From noy@atc.atccu.chula.ac.th Thu Jan 18 03:49:51 1996 Received: from atc.atccu.chula.ac.th for noy@atc.atccu.chula.ac.th by www.ccl.net (8.6.10/950822.1) id DAA19084; Thu, 18 Jan 1996 03:48:51 -0500 Received: by atc.atccu.chula.ac.th (5.57/CFTHAI-2e1.ULTRIX) id AA12979; Thu, 18 Jan 96 15:29:46 GMT From: noy@atc.atccu.chula.ac.th (Teerakiat Kerdcharoen) Message-Id: <9601181529.AA12979@atc.atccu.chula.ac.th> Subject: free energy calculation To: chemistry@www.ccl.net Date: Thu, 18 Jan 1996 15:29:45 +0000 (WET) X-Mailer: ELM [version 2.4 PL20] Content-Type: text Content-Length: 871 Dear cyberchemists, I am studying about the molecular dynamics simulation of supramolecules. Could somebody kindly point me out good references of how free energy is calculated by molecular simulations ? I would appreciate any literatures concerning perturbation free energy methods and thermodynamic integration techniques. Thank you very much in advance and have a nice time. take care, Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen, Ph.D. Address: Department of Physics, Mahidol University ,Bangkok 10400 Phone: 5790658, 5793955 ext. 114, mobile 01-4906089 E-mail: noy@atc.atccu.chula.ac.th Homepage: http://www-c724.uibk.ac.at/noy/ Research: Computer Assisted Molecular Design ----------------------------------------------------------------------------- From vkitzing@sunny.mpimf-heidelberg.mpg.de Thu Jan 18 04:19:51 1996 Received: from otto.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-heidelberg.mpg.de by www.ccl.net (8.6.10/950822.1) id EAA19329; Thu, 18 Jan 1996 04:18:57 -0500 Received: from [192.109.43.34] (mac10.mpimf-heidelberg.mpg.de) by otto.mpimf-heidelberg.mpg.de (4.1/SMI-4.1) id AA20536; Thu, 18 Jan 96 10:18:52 +0100 Message-Id: <9601180918.AA20536@otto.mpimf-heidelberg.mpg.de> Date: Thu, 18 Jan 1996 16:13:40 +0000 To: CHEMISTRY@www.ccl.net (Computational Chemistry List) From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) X-Sender: vkitzing@sunny.MPImF-Heidelberg.mpg.de (Unverified) Subject: Mobility paradox Dear colleges on the Computational Chemistry List, this morning I thought about an apparently simple problem where I do not know a solution jet. Consider a symmetric 1:1 electrolyte system with a single dielectric constant which is divided by a planar surface into a right hand and a left hand side. The cationic and anionic concentrations, cC and cA, on both sides are the same; to obtain global electro neutrality cC == cA is required. Exceptions from this rule are allowed only locally, e.g. within a few Debye length around the boundary. The ionic mobilities are mu1 > mu2 on the right hand side and mu2 and mu1 on the other for cations and anions, respectively. At equilibrium there is no problem. Now an external electric field E is applied and this creates the problem. On the first view one would write the individual ionic fluxes jC and jA far away from the central boundary: left hand side and right hand side cations jC(left) = + F mu1 E cC and jC(right) = + F mu2 E cC anions jA(left) = - F mu2 E cA and jA(right) = - F mu1 E cA where F is Faraday's constant. But this implies jC(left) != jC(right) and jA(left) != jA(right) which violates the particle conservation law. I would assume that such a problem has been discussed in literature. Has anybody some ideas? I will summarize the replies. ------------------------------------------------------------------------- Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29, D69120 Heidelberg, FRG Carl-Zuckmayer Str. 17, D69126 Heidelberg (privat) FAX : +49-6221-486 459 (work) Tel.: +49-6221-486 467 (work) Tel.: +49-6221-385 129 (home) internet: vkitzing@sunny.MPImF-Heidelberg.mpg.de http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/Eberhard.html From qojskd@uscmail.usc.es Thu Jan 18 06:34:52 1996 Received: from uscmail.usc.es for qojskd@uscmail.usc.es by www.ccl.net (8.6.10/950822.1) id GAA20306; Thu, 18 Jan 1996 06:21:47 -0500 Received: from [193.144.74.64] (qojskd.usc.es) by uscmail.usc.es (5.67b/1.34) id AA05321; Thu, 18 Jan 1996 12:22:47 +0100 Date: Thu, 18 Jan 1996 12:22:47 +0100 Message-Id: <199601181122.AA05321@uscmail.usc.es> From: "Javier Sardina" To: chemistry@www.ccl.net Subject: Freeware for NMR processing Dear netters: It is a pleasure to announce that version 3.1.1 of the NMR processing program SwaN-MR is available, as two compressed-self-expanding files, (via anonymous ftp) from : sfdzuma.usc.es (193.144.75.69) directory /pub/NMR/SwaN-MR.311 This version is a beta release and users are encouraged to test it and submit the bugs they find to the author. SwaN-MR is a FREEWARE program for the Macintosh and PowerMac. It processes and analyzes NMR spectra (1D to 4D, from Varian Gemini, Bruker nad TecMag spectrometers). It is also very useful in annotating, printing and presenting spectra. The program has been written by: Dr. Giuseppe Balacco MENARINI s.r.l. Via Sette Santi, 3 I-50131 Firenze ITALY In order to use SwaN-MR you need to write a SIGNED LETTER (no fax or e-mail messages) to Dr. Balacco requesting a LICENSE. If you want to check out the program before asking for the license you can try Snail-MR (included in the demo file). It does everything that SwaN-MR does but much more slowly. Newest features: - A converter for Nicolet spectra has been added - A module for spectral simulation (up to 9 nuclei) and fitting to experimental data has been added The program's capabilities include: Weighting (9 different window functions) FFT (real, complex, hypercompex, etcI) Phase Correction (1 manual and 2 automatic options) Magnitude representation Baseline Correction (6 options, including 5th degree polynomials and trigonometric series) BasePlane correction Integration (manual and automatic) Least Squares Fitting (to Lorentzian or Gaussian functions) Quanto-mechanical simulations Fast Linear Prediction Digital Solvent Suppression T1 calculation (inversion recovery) Spectral Editing (algebraic addition and much more) Symmetrization I hope that you will enjoy the program. F. Javier Sardina Associate Prof. of Organic Chemistry phone: (34)-81-591085 Departamento de Quimica Organica (34)-81-563100-Ext 4249 Universidad de Santiago de Compostela fax: (34)-81-595012 15706 Santiago de Compostela. SPAIN e-mail: qojskd@usc.es From owner-chemistry@ccl.net Thu Jan 18 10:34:56 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA23758; Thu, 18 Jan 1996 10:33:17 -0500 Received: from mudfence.ce.psu.edu for posting@omnibus.ce.psu.edu by bedrock.ccl.net (8.7.1/950822.1) id KAA24104; Thu, 18 Jan 1996 10:33:14 -0500 (EST) Received: from omnibus.ce.psu.edu (omnibus.ce.psu.edu [128.118.35.3]) by mudfence.ce.psu.edu (8.6.9/A/UX 3.1) with SMTP id KAA07493 for ; Thu, 18 Jan 1996 10:33:10 -0500 Message-ID: Date: 18 Jan 1996 10:32:01 -0500 From: "posting" Subject: Request post chromatography course announcement To: chemistry@ccl.net X-Mailer: Mail*Link SMTP-MS 3.0.2 Dear List Owner: Will you please consider posting the following announcement to your Chemistry-people listserv? We think it may be of interest to your subscribers. Thank you. POSTING: High Performance Liquid Chromatography (HPLC) and Gas Chromatography (GC) Intensive Short Courses The Penn State Scanticon Conference Center Hotel State College, Pennsylvania Basic HPLC: May 15-17, 1996 Advanced HPLC: May 18-19, 1996 Basic GC: June 3-5, 1996 Advanced GC: June 6-7, 1996 a continuing and distance education service of The Eberly College of Science at The Pennsylvania State University Presented in a small-group setting with a limited enrollment, these four intensive short courses combine hands-on lab experience, using commercial instruments from leading manufacturers, with lectures presented in an informal atmosphere conducive for asking questions and exchanging ideas. The short courses are designed to meet the needs of: -Industrial chemists, technicians, and managers who want to know more about analytical separation techniques; -Academic faculty and staff members who use chromatography as a research tool; -Graduate and undergraduate students who want practical experience; and -New users who have been limited to following others' methods and experienced users who want to be updated. To receive a BROCHURE, call: 1-800-PSU-TODAY or e-mail: lion@cde.psu.edu From xiaopeng@astro.ocis.temple.edu Thu Jan 18 10:35:00 1996 Received: from astro.ocis.temple.edu for xiaopeng@astro.ocis.temple.edu by www.ccl.net (8.6.10/950822.1) id KAA23488; Thu, 18 Jan 1996 10:32:06 -0500 Received: (from xiaopeng@localhost) by astro.ocis.temple.edu (8.7.1/8.7.1) id KAA00099; Thu, 18 Jan 1996 10:32:00 -0500 (EST) Date: Thu, 18 Jan 1996 10:31:58 -0500 (EST) From: Peking To: ccl Subject: Re: Further question about Gaussian 94 IRC calculation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thanks very much for all the response! I found that I may not express myself clearly in the post. I would like to ask you to help me for further information. I add more information in the relative lines below: I first use LST to get a guess structure of the transition state and then use Transition State optimization and frequency to get a first order saddle point. So this structure should be O.K as a starting point for IRC calculation. All this calculation has been saved as ."chk" file by including "%chk=ts" in the input commmand file. Then I use the following input command file to do the IRC --link1-- %chk=ts #T RHF/6-31g(d) IRC=(rcfc, stepsize=5, maxpoint=20) guess=read geom=checkpoint test run tIRC to see if the saddle point connect the starting point to the product 0 1 Could you please give me some more information? > Peking writes: > > > > Dear netters, > > Anybody can kindly point out if it is a bug or I did something wrong? > > > > I used LST and got a saddle point at rhf/6-31g* level, then I try > > to use IRC calculation to confirm that the saddle point connects my > > starting materia and the product. however, when I submitted that job, the > > computer told me that "operation on file out of range" "ER terminatnion > > in NtrErr". "NtrErr called from FileIO" But I did similar job before using > > Gaussian92. > > > > So is this a bug of G94 but not of G92? > > > > Thanks in advance!!! > > > > xiaopeng > > > > This topic is a common source of confusion, which I'd like to > clarify. > > The IRC path leads down from a transition state to the minima it > connects. It starts at a true transition structure, where the forces > are zero and the Hessian has one negative eigenvalue. The algorithm > in Gaussian also expects to start with the Hessian at the TS. > > The LST procedure does NOT locate a transition structure -- it locates > an initial guess for a transition state optimization. In particular, > it finds a point at which the Hessian has at least one negative > eigenvalue (but perhaps more) and at which the forces are far from > zero. The results of an LST calculation are not chemically > meaningful, but are only useful to start an optimization to locate the > actual transition structure. > > In Gaussian 94, LST is really obsolete, since the Opt=QST2 algorithm > both uses synchronous transit methods to locate a guess for the > transition structure and then goes on to complete the optimization. > This replaces the combination of LST and Opt=TS in G92 with a single > (and much more reliable) algorithm. > > The combination of LST and IRC without an intervening Opt=TS in G92 > would give a path, but not one satisfying the definition of the IRC > and not one containing the transition structure, so it's probably > better than G94 won't let you do it. The recommended procedure is > Opt=QST2, Freq, IRC=RCFC. The Freq step both confirms that the > structure found by Opt=QST2 is a proper first order saddle point and > provides the Hessian read by the RCFC option to the IRC. > > Mike Frisch > frisch@lorentzian.com > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: owner-chemistry@ccl.net > -- Original Sender From: Address: frisch@lorentzian.com > 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 owner-chemistry@ccl.net Thu Jan 18 15:35:00 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id PAA29530; Thu, 18 Jan 1996 15:28:48 -0500 Received: from euch4e.chem.emory.edu for morokuma@euch4e.chem.emory.edu by bedrock.ccl.net (8.7.1/950822.1) id PAA00129; Thu, 18 Jan 1996 15:28:43 -0500 (EST) From: Received: by euch4e.chem.emory.edu (AIX 3.2/UCB 5.64/4.03) id AA26738; Thu, 18 Jan 1996 15:28:42 -0500 Message-Id: <9601182028.AA26738@euch4e.chem.emory.edu> Subject: icqc 97 announcement To: molecular-dynamics-news@mailbase.ac.uk Date: Thu, 18 Jan 1996 15:27:20 -0500 (EST) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Sender: morokuma@euch4e.chem.emory.edu Content-Transfer-Encoding: quoted-printable FIRST ANNOUNCEMENT THE 9TH INTERNATIONAL CONGRESS OF QUANTUM CHEMISTRY Organized under the auspices of=20 the Internaltional Academy of Quantum Molecular Sciences EMORY CONFERENCE CENTER HOTEL EMORY UNIVERSITY, ATLANTA, GEORGIA, USA JUNE 9-14, 1997 ___________________________________________________________________ ORGANIZING COMMITTEE =20 Ernest R. Davidson Kieji Morokuma (Chair) Henry F. Schaefer, III LOCATION AND DATES =20 Emory Conference Center Hotel, Emory University Atlanta, Georgia USA >From Monday, June 9, 1997 (Gathering) to Saturday, June 14 (Closing Session, Banquet) CORRESPONDENCE =20 Keiji Morokuma 9th ICQC '97 Department of Chemistry Emory University Atlanta, GA 30322 USA Tele: (404) 727-2180 Fax: (404) 727-6586 Email: morokuma@emory.edu PROGRAM =20 The program will include plenary and invited lectures and posters. =20 The conference will be in English. PLENARY SPEAKERS =20 Reinhart Ahlrichs, Institut f=9Fr Physikalische Chemie und Elektrochemie, Karlsruhe, Germany Michele Parrinello, Max-Planck-Institut f=9Fr Festk=9Arperforschung,=20 Stuttgart, Germany Martin Quack, Laboratorium f=9Fr Physikalische Chemie, ETH , Z=9Frich,=20 Switzerland PARTIAL LIST OF INVITED SPEAKERS =20 Alml=9Af Clementi Heller Mayer Apeloig Cremer Hirao Musaev Armentrout Dixon Houk Nascimento Baerends Dunning Iwata Robb Bauschlicher Dykstra Jemmis Scuseria Becke Eisenstein Koch Shaik Bondybey Frenking Koga Stanton Bowers Fu Kozlowski Taylor Carsky Galabov Lischka Urban Cederbaum Gauss Light Yang Ceyer Hall Lorquet Zerner Cioslowski Head-Gordon Makri SESSION TOPICS =20 Methods - Parallel Computation - quantum chemistry code implementation - DFT - Perturbation, Coupled Cluster, etc. (all non-variational methods) - Multi-reference Approaches - Basis Sets and Corrections for Inadequacy - Hybrid Methods (QM/MM, etc.) Applications - Photochemistry - Non-adiabatic Effects - Electronic Structure in Condensed Media - Intermolecular Interactions - Spectroscopy - Chemical Reactivity - Organic Reactions - Homogeneous Catalysts - Solid Surface, Heterogeneous Catalysis - Materials, Solid States - Biological Applications - Dynamics of Nuclear Motion - Statistical Applications - Industrial Applications SATELLITE MEETINGS =20 1. Density-Functional Theory and Computation Dates: June 3-7, 1997 Location: Duke University Durham, North Carolina Contact: Weitao Yang Dept. of Chemistry Duke University Durham, NC 27708-0346 Organizers: Mel Levy and Weitao Yang Email: yang@chem.duke.edu 2. Theoretical Chemistry in Biology: From Molecular Structure=20 to Functional Mechanisms Dates: June 3-7, 1997 Location: Savannah, GA or Charleston, SC Contact: Michael Zerner Quantum Theory Project Univ. of Florida Gainesville, Florida 32611 Organizers: Peter Kollman, Harel Weinstein,=20 and Michael Zerner Email: zerner@qtp.ufl.edu 3. Structural and Mechanistic Organic Chemistry: A Tribute to=20 Professor Norman L. Allinger Dates: June 5-7, 1997 Location: Athens, Georgia Contact: H.F. Schaefer, III Ctr. for Comp. Quan. Chem. Univ. of Georgia Athens, Georgia 30602-2556 Organizers: H.F. Schaefer and P. Schleyer Email: hfsiii@uga.cc.uga.edu 4. Coupled Cluster Theory and Electron Correlation Workshop Dates: June 15-19, 1997 Location: Cedar Key, Florida Contact: Rodney Bartlett Quantum Theory Project University of Florida Gainesville, Florida 32611 Email: bartlett@qtp.ufl.edu=20 5. Interplay between Theory and Experiment in Molecular=20 Spectroscopy and Dynamics Dates: June 15-18, 1997 Location: Memphis, Tennessee Contact: Peter Pulay Dept. of Chem. & Biochem. Univ. of Arkansas Fayetteville, AK 72701 Organizers: Daniel Chapman, Tom Cundari, David Dixon,=20 B. Andes Hess, Bruce Hudson, Henry Kurtz and Peter Pulay Email: pulay@comp.uark.edu __________________________________________________________ Updated information concerning the congress can also be obtained=20 on the internet at http://www.chem.emory.edu/icqc/icqc.html. The second circular containing registration and accommodation=20 information will be mailed in the fall of 1996 to those who=20 return the following response form via fax, mail or email=20 [icqc@euch4g.chem.emory.edu].=20 ___________________________________________________________ Last name First Name Institution Department Address Telephone Fax E-mail ( ) I intend to aprticipate ( ) I intend to present a poster ( ) Please send the second circular