simulation: Bridging the Gap 230th National American Chemical Society Meeting, Washington, DC August 28-September 1, 2005 Sponsored by the Computers in Chemistry Division Co-sponsored by the Physical Chemistry Division With increasing accuracy and applicability of molecular modeling tools, the challenge is beginning to shift to addressing how molecular modeling can help engineer materials and processes at the macro-scale. The properties at the macro-scale not only depend on the molecular arrangement, but often on how the nanoscale arrangements of these molecules themselves cluster. Thus, molecular design of macroscale properties requires increased understanding of molecular scale, nano-scale, meso-scale and macro-scale phenomena. This symposium will focus on applications and methodology development in integrating the nano, meso and larger length scale regions. Applied large-scale atomistic molecular dynamics simulations, mesoscale simulations, and additional course grain methodology studies with focus on structure-property behavior as well as kinetic processes are requested. Applications in nanotechnology, biology, inorganic materials, catalysis, polymers, pharmaceuticals and additional life and materials science areas are encouraged. Contributions are solicited from academic, industrial, and the governmental research sectors. A poster session is planned in addition to oral presentations. A panel discussion of modeling and simulation in this area is also planned. In addition, the organizers plan to publish a proceedings pending interest > from contributing authors. A social event for contributing authors during the ACS meeting is also planned. Please submit abstracts to either Sanat Mohanty or Rick Ross (email below) at your earliest convenience to aid in session planning. Please also directly submit abstracts to the American Chemical Society via the official on-line abstract submissions system when it becomes available on Feb. 28 to officially have your presentation entered for the meeting.* Final deadline for electronic submission of abstracts is April 25th. For additional information on the symposium, please contact Sanat Mohanty or Rick Ross. Symposium Organizing Committee: Sanat Mohanty and Rick Ross 201-2E-23, Corporate Research Materials Laboratory 3M Company, St. Paul, MN 55144 smohanty _(a)_ mmm.com; rbross _(a)_ mmm.com * see http://oasys.acs.org/ for abstract submission access and guidelines. From chemistry-request@ccl.net Wed Feb 2 19:03:21 2005 Received: from schrodinger.com (thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1303ImK001233 for ; Wed, 2 Feb 2005 19:03:19 -0500 Received: from SVETLA (svetla.schrodinger.com [192.156.98.141]) by schrodinger.com (8.13.3/8.12.8) with SMTP id j12Mch45001856 for ; Wed, 2 Feb 2005 14:38:47 -0800 (PST) (envelope-from announce #%# schrodinger.com) From: Schrodinger Announcements To: CCL Subject: Schrodinger announces the release of two new products Date: Wed, 02 Feb 2005 17:38:49 -0500 Message-ID: <0202105173849.3@SVETLA> 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 Schrodinger announces the release of two new products: Phase, a high-performance program for ligand-based drug design; and Strike, powerful new software for statistical modeling and QSAR. Phase is an easily mastered pharmacophore modeling program, while Strike integrates a chemically aware statistics package into Schrodinger's modeling environment. To learn more about these new products, please visit the Schrodinger web site at http://www.schrodinger.com. Along with these two new products are new releases of all of Schrodinger's software, including Glide, Prime, MacroModel, Jaguar, Maestro, and more. To find out more about the new releases, please go to http://www.schrodinger.com.