From chemistry-request@www.ccl.net Sun Mar 28 04:28:10 1999 Received: from techunix.technion.ac.il (root@techunix.technion.ac.il [132.68.1.28]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA16162 Sun, 28 Mar 1999 04:28:09 -0500 (EST) Received: from tx.technion.ac.il (cedl09.technion.ac.il [132.68.80.95]) by techunix.technion.ac.il (8.9.1/8.8.5) with ESMTP id LAA02001 for ; Sun, 28 Mar 1999 11:27:56 +0200 (IST) Message-ID: <36FDF352.6DA00022@tx.technion.ac.il> Date: Sun, 28 Mar 1999 12:16:02 +0300 From: Irena Efremenko Organization: Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa 32000 X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: CCL Computational Chemistry List Subject: QC on PC Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear friends, We are about to buy new machine for quantum chemical calculations for catalytic applications in both cluster and periodic approximations. I would like to ask your advice about the best hardware and operation system. My first search shows that Pentium II and linux are very perspective and provide the best performance per cost ratio. Would you so kind to share your experience on this matter. I am especially interested in successful installation of quantum chemical packages for parallel calculations on PCs and on Pentium II clusters specifically. Many thanks in advance. I'll summarize your answers. Irena From chemistry-request@www.ccl.net Sun Mar 28 11:27:11 1999 Received: from nmrc.ucc.ie (nmrc.ucc.ie [143.239.64.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA16953 Sun, 28 Mar 1999 11:27:10 -0500 (EST) Received: from odessa.nmrc.ucc.ie (odessa.nmrc.ucc.ie [143.239.64.65]) by bastion.nmrc.ucc.ie (8.9.3/8.9.3) with ESMTP id RAA13276 for ; Sun, 28 Mar 1999 17:26:41 +0100 (BST) Date: Sun, 28 Mar 1999 17:27:15 +0100 From: Michael Nolan To: Jim Greer Cc: chemistry@www.ccl.net Subject: laredo Message-ID: <19990328172703.A326@rennes.nmrc.ucc.ie> References: <199903270601.OAA11530@bak-pd.online.sh.cn> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.95.1i In-Reply-To: <199903270601.OAA11530@bak-pd.online.sh.cn>; from Jiang Aiguo on Sat, Mar 27, 1999 at 02:02:23PM +0800 Howdy...... there appears to be something funny with laredo, ever since the little server problem......I ran Insight today and it's incredibly slow, even thouhg it's local...it's almost like it's going over the network. What say we bring it down today and see if that helps? yours in awe gimp From chemistry-request@www.ccl.net Sun Mar 28 18:43:35 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA20024 Sun, 28 Mar 1999 18:43:35 -0500 (EST) Received: from auric.chem.csiro.au (auric.chem.CSIRO.AU [138.194.44.10]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id SAA19375 for ; Sun, 28 Mar 1999 18:43:31 -0500 (EST) Received: by auric.chem.csiro.au id AA19476 (5.67b/IDA-1.5 for chemistry@ccl.net); Mon, 29 Mar 1999 09:43:13 +1000 Received: from cpr-46107.chem.csiro.au(138.194.46.107), claiming to be "[138.194.46.107]" via SMTP by auric.chem.CSIRO.AU, id smtpd19468aaa; Sun Mar 28 23:43:09 1999 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 29 Mar 1999 09:43:04 +1000 To: CHMINF-L@LISTSERV.INDIANA.EDU, chemistry@ccl.net From: "Dr. Dave Winkler" Subject: organic charge-transfer complexes Dear Netters, I would like to be able to calculate interaction energies and the UV-visible spectra of organic charge-transfer or charge-resonance complexes which involve parallel stacking of aromatic donor and acceptor moieties, for example chloranil/hexamethylbenzene. Will INDO methods such as ZINDO allow me to do this? I'm interested in only organic 'pi-stacked' complexes, not those involving metals. Are there any particularly helpful key papers or reviews? Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia http://www.molsci.csiro.au From chemistry-request@www.ccl.net Fri Mar 26 09:30:06 1999 Date: Fri, 26 Mar 1999 15:29:29 +0100 (CET) From: Stefan Konietzny To: chemistry@ccl.net Subject: Re: Computational Chemist vs Theoretical Chemist Hello everybody, If you take this question serious for yourself, stop reading and delete the message NOW. we are using a computer to do theoretical chemistry. I think there was a time when people did theoretical chemistry without a computer. They were theoretical chemists but not computational chemists. So what about Computational Theoretical Chemist. But Computation implements that it is theoretical; no? Or is it only theoretical, when it is really theoretical, i mean when you calculate things that man has never seen before. We can use the term Applied Theoretical Chemist, for those who calculate things the Lab-Chemist (or is it a Synthetical Chemist?) has synthesized. But there is organic, inorganic, physical... Oh my good, in the end its Physical Chemistry! I think i am falling more and more into an identity crisis. I am calculating (we are all calculators!) inorganic molecules (although there is carbon in it, they are inorganic). Until i know who or what i am, i call myself: Molecular Modeller in Applied Theoretical Inorganic Computational Quantum Chemistry. :-) Stefan. !!!!! reply to: konietz@chemie.uni-kl.de !!!!! finger or talk request: konietz@oktarin.chemie.uni-kl.de **************************************************************** * Stefan Konietzny * *--------------------------------------------------------------* *Fachbereich Chemie, AK Frank | Dept. of Chemistry * *Universitaet Kaiserslautern | University of Kaiserslautern * *Erwin-Schroedingerstr. | Erwin-Schroedingerstr. * *67663 Kaiserslautern | D-67663 Kaiserslautern * *0631/205-2964 | +49-631/205-2964 * **************************************************************** From chemistry-request@www.ccl.net Fri Mar 26 10:33:10 1999 Date: Fri, 26 Mar 1999 09:43:43 +36000 From: Richard Wood To: chemistry@ccl.net Subject: Re: CCL:CCL: Computational Chemist vs Theoretical Chemist Hi- I would say that theoretical chemistry involves either a) developing theories, or b) using theories that involve quantum chemistry. I would say that computational chemistry is the use of tools, be they quantum mechanical, or, mostly semi-empirical. Thus, IMO, computational chemistry is a sub-field of theoretical chemistry. In my "work" as a Ph. D. candidate, I do MD simulations of biologically important molecules. These simulations involve classical mechanics and other semi-empirical techniques. When people ask what I do, I say "I am a computational chemist", because i don't develop theory, I just use what theory has already been developed by others. Richard On Thu, 25 Mar 1999, STK wrote: > > Hello, > > I would like to know what the distinction is between a computational > chemist and a theoretical chemist or are they the same? Many theoretical > chemists who do vigorous computational calculations are adament that they > are "theoretical chemists" and not "computional chemists". Whereas > people in fields like QSAR, bioinformatics, and 3D modeling clearly call > themselves computational chemists and not theoretical. Does computional > chemistry encompass theoretical chemistry? Has there been any > authoritative definition on this? Please enlighten us. > > > > Thanks, > > ============================================================================== > Stephen T. Kim Phone: 613-533-2647 > Fax: 613-533-6669 > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > From chemistry-request@www.ccl.net Fri Mar 26 11:13:21 1999 From: gomide@peri.bchs.uh.edu Date: Fri, 26 Mar 1999 09:19:17 -0600 (EST) To: CHEMISTRY@www.ccl.net Subject: Re: CCL:PC-modelling > > Hi, > > I'm looking for an overview of all available molecular modelling packages on > PC(Pentium)-platforms (windows or linux). > I'm especially interested in ab initio, forcefield, dynamics packages. > Any suggestion is helpful. > Thank you, > > Steven Hi, Steven About the software for modeling, try the URL http://sal.jyu.fi/Z/2/index.shtml Luiz C Gomide Freitas ______________________________________________________________ Dr. Luiz Carlos Gomide Freitas Present address: Department of Biochemistry and Biophysical Science University of Houston Houston, TX 77204-5513, USA Permanent address: Laboratorio de Quimica Teorica Departamento de Quimica Universidade Federal de Sao Carlos CP 676 13.565-905 Sao Carlos, SP Brasil web page www.lqt.dq.ufscar.br From chemistry-request@www.ccl.net Fri Mar 26 12:14:32 1999 Date: Fri, 26 Mar 1999 12:10:45 -0500 (EST) From: Rick Venable To: chemistry@www.ccl.net Subject: Re: CCL:eisai monos ?diabase to (fwd) On Fri, 26 Mar 1999, I. Kerkines wrote: > a)I am interested in finding a program (in C or better > in Fortran), that from classical trajectory calculations > via Molecular Dynamics, is able to calculate the Raman > or/and Rayleigh spectra of a mixture not necessary > composed of monoatomics. CHARMM can perform quasiharmonic anaylis of MD trajectories, essentially determing modes of motion from the simulation data. > b)In MD we use the term "Potential Energy".Which experi- > mental quantity is very close to it and so we can > compare with it when we work in the GAS phase with > pure substances or mixtures of diatomics molecules. The MD potential is relative enthalpy-- meaning you can reasonably compute enthalpy differences, but you shouldn't trust the absolute value of the potential energy; it's different for different MD parameter sets. > c)When we have to work a mixture we usually apply > the well-known Lorentz-Berthelot rules.But it is not > too accurate.Is there any general procedure when we > have excess properties(enthalpy,volume) to calculate > a more accurate interaction L-J potential between the > dissimilar species of a mixture? CHARMM can evaluate energetic between arbitrary sets of particles, using just the VDW term in the potential, if that's what you mean. CHARMM is not freely distributed, but is available for academic license to the mostly Fortran source code for a few hundred dollars U.S. from Harvard Univ.; see http://yuri.harvard.edu -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://www.erols.com/rvenable \/ |=| see http://www.fda.gov ) From chemistry-request@www.ccl.net Sun Mar 28 20:12:50 1999 Received: from gold.truman.edu (gold.truman.edu [150.243.90.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA21098 Sun, 28 Mar 1999 20:12:50 -0500 (EST) Received: from pop.truman.edu ([150.243.64.4]) by gold.truman.edu (8.9.1/8.9.1) with ESMTP id TAA74840 for ; Sun, 28 Mar 1999 19:10:22 -0600 Message-ID: <36FED142.7B8745CA@pop.truman.edu> Date: Sun, 28 Mar 1999 19:02:59 -0600 From: sc18 Reply-To: sc18@truman.edu Organization: Truman St. Un. X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: PROAIMV on an SGI Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Has anybody compiles PROAIMV on an SBI? If you have done this on an Indy, please contact me. Thanx, Ken Fountain