From chemistry-request@server.ccl.net Mon Aug 27 08:11:06 2001 Received: from mail1.rrz.Uni-Koeln.DE ([134.95.100.208]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7RCB5M05659 for ; Mon, 27 Aug 2001 08:11:05 -0400 Received: from xenon (Xenon.AC.Uni-Koeln.DE [134.95.205.83]) by mail1.rrz.Uni-Koeln.DE (8.9.3/8.9.3) with ESMTP id OAA25792 for ; Mon, 27 Aug 2001 14:11:04 +0200 (MET DST) Date: Mon, 27 Aug 2001 14:14:08 +0200 From: Harald Bock X-Mailer: The Bat! (v1.47 Halloween Edition) Personal Reply-To: Harald Bock X-Priority: 3 (Normal) Message-ID: <176251633079.20010827141408@uni-koeln.de> To: chemistry@ccl.net Subject: combination of b3lyp and cc-pVQZ Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear reader, I have a question about combining methods and basis sets: does it make sense to run a calculation usin eg b3lyp using a cc-pVQZ basis set. I am interested in opt, freq (raman) and nbo results. Harald Born Please send answers to protactinium@gmx.de From chemistry-request@server.ccl.net Mon Aug 27 08:29:01 2001 Received: from hotmail.com ([64.4.9.167]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7RCT1M05962 for ; Mon, 27 Aug 2001 08:29:01 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 27 Aug 2001 05:28:56 -0700 Received: from 130.108.137.122 by lw9fd.law9.hotmail.msn.com with HTTP; Mon, 27 Aug 2001 12:28:55 GMT X-Originating-IP: [130.108.137.122] From: "Casey Kelly" To: CHEMISTRY@server.ccl.net Subject: PC Spartan Date: Mon, 27 Aug 2001 07:28:55 -0500 Mime-Version: 1.0 Content-Type: text/html Message-ID: X-OriginalArrivalTime: 27 Aug 2001 12:28:56.0038 (UTC) FILETIME=[D6E58060:01C12EF3]
I am currently using Spartan PC  in order to perform semi-empirical calculations in a solvent.  If anyone is familiar with the program, you may know there are a number of unpublished keywords.  If anyone knows a keyword in which a nonpolar solvent medium can be used to optimize a structure (AM1-SM4 would be the best) it would be greatly appreciated.  Thanks for your help.
 
Best regards,
Casey Kelly
 

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From chemistry-request@server.ccl.net Mon Aug 27 10:07:54 2001 Received: from info.cyf-kr.edu.pl ([149.156.4.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7RE7rM07797 for ; Mon, 27 Aug 2001 10:07:53 -0400 Received: from kinga.cyf-kr.edu.pl (IDENT:4119@kinga.cyf-kr.edu.pl [149.156.2.32]) by info.cyf-kr.edu.pl (8.11.3/8.11.3) with ESMTP id f7RE7m508303 for ; Mon, 27 Aug 2001 16:07:48 +0200 (MEST) Received: (from mykrol@localhost) by kinga.cyf-kr.edu.pl (8.9.3/8.9.3) id QAA09410; Mon, 27 Aug 2001 16:07:46 +0200 (METDST) Date: Mon, 27 Aug 2001 16:07:45 +0200 (METDST) From: Marcin Krol To: Subject: Dual AMD motherboard In-Reply-To: <176251633079.20010827141408@uni-koeln.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Sorry for another hardware question, but as I followed the discusion on AMD vs Intel processors it occured to me that the former are faster and cheaper than the latter but the problem was the lack of dual AMD motherboards. Now Tyan has delivered two dual AMD motherboards (Thunder and Tiger). As Thunder (S2462) is unfortunately too expensive (for my budget at least), I thought that a PC with Tyan Tiger (S2460) and 2 AMD MP processors would be a great computer for MD and QM/MM simulations - fast and not so expensive. However, I haven't found any benchmarks for dual AMD computers on any MD code. Does anyone use such a computer for MD and/or QM calculations? Is it good, or is it better to buy dual PentiumIII system? Or maybe wait for other dual AMD motherboards (MSI and ASUS are said to be preparing such motherboards)? Any comment on dual AMD configuration and/or performance would be appreciated. Thank you in advance Sincerely Marcin Krol From chemistry-request@server.ccl.net Mon Aug 27 11:48:46 2001 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7RFmkM09501 for ; Mon, 27 Aug 2001 11:48:46 -0400 Received: from trentu.ca ([204.225.12.60]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01K7MLMS05LA0024XV@trentu.ca> for chemistry@ccl.net; Mon, 27 Aug 2001 11:48:15 EDT Date: Mon, 27 Aug 2001 11:54:20 -0400 From: elewars Subject: Re: CCL:combination of b3lyp and cc-pVQZ To: chemistry@ccl.net Message-id: <3B8A6D2C.66544C09@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en References: <176251633079.20010827141408@uni-koeln.de> Hello, DFT calc's seem to be "saturated" by basis sets more quickly than are ab initio: Merril et al noted that "Once the double split-valence level [e.g. 6-31G*] is reached, further improvement in basis set quality offers little in the way of structural or energetic improvement.' [1]. Stephens et al. report that "B3LYP calculations converge rapidly with increasing basis set size and that the cost-to-benefit ratio is optimal at the 6-31G* basis set level. 6-31G* will be the basis set of choice in B3LYP calculations on much larger molecules [than C5H6O2]." [2]. We have found (albeit in a limited number of calculations) only very small differences (up to 4 kJ mol-1) between 6-31G* and 6-311G* basis sets with the BP86 functional. But you could do some test calculations using B3LYP/6-31G* and B3LYP/cc-pVQZ. [1] G. N. Merrill, S. Gronert, S. R. Kass, J Phys Chem A, 1997, 101, 208. [2] P. J. Stephens, F. J. Devlin, C. F. Chablowski, M. J. Frisch, J Phys Chem 1994, 98, 11623, and refs therein. E. Lewars ========= Harald Bock wrote: > Dear reader, > I have a question about combining methods and basis sets: > > does it make sense to run a calculation usin eg b3lyp using a cc-pVQZ > basis set. I am interested in opt, freq (raman) and nbo results. > > Harald Born > > Please send answers to > > protactinium@gmx.de > > -= 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 Mon Aug 27 17:06:41 2001 Received: from ccmsi.jsums.edu ([143.132.231.21]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7RL6eM13403 for ; Mon, 27 Aug 2001 17:06:41 -0400 Received: from Falcon [10.30.4.199] by ccmsi.jsums.edu with ESMTP (SMTPD32-7.03) id A66224C20144; Mon, 27 Aug 2001 16:06:42 -0500 From: "Yevgeniy Podolyan" To: Subject: 01.11.01 10th Conference on Current Trends in Computational Chemistry, Jackson MS USA Date: Mon, 27 Aug 2001 16:06:42 -0500 Organization: Jackson State University Message-ID: <001501c12f3c$2c0c6e80$c7041e0a@ccmsi.jsums.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2616 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2462.0000 Importance: Normal Dear Colleague: This is a second announcement of the decennial Conference on Current Trends in Computational Chemistry (CCTCC). This year, the meeting organized annually by Jackson State University will be held at Jackson Hilton Hotel, Jackson, Mississippi on November 1-3, 2001. The 10th CCTCC will cover all areas of computational chemistry as well as quantum chemistry. The format consists of a series of plenary lectures and poster presentations (Thursday 2pm - Saturday 7pm) covering applications as well as theory. Within two and a half days we will accommodate 32 talks of the previous CCTCC speakers as well as three poster sessions. The scope of the talks will be different from the previous meetings. We have asked invited speakers to cover the progress of their research areas over the last decade. As usual, poster presentations will cover results of current research activities. I am also glad to inform you, that fourteen invited speakers contributed their reviews to a special "Perspectives on a Decade of Trends in Computational Chemistry" issue of THEOCHEM. This issue will appear in October 2001, and will be distributed among all registered participants. We are planning to publish extended abstracts (up to four pages each) of all invited talks and poster presentations. Original scientific contributions will be published in a special issue of the Journal of Molecular Structure (THEOCHEM). Manuscripts for inclusion in the special issue should be submitted in triplicate upon arrival at the registration desk. Submitted papers will be subject to the journal's standard referee procedures. The detail information, registration forms and deadlines are available at the WebPage: http://ccmsi.jsums.edu/cctcc/. Sincerely, Jerzy Leszczynski Chairman of the Organizing Committee List of Invited Oral Presentations Rodney J. Bartlett - University of Florida, USA Ab Initio DFT David Buckingham - Cambridge University, UK TBA Ernest R. Davidson - Indiana University, USA The Cope Rearrangement in Theoretical Retrospect Thom H. Dunning , Jr. - Pacific Northwest Laboratories, USA TBA Clifford Dykstra - Indiana University, USA Intermolecular Electrical Effects Joseph S. Francisco - Purdue University, USA The Atmospheric Chemistry of Halogens: Insights from Computational Chemistry Gernot Frenking - Phillips-Universitat Marburg, Germany Insight into the Chemical Bond of Transition Metal Complexes Nicholas C. Handy - Cambridge University, UK Exchange and Correlation in Density Functional Theory Istvan Hargittai - Budapest University of Technology, Hungary Shifting Balance between Computation and Experiment Herbert A. Hauptman (Noble Prize Laureate) - Hauptman-Woodward Medical Research Institute, USA (After-Dinner Noble Lecture Series) X-Ray Crystallography. A History of Ideas Kimihiko Hirao - University of Tokyo, Japan Research Activities of Theoretical Chemistry Group at the University of Tokyo: Recent Advances in Multireference based Perturbation Theory and Relativistic Molecular Theory Kendall N. Houk - University of California Los Angeles, USA Pericyclic Reaction Transition States Yasuyuki Ishikawa - University of Puerto Rico, Puerto Rico Relativistic Many-Body Perturbation Theory for Many-Electron Systems William Jorgensen - Yale University, USA Computational Studies for Protein-Ligand Binding and Drug Design William Lester, Jr. - University of California at Berkeley, USA Overview of Quantum Monte Carlo Developments for the Past Decade William H. Miller - University of California at Berkeley, USA Using Semiclassical Theory to Add Quantum Effects to Classical Molecular Dynamics Simulations Keiji Morokuma - Emory University, USA TBA Vicent Ortiz - Kansas State University, USA TBA Robert G. Parr - University of North Carolina, USA What is an Atom in a Molecule? Peter Politzer - University of New Orleans, USA Computational Characterization of Energetic Materials John A. Pople (Noble Prize Laureate) - Northwestern University, USA Theoretical Chemical Models for 3rd Row Elements Peter Pulay - University of Arkansas, USA TBA Mario Raimondi - University of Milan, Italy Developments and Applications of Modern Forms of Valence Bond Theories and Related Methods Krishnan Raghavachari - Bell Laboratories, USA Electronic Structure Studies of Semiconductor Surface Chemistry Jean-Louis Rivail - Universite Henri Poincare, France Liquid State Quantum Chemistry, More on Continuum Models Andrzej Sadlej - Nicolaus Copernicus University, Poland TBA Henry F. Schaefer, III - University of Georgia, USA TBA Harold Scheraga - Cornell University, USA Search for an Efficient Global Optimization Procedure for Protein Folding George C. Schatz - Northwestern University, USA Electrodynamics of Metal Nanoparticles and Nanostructured Materials Jack Simons - University of Utah, USA Unusual Negative Molecular Ions and Dianions and Chemical Bonds Involving Rydberg Orbitals Donald Truhlar - University of Minnesota, USA Quantum Mechanical Effects on Chemical Reaction Dynamics From chemistry-request@server.ccl.net Mon Aug 27 10:33:16 2001 Received: from epimetheus.hosting4u.net ([209.15.2.70]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7REXGM08216 for ; Mon, 27 Aug 2001 10:33:16 -0400 Received: (qmail 28995 invoked from network); 27 Aug 2001 14:05:11 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 27 Aug 2001 14:05:11 -0000 Received: from yersina ([210.50.56.124]) by proinformatix.com ; Mon, 27 Aug 2001 09:05:04 -0500 Reply-To: From: "Sergio Manzetti" To: "Chemistry Discussion G" Subject: GROMACS and Energy Minimization Date: Tue, 28 Aug 2001 00:03:37 -0700 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Hi all. I am trying to minimize a complex of two chains using the GROMACS package, following the Getting Started Guide. Unfurtunately, the specific molecular dynamics parameter file (*mdp) for energy minization is not available from the net. Does anyone have a spare copy of such a parameter file for the specific energy minimization process? In case I got something wrong here, all hints and tricks are warmly welcome. Thank you Sergio Manzetti ____________________________________________________________________________ ___________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Mon Aug 27 11:46:11 2001 Received: from alcides.host4u.net ([216.71.64.98]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7RFkBM09469 for ; Mon, 27 Aug 2001 11:46:11 -0400 Received: from mars (cr808583-b.shprd1.on.wave.home.com [24.43.18.40]) by alcides.host4u.net (8.9.3/8.9.3) with SMTP id KAA10909; Mon, 27 Aug 2001 10:43:13 -0500 Message-ID: <008301c12f0f$2bf90700$05d5a8c0@simbiosys.ca> From: "Owen Lewis" To: "Marcin Krol" , References: Subject: Re: CCL:Dual AMD motherboard Date: Mon, 27 Aug 2001 11:44:23 -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 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 Try www.tomshardware.com for benchmarks and performance comments on the two Tyan motherboards - there may be something there. I can unfortunately only personally comment on the performance of the motherboard itself - we have used the Tyan Tiger board with twin PIII 733 chips and the performance is excellent. I would imagine one would obtain excellent results using AMD processors. cheers, Owen Lewis Molecular Modelling Product Developer SimBioSys Inc. Toronto, Ontario owen@simbiosys.ca----- Original Message ----- From: "Marcin Krol" To: Sent: Monday, August 27, 2001 10:07 AM Subject: CCL:Dual AMD motherboard > Dear CCLers, > > Sorry for another hardware question, but as I followed the discusion on > AMD vs Intel processors it occured to me that the former are faster and > cheaper than the latter but the problem was the lack of dual AMD > motherboards. Now Tyan has delivered two dual AMD motherboards (Thunder > and Tiger). As Thunder (S2462) is unfortunately too expensive (for my > budget at least), I thought that a PC with Tyan Tiger (S2460) and 2 AMD MP > processors would be a great computer for MD and QM/MM simulations - fast > and not so expensive. However, I haven't found any benchmarks for dual AMD > computers on any MD code. Does anyone use such a computer for MD and/or QM > calculations? Is it good, or is it better to buy dual PentiumIII system? > Or maybe wait for other dual AMD motherboards (MSI and ASUS are > said to be preparing such motherboards)? > > Any comment on dual AMD configuration and/or performance would be > appreciated. > > Thank you in advance > Sincerely > Marcin Krol > > > -= 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 Mon Aug 27 14:14:44 2001 Received: from email01.aon.at ([195.3.96.115]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7RIEhM11658 for ; Mon, 27 Aug 2001 14:14:43 -0400 Received: (qmail 136626 invoked from network); 27 Aug 2001 18:14:37 -0000 Received: from n783p023.adsl.highway.telekom.at (HELO pc1.eidolon.net) ([62.47.41.215]) (envelope-sender ) by qmail1.highway.telekom.at (qmail-ldap-1.03) with SMTP for ; 27 Aug 2001 18:14:37 -0000 Sender: hal@pc1.eidolon.net To: chemistry@ccl.net Subject: Where can I find the cc-pVXZ basis sets for Li? From: Hannes Loeffler Date: 27 Aug 2001 20:14:37 +0200 Message-ID: <87ofp1jroy.fsf@pc1.eidolon.net> Lines: 10 User-Agent: Gnus/5.0808 (Gnus v5.8.8) XEmacs/21.4 (Artificial Intelligence) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, does anybody know where I can find the cc-pVXZ basis sets for Li? Interestingly the EMSL database doesn't have them and Gaussian doesn't support them either but all other elements of the first row. These basis sets have been used quite often in the literature so I wonder why they aren't there. Any help appreciated, Hannes.