From Robert.Franke@ruhr-uni-bochum.de Thu Apr 23 07:26:32 1998 Received: from sunu450.rz.ruhr-uni-bochum.de for Robert.Franke@ruhr-uni-bochum.de by www.ccl.net (8.8.3/950822.1) id HAA00356; Thu, 23 Apr 1998 07:20:10 -0400 (EDT) From: Received: (qmail 21052 invoked from network); 23 Apr 1998 11:20:05 -0000 Received: from sgi249.rz.ruhr-uni-bochum.de (134.147.222.1) by mailhost.rz.ruhr-uni-bochum.de with SMTP; 23 Apr 1998 11:20:05 -0000 Received: (qmail 5010 invoked by uid 10796); 23 Apr 1998 11:20:05 -0000 Date: Thu, 23 Apr 1998 13:20:04 +0200 (MSZ) To: ccl Subject: SUMMARY: c++ class for linear algebra Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 7 Apr 1998 09:46:32 -0400 From: "Dimitris K. Agrfiotis" To: "'Robert.Franke@ruhr-uni-bochum.de'" Subject: RE: c++ class for linear algebra We use RogueWave's Math.h++ and Lapack.h++ and we are very happy with them. They are commercial, of course. There is a public version of Lapack from Oak Ridge but I believe they are in the process of changing the interface. We used to use the Oak Ridge version but decided to switch to a commercial package for obvious reasons. Hope that helps. Date: Tue, 7 Apr 1998 16:03:52 +0200 (MDT) From: Lutz.Ehrlich@EMBL-Heidelberg.de To: Robert.Franke@ruhr-uni-bochum.de Subject: Re: CCL:c++ class for linear algebra Hi, Robert, versuch mal LAPACK++ http://math.nist.gov/lapack++/ Sollte demn"achst aber von Template Numerical Toolkit ersetzt werden. Sehr viel sch"oner f"ur die konkrete Arbeit sind nat"urlich die NumericPython-Module, die ebenfalls LAPACK f"ur Matrixobjekte wrappen. Infos unter: http://www.sls.lcs.mit.edu/jjh/numpy/ Das ganze ist in den MolecularModellingToolkit von Konrad Hinsen integriert (http://starship.skyport.net/crew/hinsen/mmtk.html), so da"s viele CompChem-Sachen schon vorliegen. Cheers, Lutz --------------------- Lutz Ehrlich Structural Biology EMBL Meyerhofstr. 1 D-69012 Heidelberg Germany Date: Tue, 7 Apr 1998 10:39:02 -0400 (EDT) From: yliu@wesleyan.edu To: Robert.Franke@ruhr-uni-bochum.de Subject: Re: CCL:c++ class for linear algebra Hi, There is a lapack++ at http://www.netlib.org Date: Tue, 7 Apr 1998 11:42:44 -0400 From: Peter Shenkin To: Robert.Franke@ruhr-uni-bochum.de Subject: Re: CCL:c++ class for linear algebra There is something called blitz++ -- but I've never used it. It is well spoken of by those who have. -P. Date: Tue, 07 Apr 1998 20:40:54 +0200 From: Olivier Quinet To: Robert.Franke@ruhr-uni-bochum.de Subject: Re: CCL:c++ class for linear algebra Hi, Here is a site with some good libraries, some are in C other are in C++ http://www.devinfo.com/archives/x2ftp/math/ Olivier Date: Tue, 07 Apr 1998 14:30:01 -0400 From: Lutfur Khundkar To: Robert.Franke@ruhr-uni-bochum.de Subject: Re: CCL:c++ class for linear algebra You could look for the things you need at Netlib (http://www.netlib.org). -- Lutfur Khundkar Assistant Professor Department of Chemistry, 102 HT Northeastern Unversity Boston, MA 02115 ------------------------------------ Voice: (617) 373-2382 FAX: (617) 373-8795 Email: lkhundkr@neu.edu Date: Tue, 7 Apr 1998 16:08:06 -0400 (CDT) From: Norge Cruz Hernndez To: Robert.Franke@ruhr-uni-bochum.de Subject: Re: CCL:c++ class for linear algebra You may use the IMSL Library in FORTRAN 77. You want to use the code written in c++. well OK !! In Linux Sistem is the conver fortran-c f2c command that can help you to pass tha routines in fortran to c or c++ I think. Best regard Norge Date: Wed, 8 Apr 1998 08:51:10 GMT + 2:00 From: Leslie Glasser To: Robert.Franke@ruhr-uni-bochum.de Subject: Re: CCL:c++ class for linear algebra The computer algebra program, Maple, can generate C code for any desired operations. Presumably, Mathematica will do the same. > I would like to know if anyone has a source for a powerfull c++ > class concerning linear algebra features like matrix multiplication etc. Leslie ============================================================== (Prof.) Leslie Glasser Dept. of Chemistry E-mail: glasser@aurum.chem.wits.ac.za Univ. of Witwatersrand Tel: Intl + 27 11 716-2070 P. O. WITS 2050 Fax: Intl + 27 11 339-7967 South Africa Home Pages: University http://sunsite.wits.ac.za Chemistry http://www.chem.wits.ac.za ====================================================================== Date: Wed, 08 Apr 1998 10:44:09 +0100 From: Peter Tebbutt To: robert.franke@rz.ruhr-uni-bochum.de Subject: C++ libraries Dear Dr Franke, In response to your query we have a couple of suggestions which might be useful. The C++ Library of Efficient Datatypes and Algorithms (LEDA) is very good. Its free within academia, and has a linear algebra class. The homepage is: http://www.mpi-sb.mpg.de/LEDA/ Also NAG http://www.nag.co.uk NAG do not provide c++ classes but do sell libraries of FORTRAN and C functions for a wide range of maths applications With regards Peter Tebbutt ChemSymphony Consultant Cherwell Scientific Publishing Oxford UK Date: Mon, 13 Apr 1998 10:18:30 -0500 (MEX) From: Joaquin Hernandez Perez To: Robert.Franke@ruhr-uni-bochum.de Cc: Rafael Fernandez Subject: Re: CCL:c++ class for linear algebra Robert, here is a list oF C++ libraries that includes a good core of routines for linear algebra: PETSc - The Portable, Extensible Toolkit for Scientific Computation http://www.mcs.anl.gov/petsc/petsc.html The Diffpack Home Page http://www.oslo.sintef.no/avd/33/3340/diffpack/ The FEAT site of life http://gaia.iwr.uni-heidelberg.de/~featflow/ VECFEM http://www.uni-karlsruhe.de/~vecfem/ You can also check netlib home page http://netlib.no/ I hope this could help you. Regards. - - - - - - - - - - - - - - - - -- - - - - - - - - - - - - - - - - - - Joaquin Hernandez jrhp@labvis.unam.mx http://www.labvis.unam.mx/ #: (5)-622-8582 fax: (5) 622-8043 - - - - - - - - - - - - - - - - -- - - - - - - - - - - - - - - - - - - /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ /\ /\ /\ Robert Franke /\ /\ Fakultaet fuer Chemie /\ /\ Lehrstuhl fuer Theoretische Chemie /\ /\ Ruhr-Universitaet Bochum /\ /\ D-44780 Bochum /\ /\ Phone: 049-234-7006751 or /\ /\ 049-234-7005294 /\ /\ Fax: 049-234-7094109 /\ /\ email: robert.franke@rz.ruhr-uni-bochum.de /\ /\ /\ /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ From yliu@mail.wesleyan.edu Thu Apr 23 10:26:30 1998 Received: from mail.wesleyan.edu for yliu@mail.wesleyan.edu by www.ccl.net (8.8.3/950822.1) id KAA01361; Thu, 23 Apr 1998 10:07:29 -0400 (EDT) Received: from dkombo.wesleyan.edu (jellyfish.chem.wesleyan.edu [129.133.20.75]) by mail.wesleyan.edu (8.8.6/8.7.3) with SMTP id KAA05809; Thu, 23 Apr 1998 10:07:14 -0400 (EDT) Date: Thu, 23 Apr 1998 10:07:14 -0400 (EDT) Message-Id: <199804231407.KAA05809@mail.wesleyan.edu> X-Sender: yliu@wesleyan.edu X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: Vagster From: yliu@wesleyan.edu Subject: Re: CCL:another book request... TCl this time Cc: CHEMISTRY@www.ccl.net Hi, Check out at http://www.sunlabs.com/~bwelch/book/. At 09:09 AM 4/22/98 +0100, you wrote: >Hello all > >I was wondering if anyone out there could recommend a good book on TCl >as I'm just trying to learn the language. > >Cheers > >Steve > > > mail to : S.M.Todd@chem.hull.ac.uk > web-site: http://www.hull.ac.uk/php/chpsmt/ > > > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: s.m.todd@chem.hull.ac.uk >-- Original Sender From: Address: s.m.todd@chem.hull.ac.uk >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 > > > ---------------------------------------------- Yongxing Liu Wesleyan University Middletown CT 06459 Tel: (860)-343-7330 E-Mail yliu@wesleyan.edu URL http://linus.chem.wesleyan.edu ---------------------------------------------- From sadowski@zhs4.zh.basf-ag.de Thu Apr 23 02:26:22 1998 Received: from basfzgw for sadowski@zhs4.zh.basf-ag.de by www.ccl.net (8.8.3/950822.1) id CAA29216; Thu, 23 Apr 1998 02:03:14 -0400 (EDT) Received: from basfygw.basf-corp.com (actually host basfygw) by basfzgw with SMTP (MMTA) with ESMTP; Thu, 23 Apr 1998 01:55:10 -0400 Received: from zhs8.zh.basf-ag.de by basfygw with SMTP (MMTA); Thu, 23 Apr 1998 01:55:03 -0400 Received: from zhs4.zh.basf-ag.de by zhs8.zh.basf-ag.de via ESMTP (950413.SGI.8.6.12/940406.SGI) for <@zhs8.zh.basf-ag.de:CHEMISTRY@www.ccl.net> id HAA05738; Thu, 23 Apr 1998 07:56:08 +0200 Received: (from sadowski@localhost) by zhs4.zh.basf-ag.de (950413.SGI.8.6.12/950213.SGI.AUTOCF) id HAA05898 for CHEMISTRY@www.ccl.net; Thu, 23 Apr 1998 07:55:47 +0200 Date: Thu, 23 Apr 1998 07:55:47 +0200 From: sadowski@zhs4.zh.basf-ag.de (Jens Sadowski) Message-Id: <199804230555.HAA05898@zhs4.zh.basf-ag.de> To: CHEMISTRY@www.ccl.net Subject: Darmstadt98 The 12th. Molecular Modelling Workshop at Darmstadt will take place on May 19.-20. at the University of Darmstadt. The final program and all abstracts are now available on the net: http://www.pc.chemie.tu-darmstadt.de/mmws See below for the list of speakers. Thanks, Jens Sadowski ----------------------------------------------------------------------------- May 19, 1998 ----------------------------------------------------------------------------- 8.00-9.00 registration 9.00-9.10 opening 9.10-9.30 M. Stahl (Hoffmann-La Roche) Filter Functions for Protein-Ligand Docking 9.30-9.50 M. Rarey (GMD St. Augustin) The particle concept: Considering water molecules in protein-ligand docking 9.50-10.10 T. Fox (Boehringer Ingelheim) Structure Based Computer Screening of Compound Databases 10.10-10.40 break 10.40-11.00 A. Bergner (MPI Martinsried) Crystal structure of human beta-tryptase: A attractive target for drug design and modeling studies 11.00-11.20 P. van Hooft (Uni Duesseldorf) Development of a 3D Model of E. coli PBP3 11.20-11.40 P. Monecke (Uni Halle) Molecular Modelling Studies on Candida Rugosa Lipase 11.40-12.00 S. Luedemann (EMBL Heidelberg) Substrate access to Cytochrome P450cam investigated by by molecular dynamics simulations 12.00-13.30 lunch 13.30-13.50 B. Beck (Uni Erlangen) Quantum QSAR: A Proof of Concept for Databases 13.50-14.10 A. Klinsky (Uni Wien) Ab initio molecular electrostatic potential grid maps for quantitative similarity calculations of organic compounds 14.10-14.30 A. Parusel (Uni Wien) Light Driven Molecular Machines: A Semiempirical Analysis of a Novel Flavin-Porphyrin Dyad 14.30-14.50 L. Hilfert (Uni Potsdam) GIAO-calculations of chemical shifts in heteroaromatic substituted quinoxalines - a comparison of theory and experiment 14.50-15.10 N. Jaeger (Uni Potsdam) Description of molecular structure and bonding conditions of oxo- rhenium-(V)-chelates with diacidic tridentate ligands by molecular mechanics and quantum chemical calculations 15.10-16.40 posters, hard- and software presentation 16.40-17.00 M. Krug (Merck) Application of Genetic Algorithms for Compound Selection: Library Design and Series 17.00-17.20 H.-J. Boehm (Hoffmann-La Roche) Combinatorial Docking and Combinatorial Chemistry: De Novo Design of Potent Non-Peptide Thrombin Inhibitors 17.20-17.40 C. Lemmen (GMD St. Augustin) FlexS : A Method for Fast Flexible Ligand Superposition 17.40-18.00 O. Kraemer (Uni Marburg) Field-Based Pharmacophores 18.00-19.00 MGMS/German speaking section: annual meeting, posters, hard- and software presentation 19.00 buffet ----------------------------------------------------------------------------- May 20, 1998 ----------------------------------------------------------------------------- 9.00-9.20 K.-J. Schleifer (Uni Duesseldorf) Binding Site Models of the Resting and the Activated/Inactivated State of Voltage-Gated Calcium Channels Elucidated by a 3D-QSAR Study of 1,4-Dihydropyridines 9.20-9.40 M. Schaefer (Uni Strasbourg) Solution conformation of structured peptides: Molecular dynamics simulations with an implicit solvent potential 9.40-10.00 J. Schlitter (Uni Bochum) Simulation of Protein Unfolding: The ApoMb pH4 Molten Globule 10.00-10.20 J. Junker (Uni Frankfurt) Systematic investigation of the ensemble method applied to conformational heterogenity of organic compounds 10.20-10.50 break 10.50-11.10 A. Goeller (Uni Jena) Oxidation of an alkane by Cytochrome P450 - SAM1 semiempirical calculations 11.10-11.30 H. Mauser (Uni Erlangen) Endohedral and Exohedral Chemistry of C60 11.30-11.50 D. Bougeard (Uni Lille) Potentials for spectroscopic studies in materials modelling 11.50-12.10 E. Gemmel (Uni Frankfurt) Parametrization of Force Fields with Evolutionary Strategic Algorithms 12.10-13.20 lunch 13.20-13.40 P. Krueger (TH Aachen) Simulations as tool to explore 'undiscovered' parts of the conformational space 13.40-14.00 N. Oezguen (TH Aachen) Investigation of the Segmental Mobility for Bisphenol-A-Polycarbonate and Bisphenol-Z-Polycarbonate from MD-Simulations at Various Temperatures 14.00-14.20 G. Boks (Uni Utrecht) Structure and Conformational Behaviour of Peptoid Peptidomimetics 14.20-14.40 H. Scheib (Uni Stuttgart) A simple solution to a complex problem: the stereoselectivity of Mucorales lipases toward triradylglycerols 14.40-15.00 B. Fodi (MPI Mainz) Simulated Phase Behaviour of Model Surfactant Solutions 15.00 final discussion +-----------------------------------------------------------------------+ | Dr. Jens Sadowski | | Molecular Modelling, ZHF/G - A 30 Phone: +49 (0)621-6049338 | | BASF AG Fax: +49 (0)621-6020440 | | D-67056 Ludwigshafen, Germany Email: sadowski@zhs4.zh.basf-ag.de | +-----------------------------------------------------------------------+ From sadowski@zhs8.zh.basf-ag.de Thu Apr 23 06:26:25 1998 Received: from basfzgw for sadowski@zhs8.zh.basf-ag.de by www.ccl.net (8.8.3/950822.1) id FAA29858; Thu, 23 Apr 1998 05:35:47 -0400 (EDT) Received: from basfygw.basf-corp.com (actually host basfygw) by basfzgw with SMTP (MMTA) with ESMTP; Thu, 23 Apr 1998 05:31:25 -0400 Received: from zhs8.zh.basf-ag.de by basfygw with SMTP (MMTA); Thu, 23 Apr 1998 05:31:13 -0400 Received: by zhs8.zh.basf-ag.de (950413.SGI.8.6.12/940406.SGI) id LAA16503; Thu, 23 Apr 1998 11:32:23 +0200 From: Jens Sadowski Message-Id: <9804231132.ZM16501@zhs8.zh.basf-ag.de> Date: Thu, 23 Apr 1998 11:32:22 -0600 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Darmstadt 98 Cc: sadowski@zhs8.zh.basf-ag.de MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Just an addendum to my recent posting with respect to the 12th Molecular Modelling Workshop, May 19.-20., Technical University Darmstadt, Germany: Conference language will be GERMAN. The ENGLISH program and abstracts are on the web: http://www.pc.chemie.tu-darmstadt.de Sorry, Jens Sadowski -- +-----------------------------------------------------------------------+ | Dr. Jens Sadowski | | Molecular Modelling, ZHF/G - A 30 Phone: +49 (0)621-6049338 | | BASF AG Fax: +49 (0)621-6020440 | | D-67056 Ludwigshafen, Germany Email: sadowski@zhs4.zh.basf-ag.de | +-----------------------------------------------------------------------+ From l.cruzeiro-hansson@mail.cryst.bbk.ac.uk Tue Apr 21 14:39:07 1998 Received: from iona.cryst.bbk.ac.uk for l.cruzeiro-hansson@mail.cryst.bbk.ac.uk by www.ccl.net (8.8.3/950822.1) id NAA17566; Tue, 21 Apr 1998 13:43:36 -0400 (EDT) Received: from hindy.cryst.bbk.ac.uk by iona.cryst.bbk.ac.uk (5.65v4.0/2.1/09Sep96-1332PM) with SMTP id <199804211747.AA01753@iona.cryst.bbk.ac.uk>; Tue, 21 Apr 1998 18:47:41 +0100 Received: from localhost by hindy.cryst.bbk.ac.uk (940816.SGI.8.6.9/slave-1.2/29Aug96-1209PM) id SAA22731; Tue, 21 Apr 1998 18:47:40 +0100 Date: Tue, 21 Apr 1998 18:47:40 +0100 (BST) From: "L. Cruzeiro_Hansson" X-Sender: ubcg02h@hindy.cryst.bbk.ac.uk To: chemistry@www.ccl.net Subject: CCL Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII -------------------------------------------- Energy Transduction in Biological Systems --------------------------------------------- Summer School ITQB, Oeiras, Portugal June 15 to 27, 1998 This summer school is part of a program on "Spatio-temporal coherence in the solid state and in living matter" promoted by the Institute for Scientific and Technological Advanced Studies- Portugal (ISTAS - Portugal), and financed by the TMR programme of the European Community. - Scope: The phenomenon of energy transduction, that is, the manner in which energy is stored, transported and used to perform work in biological systems, is fundamental for the understanding of many biological processes. This school will reflect the many approaches that can be used in order to study energy transduction in biological systems. It will include lectures on the biological detail of specific systems, as well as some of the experimental techniques used in their study. Furthermore, theoretical frameworks will also be described, ranging from the detail which can be obtained in molecular mechanics and molecular dynamics simulations, to the identification of functional modes and the hierarchies in biological organization. The level of presentation is appropriate for young post-docs and advanced PhD students, interested in biology, who can have a variety of backgrounds, such as biological, physical, chemical or mathematical. - Topics - Single molecule studies of muscle contraction - Energy transduction from fluctuations and electromagnetic fields - Electron and proton transfer in cytochrome c oxidase - Effects of long range interactions and two-dimensional energy transfer - Proteins as quantum mechanical and nonlinear machines - Effects of electron (ion) conformational interactions on charge and energy transport in biological systems - Proton migration and energy transduction in proton pumps - Energy transduction by Photosytem Two: a balance of regulation and efficiency - Acid-base reactions as driving-force in metabolism, ATP synthases and ion-motive ATPases - Dynamical hierarchies in biological function - Coherent control of chemical reactions: applications to photosynthetic centers - Molecular ratchets in nonequilibrium statistical environments - Electroconformational coupling and biological energy transduction - The Lipid bilayer as a modulator of protein function - The Redox-Bohr effect: a model for energy transduction mechanisms - Invited Lecturers in alphabetic order: - M. Anson, NIMR, Mill Hill, UK - R.D. Astumian, University of Chicago, Chicago, USA - P. Brzezinski, University of Gal Physics Institute, Kiev,Ukraine - P.L. Christiansen, Technical University of Denmark, Lyngby, Denmark - Y. Gaididei, Bogolyubov Theoretical Physics Institute, Kiev,Ukraine - J. Heberle, Forschungszentrum Julich, Julich, Germany - D. Klug, Imperial College, London, UK - V.M.C. Madeira, Centro Neurociencias, Coimbra, Portugal - A.C. Scott, Tehnical Univ. Denmark, Lyngby, Denmark - M. Shapiro, Weizmann Institute, Rehovot, Israel - G. P. Tsironis, University of Crete, Crete, Greece - T. Y. Tsong, University Minnesota, (Department of Biochemistry, St. Paul, USA) - W.L.C. Vaz, Universidade do Algarve, Faro, Portugal - Organizing Committee: Leonor Cruzeiro-Hansson Cristallography Department, Birkbeck College, Malet Street, London , WC1E 7HX, UK Antonio Xavier e Ricardo O. Louro Universidade Nova de Lisboa,ITQB Apt 127, P-2780 Oeiras , Portugal - Grants: A number of grants will be available for participants from EU countries. These grants will be given preferentially to young participants (graduate students, post-docs, etc.)and may cover travel and living expenses. Applications including a short C.V. (with a list of publications) should be included with the registration form. The deadline for grant application is April 30, 1998. The applicants will be notified before May 17, 1998 by E-mail or fax whether their applications were successful. - Deadlines: Application for grants --- April 30, 1998 School registration --- April 30, 1998 Abstract submission --- May 9, 1998 - Sponsors: This School is financed by the European Commission through the TMR programme and ISTAS - Portugal and co-sponsored by: - Ministerio da Ciencia e Tecnologia (MCT) - Luso- Americain Foundation - Institute of Technology for Chemistry and Biology (ITQB) - Oeiras City Hall - Registration: There is a registration fee for the school of 300 US dollars. Payment will be requested after acceptance of registration. You may register on-line at the web address: http://milu.ipn.pt/~istas or contact the school secretariat at istas@ipn.pt fax +351 2 441 1277 and we will fax you the registration and grant application form. Grants may cover the registration fee. - Correspondance Address: Summer School June 1998 ISTAS - Portugal Apartado 106 P- 2780 Oeiras, Portugal Fax: +351 1 441 1277 E-mail: istas@ipn.pt URL: http://milu.ipn.pt/~istas ------------ End of announcement ---------------------------------------- From Anthony.Scott@anu.edu.au Tue Apr 21 20:28:41 1998 Received: from anugpo.anu.edu.au for Anthony.Scott@anu.edu.au by www.ccl.net (8.8.3/950822.1) id TAA20335; Tue, 21 Apr 1998 19:44:53 -0400 (EDT) Received: from [150.203.35.14] (rscqc1.anu.edu.au [150.203.35.14]) by anugpo.anu.edu.au (8.8.8/8.8.8) with SMTP id JAA21015; Wed, 22 Apr 1998 09:44:52 +1000 (EST) X-Sender: e910603@pophost.anu.edu.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 22 Apr 1998 09:45:12 +1000 To: chemistry@www.ccl.net From: Anthony.Scott@anu.edu.au (Anthony P. Scott) Subject: QCISD energy lower than QCISD(T) energy! Cc: Anthony.Scott@anu.edu.au We recently have such a case. The molecule in question is CaO. Both G94, molpro96 and ACES2 agree on this, although the molpro results are different >from the G94 and ACES2. (we are investigating this still). The basis used is 6-311+G(3df,2p). When the 6-311G** or 6-311+G** basis is used the QCISD energy is lower than the QCISD(T) energy as I would normally have expected. Can someone shed some light on this strange result. Is such a result even physically meaningful? and if so what exactly does it mean? A possible reason is linear dependency in the large basis set, however for BeO and Ca(OH)2 such a strange thing does not happen. Thanks for your help. tony ______________________________________________________________________________ Dr. Anthony P. Scott, Computational Quantum Chemistry Group, Office Ph.: 61-2-6249-3573 Research School of Chemistry, Dept. Ph.: 61-2-6249-3637 Australian National University, Fax: 61-2-6249-0750 Canberra, ACT 0200, E-mail: Anthony.Scott@anu.edu.au AUSTRALIA. ____________________________________________________________________________ __ From walterse@mis.finchcms.edu Thu Apr 23 14:26:30 1998 Received: from mis.finchcms.edu for walterse@mis.finchcms.edu by www.ccl.net (8.8.3/950822.1) id NAA03565; Thu, 23 Apr 1998 13:54:28 -0400 (EDT) Received: from [192.217.100.91] by mis.finchcms.edu (SMI-8.6/SMI-SVR4) id MAA12413; Thu, 23 Apr 1998 12:48:48 -0500 Message-Id: In-Reply-To: <199804212114.QAA12501@tw515a.chem.mu.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 23 Apr 1998 12:56:13 -0500 To: judithkl@MIT.EDU From: "Dr. Eric Walters" Subject: Re: CCL:Books on C Programming and Unix Cc: "Dr. Nagamani Sukumar" , CHEMISTRY@www.ccl.net >I am posting this on behalf of a friend: >Do you know a good book about Programming in C and about using >Unix that you could recommend me? >Judith My favorite C programming book is "C Programming: A Modern Approach" by K.N. King. Below is a review I wrote for J. Chem. Inf. Computer Sci. Hope this is helpful. Eric Walters --------- C Programming. A Modern Approach. By K.N. King. W.W. Norton & Company: New York. 1996. 661 pp. $39.95. ISBN 0-393-96945-2. Changing one's programming language is a little like changing one's religious convictions--not something to be done on a whim. A few years ago, I decided to switch from Fortran (which I had used for over 20 years) to C. I purchased about a dozen different books purporting to explain how to use the C language. Most were densely unreadable, few had a usable index, and some were riddled with errors. The learning curve was unnecessarily steep. Now comes the book I really wanted, by Prof. Kim King of Georgia State University. It is apparent that this book was written by someone who has spent time teaching the subject. The writing style is entertaining and clear. There are many good examples throughout the book. Each chapter includes a "Q & A" section which addresses frequently asked questions as well as tangential issues which would detract from the flow of the text. There are frequent cross-references to related material in other parts of the book. Source code for the book's programs, as well as errata, are available on the author's World-Wide Web page. And each chapter has a variety of exercises, enabling the reader to evaluate the learning process. Best of all, the index takes you right to the part of the book you need--it's not too sparse, and it's not cluttered with tangential references. The first time I picked up this book I quickly found the solution to a file-reading bug which had perplexed me for months. I am placing this book at the top of my heap of programming texts, and I am recommending it to all of my programming colleagues. * D. Eric Walters, Ph.D., Associate Professor, Biological Chemistry * Finch University of Health Sciences/The Chicago Medical School * 3333 Green Bay Road, North Chicago, IL 60064 * ph 847-578-8613;fax 847-578-3240; email: walterse@mis.finchcms.edu * "A man would do nothing if he waited until he could do it so well that * no one would find fault with what he had done." --Cardinal Newman * * visit my web page! http://www.finchcms.edu/biochem/walters.html * * From yubofan@guomai.sh.cn Wed Apr 22 02:26:10 1998 Received: from guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id BAA21872; Wed, 22 Apr 1998 01:35:13 -0400 (EDT) Received: from guomai.sh.cn (Email-22 [210.0.0.22]) by guomai.sh.cn (8.8.8/8.8.8) with ESMTP id NAA18514 for ; Wed, 22 Apr 1998 13:33:02 +0900 (CDT) Message-ID: <353D824D.B30313E1@guomai.sh.cn> Date: Wed, 22 Apr 1998 13:38:22 +0800 From: Yubo Fan X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Which one is better for geometry optimization, B3LYP/4-31G or HF/6-31G*? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I have been doing calculations on geometry optimizing of some organic molecules with great ring constraints. I tried some semi-empirical methods, for example, MNDO and PM3, but the results were rather different with the corresponding XRD crystal datas. So I have to use non-empirical ab initio methods to do the same work. My question is which method is better, B3LYP/4-31G or HF/6-31G*? With best wishes Y. Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab yubofan@fudan.edu.cn The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From rachelle@odo.niehs.nih.gov Wed Apr 22 16:26:24 1998 Received: from odo.niehs.nih.gov for rachelle@odo.niehs.nih.gov by www.ccl.net (8.8.3/950822.1) id QAA26948; Wed, 22 Apr 1998 16:17:59 -0400 (EDT) Received: from odo (localhost [127.0.0.1]) by odo.niehs.nih.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id QAA01190 for ; Wed, 22 Apr 1998 16:17:23 -0400 Sender: rachelle@odo.niehs.nih.gov Message-ID: <353E5053.6201@odo.niehs.nih.gov> Date: Wed, 22 Apr 1998 16:17:23 -0400 From: rachelle bienstock Organization: NIH/NIEHS X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP30) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Dock 4.0 successful compilation under Irix 6.4 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thanks to the many people who volunteered advice concerning Dock 4.0 compilation under Irix 6.4. In case others encounter problems, here are some things which need to be done for successful compilation: (1) There is a problem with the number of continuation lines in the elements.h file under Irix 6.4. (Note that there are two elements.h files, one in the database directory and one in the accessories directory). You need to edit both of these and change the number of lines by placing the last data entry on one line e.g. + 252.00000,257.00000,258.00000,259.00000,260.00000/ (2) There are several old object files which are not deleted by "make clean". You will need to hand delete these files. They include writeSDF.o and readSDF.o in the accessories directory. (3) You will need a -n32 flag on the compile and will need to add this to all the Makefiles. You may not need this if you figure out #2 above first and delete all the old object files. I got a fatal linker error because it was trying to link old 32-bit objects with -n32 links. This could have been because there were some old remaining object files. I still received some warnings on compilation, and will have to see how serious they are once I begin playing with the program. Again, thanks to all those who gave me advice. -- ******************************* Dr. Rachelle J. Bienstock Molecular Modeler and Computational Chemist NIH/NIEHS 111 T.W. Alexander Drive P.O. Box 12233 MD F0-01 Research Triangle Park, NC 27709 Tel.: (919) 541-3397 e-mail: rachelle@picard.niehs.nih.gov or rachelle@odo.niehs.nih.gov ******************************** From lim@rani.chem.yale.edu Thu Apr 23 19:26:32 1998 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by www.ccl.net (8.8.3/950822.1) id TAA06125; Thu, 23 Apr 1998 19:24:03 -0400 (EDT) Received: by rani.chem.yale.edu; Thu, 23 Apr 98 19:24:05 -0400 From: Dongchul Lim Message-Id: <9804232324.AA14118@rani.chem.yale.edu> Subject: BOSS/MCPRO output analyzer To: chemistry@www.ccl.net (Computational Chemistry) Date: Thu, 23 Apr 98 19:24:05 EDT X-Mailer: ELM [version 2.3 PL11] A web-based analysis tool for the BOSS/MCPRO program, which has been develped in W. L. Jorgensen group, is now available on our web page (http://zarbi.chem.yale.edu/~lim/chem/boss/index.html). The BOSS/MCPRO is a Monte Carlo simulation program for organic molecules and proteins. This analysis tool gives you plots of solvent-solvent and solvent-solute radial distribution functions, solvent-solvent and solvent-solute energy and energy pair distributions, dihedral angle distributions, total energy, heat capacity, volume, enthalpy, themal compressibility, solute-solute and solvent-solute interaction energies, intrasolute Coulombic and Lennard-Jones energies, etc. Sample BOSS/MCPRO output files are available for download. D. Lim, Dept of Chemistry, Yale University lim@doctor.chem.yale.edu