From chemistry-request@server.ccl.net Wed Feb 7 01:21:45 2001 Received: from ksmail.netcologne.de (ksmail.netcologne.de [194.8.194.97]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f176Liw28984 for ; Wed, 7 Feb 2001 01:21:44 -0500 Received: from cosmologic.de (dial-213-168-88-201.netcologne.de [213.168.88.201]) by ksmail.netcologne.de (8.9.3/8.9.3) with ESMTP id HAA05096; Wed, 7 Feb 2001 07:21:39 +0100 (MET) Message-ID: <3A80E9BD.F15D1159@cosmologic.de> Date: Wed, 07 Feb 2001 07:22:53 +0100 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG X-Mailer: Mozilla 4.7 [de] (Win98; I) X-Accept-Language: en,pdf MIME-Version: 1.0 To: Olegas Eicher-Lorka , chemistry@ccl.net Subject: Re: CCL:Gaussian Raman Intensities in Solution References: <000e01c08f7b$4d114260$ae0e3bd4@ktl.mii.lt.lorka.ktl.mii.lt> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Although I am not familiar with the details of the COSMO implementation in Gaussian, being the author of the original COSMO I like to shortly comment on the general question of Raman intensities in solution: Note, that high vibrational frequencies in solution are definitely not in equilibrium with the reorientational part of the solvent polarization. Therefore calculation of second derivatives of the total energy are not adequate for vibrational frequencies. The best way to calculate the Raman frequencies in solution would be - to first do geometry optimization in the solvent - then freeze the polarization charges - do second derivatives while treating the (molecule + frozen equilibrium polarization charges) as embedded in a medium of electronic polarizability (eps=2). I am not sure, whether such treatment is possible in Gaussian, but it efinitely would be the physically most correct way to do it. Andreas Klamt -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Feb 7 04:41:33 2001 Received: from as1200.organik.uni-erlangen.de (as1200-1.organik.uni-erlangen.de [131.188.128.6]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f179fWw29900 for ; Wed, 7 Feb 2001 04:41:32 -0500 Received: from chemie.uni-erlangen.de (indigo11.chemie.uni-erlangen.de [131.188.128.69]) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id KAA04951 for ; Wed, 7 Feb 2001 10:41:31 +0100 (MET) Sender: Harald.Lanig@Organik.Uni-Erlangen.DE Message-ID: <3A81184B.BEFCF218@chemie.uni-erlangen.de> Date: Wed, 07 Feb 2001 10:41:31 +0100 From: Harald Lanig Organization: Computer-Chemie-Centrum Uni Erlangen/Nbg X-Mailer: Mozilla 4.08 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Conference announcement: Model(l)ing 2001 in Erlangen/Germany Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 7bit We are pleased to announce Model(l)ing 2001, the second MGMS annual meeting to be held in Erlangen/Germany (after Model(l)ing '97). In the tradition of its predecessor, Model(l)ing 2001 will treat a broad range of topics associated with computational chemistry, modeling, bioinformatics and cheminformatics. The individual sessions are as follows: Sunday, Sept 16 Registration Monday, Sept 17 Library Design/ADME Tuesday, Sept 18 Enzymes/DNA Wednesday, Sept 19 New Techniques Thursday, Sept 20 Modeling/QSAR Friday, Sept 21 Genomics Poster sessions will be held on the evenings of Sept. 17. and 18. Registration for the conference is now open at the conference web site http://www.ccc.uni-erlangen.de/model2001/, where details of the schedule, hotels, travel etc. can also be found. We are looking forward to see you in Erlangen! Harald Lanig and Tim Clark -- ------------------------------------------------------------------------ Dr. Harald Lanig Universitaet Erlangen/Nuernberg Lehrstuhl fuer Schuhstrasse 19 Pharmazeutische Chemie D-91052 Erlangen, Germany oder Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen Phone +49(0)9131-85 26525 Mailto:lanig@chemie.uni-erlangen.de Fax +49(0)9131-85 26565 http://www.ccc.uni-erlangen.de/clark/lanig ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Wed Feb 7 06:31:38 2001 Received: from mail.zrz.tu-berlin.de (mail.zrz.TU-Berlin.DE [130.149.4.15]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f17BVcw30259 for ; Wed, 7 Feb 2001 06:31:38 -0500 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail.zrz.tu-berlin.de with esmtp (exim-3.22) id 14QSnS-0001LQ-00; Wed, 07 Feb 2001 12:30:02 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.42.210]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.22) id 14QSnR-0004hQ-00; Wed, 07 Feb 2001 12:30:01 +0100 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: In-Reply-To: <01020613084300.26802@coch11> References: <01020613084300.26802@coch11> Date: Wed, 7 Feb 2001 12:07:47 +0100 To: Matthias Mann From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:Linux 2.4.0 and 2 GB promlem Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" Files larger than 2GB on 32-bit unix systems need new system calls, e.g. read64(), lseek64() etc., to handle large files. In these system calls, "long long" parameters instead of the standard "int" are used for passing the offset, and for passing return values. The calling (FORTRAN) program must access the file in blocks (if it is direct access) and use I/O procedures written in C, then you can use the new system calls. If a FORTRAN integer has to specify a *byte* offset in the file, the new system calls are of no use. -- +---------------------------------+-------------------------------------+ | Prof. Christoph van Wullen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universitat Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Strasse des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+-------------------------------------+ From chemistry-request@server.ccl.net Wed Feb 7 10:30:24 2001 Received: from admin.cnrs-orleans.fr (admin.cnrs-orleans.fr [163.9.1.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f17FUNw31410 for ; Wed, 7 Feb 2001 10:30:23 -0500 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id OAA04725 ; Wed, 7 Feb 2001 14:34:33 +0100 (MET) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id OAA10116; Wed, 7 Feb 2001 14:33:03 +0100 Date: Wed, 7 Feb 2001 14:33:03 +0100 Message-Id: <200102071333.OAA10116@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: avijit@CS.Cornell.EDU CC: chemistry@ccl.net In-reply-to: (message from Avijit Ghosh on Wed, 31 Jan 2001 18:42:02 -0500 (EST)) Subject: Re: CCL:GPL'd MD packages References: > I was wondering whether anyone has any GPL'd code for MD? > Particularly, whether there are any GPL'd force field > implementations out there (I.E. MM*/OPLS*/AMBER* ). Cornell U. has a The Molecular Modelling Toolkit, available from http://dirac.cnrs-orleans.fr/MMTK/ has a less restrictive license than GPL and includes an implementation of the Amber force field as well as MD and many other molecular simulation techniques. As for the language question, it is written in a mixture of Python and C, with C for the time-critical sections (mostly energy evaluation) and Python for everything else. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Feb 7 03:13:36 2001 Received: from radon.pc.helsinki.fi (root@radon.pc.helsinki.fi [128.214.14.200]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f178DZw29480 for ; Wed, 7 Feb 2001 03:13:35 -0500 Received: (from jonas@localhost) by radon.pc.helsinki.fi (8.9.3/8.9.3/Debian 8.9.3-21) id KAA21944; Wed, 7 Feb 2001 10:11:47 +0200 Date: Wed, 7 Feb 2001 10:11:47 +0200 From: Jonas Juselius To: Matthias Mann Cc: CHEMISTRY@ccl.net, q_timerg@alcor.concordia.ca Subject: Re: CCL:Linux 2.4.0 and 2 GB promlem Message-ID: <20010207101147.A21758@chem.helsinki.fi> References: <01020613084300.26802@coch11> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii User-Agent: Mutt/1.0.1i In-Reply-To: <01020613084300.26802@coch11>; from Matthias.Mann@chemie.tu-dresden.de on Tue, Feb 06, 2001 at 12:45:35PM +0100 The 2GB limit is a thing of the past in 2.4.1, but you must use ReiserFS (or XFS from SGI) to get past the limit. AFAIK ext2 does still not handle files larger than 2GB. I have been using ReiserFS together with LVM (www.sistina.com) for some time now, and I'm extermely happy with the setup. If I do a one finger boot, the filesystem check on my 25 GB work partition (ReiserFS) takes about 2-3 seconds :-) -jonas- On Tue, Feb 06, 2001 at 12:45:35PM +0100, Matthias Mann wrote: > Hallo, > > > Dear CCL'ers, > > I've heard that new Linux kernel 2.4.0 can handle files larger than 2 GB. > > Have anybody tried to test 2.4.0 kernel with quantum-chemical programs? > > it seems, nobody has experience with this until now ? > Because I'm also very interested to solve this problem, I asked Gaussian > according the LFS support in G98. Here is the answer: > > > The limit is partly relieved in Rev. A.7. We have further > > changes expected in the next minor revision which should > > remove it entirely for machines with native 64 bit integers. > > For A.7 the limit is around 20GB due to a limit in the bin > > sort required for post-MP2 methods. > > > > This does not extend to Linux on Intel platforms because here > > 32 bit integers are still used to maintain good performance. > > We have not yet tested with the 2.4 kernels but since we see > > as bad as 30% penalty for using 64 bit integers on machines > > like the IBM Power3 when using 64 bit integers we don't plan on > > releasing a version for Linux on Intel. > > This is not totally clear, because it is possible to support large > files also on 32 bit systems. For example, large files are supported > with 32bit IBM AIX 4.2 on RS/6000 (without reducing performance). > > Because the 2 GB limit is one of the remaining disadvantages in > comparison of Linux systems with commercial workstations, > we should try to solve this for quantum chemical programs ?! > > Greetings, > Matthias > > -- > Dr. Matthias Mann > Institut fuer Organische Chemie, TU Dresden > D-01069 Dresden, Mommsenstr. 13 > Tel.: +49 (351) 463-4286 / Fax: -3162 > Email: Matthias.Mann@chemie.tu-dresden.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 > > > > -- And what is good, Phaedrus, And what is not--- Need we ask anyone to tell us these things? [ PGP public key: http://www.iki.fi/jonas/pubkey.asc ] From chemistry-request@server.ccl.net Wed Feb 7 04:13:29 2001 Received: from post.tau.ac.il (post.tau.ac.il [132.66.16.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f179DSw29806 for ; Wed, 7 Feb 2001 04:13:28 -0500 Received: from post.tau.ac.il (pico.tau.ac.il [132.66.145.20]) by post.tau.ac.il (8.11.2/8.11.2) with ESMTP id f179DPe26427 for ; Wed, 7 Feb 2001 11:13:26 +0200 (IST) Sender: silviu@post.tau.ac.il Message-ID: <3A8111B3.4A562394@post.tau.ac.il> Date: Wed, 07 Feb 2001 09:13:23 +0000 From: Zilberman Silviu Organization: TAU To: ccl Subject: 2D dipoles simulations Hi, I'm looking for a free code for simulating a system of electrical dipoles in 2 dimensions. Is there something around? Thanks, Silviu. -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Zilberman Silviu School of Chemistry, Tel Aviv University Ramat Aviv, Tel-Aviv, Israel 61391 Phones 972-3-6407634 972-3-6409293 (fax 1) 972-3-6423765 (fax 2) mailto:silviu@post.tau.ac.il Home Page: http://femto.tau.ac.il/~silviu %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From chemistry-request@server.ccl.net Wed Feb 7 10:30:22 2001 Received: from admin.cnrs-orleans.fr (admin.cnrs-orleans.fr [163.9.1.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f17FUMw31406 for ; Wed, 7 Feb 2001 10:30:22 -0500 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id PAA06493 ; Wed, 7 Feb 2001 15:07:26 +0100 (MET) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id PAA10157; Wed, 7 Feb 2001 15:05:54 +0100 Date: Wed, 7 Feb 2001 15:05:54 +0100 Message-Id: <200102071405.PAA10157@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: salzner@fen.Bilkent.EDU.TR CC: chemistry@ccl.net In-reply-to: (message from Ulrike Salzner on Wed, 31 Jan 2001 11:46:29 +0200 (EET)) Subject: Re: CCL:programming language References: > We are a chemistry department and our first year students take a computer > science cours learning JAVA. They told me that they don't think it is of > any use to them. > > I would like to collect opinions which programming language is most useful > for chemists. Let's assume they are learning only one. Only one in the course is fine. Only one for life definitely isn't. My criteria for a *first* language would be: 1) Simplicity: students should concentrate on programming concepts, not on language idiosyncracies. That rules out languages with significant historical ballast, such as Fortran or C++, as well as particularly complicated languages, such as C++ (again) or Ada, and those with weird syntax features, such as Perl or APL. 2) Immediate applicability: Students can rightfully expect to be able to apply the language they learn to the problems that will occur during their studies. This will be mostly data analysis, perhaps simple simulations, but for most of them neither Web site programming nor heavy number crunching. 3) Support for modern programming techniques: Even though many scientists don't want to admit it, modern software development techniques do have advantages. You may not want to teach them directly, but you should give the students a chance to look at them for themselves. So pick a language that doesn't get in the way of OOP, functional programming, etc. 4) Generality: Special-purpose languages, even if very convenient, don't make for a good introduction to programming because they are too limited. This rules out Matlab and friends. 5) Portability: nobody knows what platforms will be popular when these students graduate. Better avoid platform-specific languages, such as Visual Basic. My personal choice would be Python, which has proven very useful in general scientific tasks such as data analysis, and permits interfacing to C, C++, and Fortran, the three most common languages for number crunching. An additional argument is the availability of VPython, which is the simplest 3D graphics programming environment I know, and 3D graphics is immensely useful in many scientific domains. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Feb 7 10:42:00 2001 Received: from mailhub.usp.br (serv1.uspnet.usp.br [143.107.253.61]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f17Ffxw31572 for ; Wed, 7 Feb 2001 10:42:00 -0500 Received: (qmail 29985 invoked from network); 7 Feb 2001 15:14:57 -0000 Received: from unknown (HELO sergio) (143.107.194.151) by mailhub.usp.br with SMTP; 7 Feb 2001 15:14:57 -0000 Message-ID: <00a201c09118$2a77a2a0$97c26b8f@ligquim.ffclrp.usp.br> Reply-To: =?Windows-1252?Q?S=E9rgio_Emanuel_Galembeck?= From: =?Windows-1252?Q?S=E9rgio_Emanuel_Galembeck?= To: Subject: G98 in K6-II 500 MHz Date: Wed, 7 Feb 2001 13:10:53 -0200 Organization: =?Windows-1252?Q?Universidade_de_S=E3o_Paulo?= MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear netters, I am planning an undergraduate course of molecular modelling. The undergraduate laboratory has K6-II 500 MHz with 64 MB of memory and with Red Hat 6.2. Is it possible to compile and run G98 in this computer? Thank you, Sergio ============================================================== Sergio Emanuel Galembeck Assistant Professor in Physical Chemistry Laboratório de Modelagem Molecular Departamento de Química Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto Universidade de São Paulo Av Bandeirantes, 3900 Ribeirão Preto, SP Brasil phone: +55-16-602-37-65 fax: +55-16-633-81-51 e-mail: segalemb@usp.br ============================================================== From chemistry-request@server.ccl.net Wed Feb 7 10:45:25 2001 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f17FjOw31602 for ; Wed, 7 Feb 2001 10:45:24 -0500 Received: from vega (vega.farma.unimi.it [159.149.79.32]) by mailserver.unimi.it (8.9.3/8.9.3) with SMTP id MAA02713 for ; Wed, 7 Feb 2001 12:53:44 +0100 (MET) Message-ID: <001f01c090fc$87a88320$204f959f@farma.unimi.it.farma.unimi.it> From: "Giulio Vistoli" To: References: <3A8046B4.ED67389F@cornell.edu> Subject: Re: CCL:Some more CHARMM questions Date: Wed, 7 Feb 2001 12:53:04 +0100 Organization: Ist. Chimica Farmaceutica 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 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear Richard, Our software VEGA (http://users.unimi.it/~ddl) can analyze the CHARMM trajectories (DCD files) and it can calculate distances, angles, torsions, angles between planes and several molecular properties, like molecular surface area, SAS, volume, dipole, etc. Best regards Giulio Vistoli -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39-02-29502230 Fax +39-02-29514197 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Wed Feb 7 11:08:31 2001 Received: from hermes.csd.unb.ca (root@hermes.csd.unb.ca [131.202.3.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f17G8Vw31802 for ; Wed, 7 Feb 2001 11:08:31 -0500 Received: from mailserv.unb.ca (root@mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.9.3/8.9.3) with ESMTP id KAA28383 for ; Wed, 7 Feb 2001 10:53:47 -0400 (AST) Received: from bongo (bongo.chem.unb.ca [131.202.162.240]) by mailserv.unb.ca (8.8.8+Sun/8.8.8) with SMTP id KAA12629 for ; Wed, 7 Feb 2001 10:53:46 -0400 (AST) Message-Id: <3.0.6.32.20010207105429.00900460@newpop.unb.ca> X-Sender: ajit@newpop.unb.ca X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Wed, 07 Feb 2001 10:54:29 -0400 To: chemistry@ccl.net From: "Ajit J. Thakkar" Subject: CCL: Second announcement - CSTC 2001 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Second Announcement: CSTC2001 14th Canadian Symposium on Theoretical Chemistry Carleton University, Ottawa, Canada August 4-9, 2001 Call for Papers, Registration, Accommodations You are cordially invited to attend CSTC2001, the 14th Canadian Symposium on Theoretical Chemistry. This is an international meeting which is held every 3 years in Canada. This year's meeting will take place in scenic Ottawa, the nation's capital. A complete guide to the conference Web Site, which highlights most of the important details may be found at http://chemistry.carleton.ca/theory/cstc2001/Announcement2.htm All necessary email addresses, registration and room reservation information may be found at the site above. The year 2001 promises to be a special one in the series of Canadian Theoretical Chemistry meetings. An outstanding list of speakers, including most of their titles, can be found at: http://chemistry.carleton.ca/theory/cstc2001/speakertable.htm Note that we have included a number of experimental scientists in the program, as well as some very intriguing titles to the talks. Please attend and help us to make this an excellent start to the new millenium...hope to see you there! Conference Co-Chairs: Jim Wright (Carleton University, Ottawa) Fred McCourt (University of Waterloo, Waterloo) Conference Secretariat: Nancy Coll James S. Wright Professor of Chemistry Office: (613) 520-2600 ext. 3645 Department of Chemistry Carleton University FAX: (613) 520-3749 1125 Colonel By Dr. email: jim_wright@carleton.ca Ottawa ON K1S 5B6 www: http://www.carleton.ca/chemistry/wright.html We apologize if you have received multiple mailings of this message...you are on several lists! From chemistry-request@server.ccl.net Wed Feb 7 11:13:32 2001 Received: from mercury.chem.nwu.edu (hutchisn@mercury.chem.nwu.edu [129.105.116.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f17GDWw31847 for ; Wed, 7 Feb 2001 11:13:32 -0500 Received: from localhost by mercury.chem.nwu.edu (8.9.1/8.9.1) with SMTP id KAA18654 for ; Wed, 7 Feb 2001 10:13:42 -0600 (CST) Date: Wed, 7 Feb 2001 10:13:42 -0600 (CST) From: Geoff Hutchison Reply-To: Geoff Hutchison To: chemistry@ccl.net Subject: Announce: Ghemical 0.40 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Ghemical version 0.40 Release Announcement ------------------------------------------ Ghemical is a molecular modelling software package with GNOME and GLUT front-ends and some nice 3D-visualization tools. It can do all-atoms molecular mechanics and dynamics, with an experimental Tripos-like parameter set. It can also be used as a graphical front-end for the quantum chemistry program MPQC. Ghemical is written in C++, and hopefully offers a good framework for a generic freeware molecular modelling tool. Ghemical uses the OELib/Babel C++ framework for import and export of a range of chemical file formats. As the version number indicates, Ghemical is still very much in development, though it is already quite usable. Feedback and suggestions are very welcome. The program is made available under the GNU GPL and is free software. For more information (and screenshots) of Ghemical, see the Ghemical homepage: To download Ghemical 0.40 (current only in source form): For more information on the Open Eye Scientific OELib library: -- -Geoff Hutchison Northwestern Chemistry From chemistry-request@server.ccl.net Wed Feb 7 11:37:55 2001 Received: from fecit-gate.fecit.co.uk (firewall-user@[193.119.134.250]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f17Gbsw32303 for ; Wed, 7 Feb 2001 11:37:54 -0500 Received: by fecit-gate.fecit.co.uk; id QAA13442; Wed, 7 Feb 2001 16:46:40 GMT Received: from suisei(192.168.101.50) by fecit-gate.fecit.co.uk via smap (V5.0) id xma013437; Wed, 7 Feb 01 16:45:58 GMT Received: from fecit.co.uk (NT11.fecit.co.uk [192.168.101.116]) by suisei.fecit.co.uk (8.6.9/8.6.9) with ESMTP id QAA07500 for ; Wed, 7 Feb 2001 16:32:00 GMT Message-ID: <3A81798E.9AE9083D@fecit.co.uk> Date: Wed, 07 Feb 2001 16:36:30 +0000 From: Herbert Fruchtl Organization: Fujitsu European Centre for Information Technology X-Mailer: Mozilla 4.75 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Re:Linux 2.4.0 and 2 GB promlem References: <01020613084300.26802@coch11> <20010207101147.A21758@chem.helsinki.fi> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Jonas Juselius wrote: > > The 2GB limit is a thing of the past in 2.4.1, but you must use ReiserFS > (or XFS from SGI) to get past the limit. AFAIK ext2 does still not handle > files larger than 2GB. I have been using ReiserFS together with LVM > (www.sistina.com) for some time now, and I'm extermely happy with the setup. > If I do a one finger boot, the filesystem check on my 25 GB work partition > (ReiserFS) takes about 2-3 seconds :-) Does anybody have performance information about this? What's the penalty compared to ext2? Does it run on any old EIDE, or are there hardware requirements? How does compiler support look like (you probably have to have 64-bit file pointers)? Thanks in advance, Herbert From chemistry-request@server.ccl.net Wed Feb 7 12:19:07 2001 Received: from mail2.organik.uni-erlangen.de (lesath.chemie.uni-erlangen.de [131.188.127.212]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f17HJ6w32530 for ; Wed, 7 Feb 2001 12:19:06 -0500 Received: from ccc.chemie.uni-erlangen.de (wtewael [131.188.127.223]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with ESMTP id SAA01006; Wed, 7 Feb 2001 18:18:48 +0100 (MET) Sender: Wolf-Dietrich.Ihlenfeldt@ccc.chemie.uni-erlangen.de Message-ID: <3A818377.13A6841D@ccc.chemie.uni-erlangen.de> Date: Wed, 07 Feb 2001 18:18:47 +0100 From: Wolf-Dietrich Ihlenfeldt Organization: Computer Chemistry Center X-Mailer: Mozilla 4.7 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: Jonas Juselius , CHEMISTRY@ccl.net Subject: Re: CCL:Linux 2.4.0 and 2 GB promlem References: <01020613084300.26802@coch11> <20010207101147.A21758@chem.helsinki.fi> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Jonas Juselius wrote: > > The 2GB limit is a thing of the past in 2.4.1, but you must use ReiserFS > (or XFS from SGI) to get past the limit. AFAIK ext2 does still not handle > files larger than 2GB. I have been using ReiserFS together with LVM > (www.sistina.com) for some time now, and I'm extermely happy with the setup. > If I do a one finger boot, the filesystem check on my 25 GB work partition > (ReiserFS) takes about 2-3 seconds :-) > > -jonas- This statement is not correct. We operate a 3.5 GB single file database successfully under Linux2.4 on an ext2 filesystem. However, there are a number of issues which we observed in our SuSE7.0 distribution setup (some of these problems may be resolved in newer releases, SuSE 7.0 contains a prerelease 2.4 kernel) a) quota support is broken b) regardless of user limit settings, only root can actually write files larger than 2 Gb. Otherwise, a file size exceeded signal will be generated and no bytes are written. c) ftell64() will return negative position values if the file pointer is beyond 2Gb, regardless of compilation flags. Add 4Gb to compensate if the value is negative (and of course use int64_t/off64_t vars for this kind of arithmetic). I don't know what happens if your file is larger than 4Gb. d) Accroding to our measurements, the performance of mmap64()ed memory from extended segments of a big file is atrocious and leads to severe paging, even if only a small section of the mapped area is actually touched. The vmem memory page swapping mechanisms desparately require improvements for this kind of application (IRIX does much better with the same software) -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, Institute for Organic Chemistry, University of Erlangen-Nuremberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 http://www2.ccc.uni-erlangen.de/wdi/ From chemistry-request@server.ccl.net Wed Feb 7 15:43:38 2001 Received: from mserve1.acs.ucalgary.ca (postfix@mserve1.acs.ucalgary.ca [136.159.34.51]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f17Khcw01562 for ; Wed, 7 Feb 2001 15:43:38 -0500 Received: from ucalgary.ca (acs1.acs.ucalgary.ca [136.159.34.221]) by mserve1.acs.ucalgary.ca (Postfix) with ESMTP id 283C210DA; Wed, 7 Feb 2001 13:43:36 -0700 (MST) Received: from localhost (patchkov@localhost) by ucalgary.ca (AIX4.3/8.9.3/8.8.8) with ESMTP id NAA115606; Wed, 7 Feb 2001 13:43:35 -0700 Date: Wed, 7 Feb 2001 13:43:30 -0700 (MST) From: Serguei Patchkovskii X-Sender: patchkov@acs1.acs.ucalgary.ca To: Jonas Juselius Cc: Matthias Mann , CHEMISTRY@ccl.net, q_timerg@alcor.concordia.ca Subject: Re: CCL:Linux 2.4.0 and 2 GB promlem In-Reply-To: <20010207101147.A21758@chem.helsinki.fi> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 7 Feb 2001, Jonas Juselius wrote: > The 2GB limit is a thing of the past in 2.4.1, but you must use ReiserFS > (or XFS from SGI) to get past the limit. AFAIK ext2 does still not handle > files larger than 2GB. This is most certainly false. ext2 does support files larger than 2Gbytes; moreover, such files have been supported since at least 2.2 kernels: # dd if=/dev/zero of=xxx seek=4096k bs=4k count=1 1+0 records in 1+0 records out # ls -l xxx -rw-r--r-- 1 ps ftp 17179873280 Feb 7 13:58 xxx # uname -a Linux CeNsOrEd 2.2.14-6.0 #1 Tue Mar 28 16:56:56 EST 2000 alpha unknown # df -T . Filesystem Type 1k-blocks Used Available Use% Mounted on /dev/sda4 ext2 2080939 51 1973317 0% /usr2 /Serge.P --- Home page: http://www.cobalt.chem.ucalgary.ca/ps/ From chemistry-request@server.ccl.net Wed Feb 7 15:37:12 2001 Received: from mailrelay1.lrz-muenchen.de (mailrelay1.lrz-muenchen.de [129.187.254.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f17KbBw01524 for ; Wed, 7 Feb 2001 15:37:11 -0500 Received: from [129.187.43.199] by mailout.lrz-muenchen.de with ESMTP; Wed, 7 Feb 2001 21:37:10 +0100 Sender: Eugene.Leitl@lrz.uni-muenchen.de Message-Id: <3A81B187.14EA692A@lrz.uni-muenchen.de> Date: Wed, 07 Feb 2001 21:35:19 +0100 From: Eugene.Leitl@lrz.uni-muenchen.de X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.17-21mdksecure i586) X-Accept-Language: en, de-DE, ru MIME-Version: 1.0 To: =?iso-8859-1?Q?S=E9rgio?= Emanuel Galembeck CC: chemistry@ccl.net Subject: Re: CCL:G98 in K6-II 500 MHz References: <00a201c09118$2a77a2a0$97c26b8f@ligquim.ffclrp.usp.br> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f17KbCw01525 I don't see why not, but you can't expect good numeric performance from the Sharptooth core based AMDs. Go for a Duron or a Thunderbird core processors, these should be several 100% faster. Sérgio Emanuel Galembeck wrote: > > Dear netters, > > I am planning an undergraduate course of molecular modelling. The > undergraduate laboratory has K6-II 500 MHz with 64 MB of memory and with Red > Hat 6.2. Is it possible to compile and run G98 in this computer? > > Thank you, > > Sergio > > ============================================================== > Sergio Emanuel Galembeck > Assistant Professor in Physical Chemistry > Laboratório de Modelagem Molecular > Departamento de Química > Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto > Universidade de São Paulo > Av Bandeirantes, 3900 > Ribeirão Preto, SP > Brasil > > phone: +55-16-602-37-65 > fax: +55-16-633-81-51 > e-mail: segalemb@usp.br > ============================================================== > > -= 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 -- ______________________________________________________________________________ icbmto:N 48 10'07'' E 011 33'53'' http://www.lrz.de/~ui22204 ED 90 04 33 EB 74 E4 A9 53 7F CF F5 86 E7 62 9B 57 F9 CF D3 From chemistry-request@server.ccl.net Wed Feb 7 16:23:36 2001 Received: from email01.aon.at (WARSL401PIP1.highway.telekom.at [195.3.96.69]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f17LNZw02456 for ; Wed, 7 Feb 2001 16:23:36 -0500 Received: (qmail 215844 invoked from network); 7 Feb 2001 21:21:35 -0000 Received: from n773p005.adsl.highway.telekom.at (HELO pc1.eidolon.net) ([62.47.40.133]) (envelope-sender ) by qmail1.highway.telekom.at (qmail-ldap-1.03) with SMTP for ; 7 Feb 2001 21:21:35 -0000 Sender: hal@pc1.eidolon.net To: chemistry@ccl.net Subject: Re: CCL:Linux 2.4.0 and 2 GB promlem References: From: Hannes Loeffler Date: 07 Feb 2001 22:17:03 +0100 In-Reply-To: Serguei Patchkovskii's message of "Wed, 7 Feb 2001 13:43:30 -0700 (MST)" Message-ID: <87y9vi9os0.fsf@pc1.eidolon.net> Lines: 21 User-Agent: Gnus/5.0807 (Gnus v5.8.7) XEmacs/21.1 (Cuyahoga Valley) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Serguei Patchkovskii writes: > This is most certainly false. ext2 does support files larger than 2Gbytes; > moreover, such files have been supported since at least 2.2 kernels: > > # dd if=/dev/zero of=xxx seek=4096k bs=4k count=1 > 1+0 records in > 1+0 records out > # ls -l xxx > -rw-r--r-- 1 ps ftp 17179873280 Feb 7 13:58 xxx > # uname -a > Linux CeNsOrEd 2.2.14-6.0 #1 Tue Mar 28 16:56:56 EST 2000 alpha unknown ^^^^^ Yes, it works on Linux/Alpha but not Linux/i386. > # df -T . > Filesystem Type 1k-blocks Used Available Use% Mounted on > /dev/sda4 ext2 2080939 51 1973317 0% /usr2 Hannes. From chemistry-request@server.ccl.net Wed Feb 7 22:52:33 2001 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f183qXw05210 for ; Wed, 7 Feb 2001 22:52:33 -0500 Received: from mail.chem.tamu.edu ([165.91.177.32]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Wed, 7 Feb 2001 22:03:55 -0600 Sender: yubo@ccl.net Message-ID: <3A81C3E2.3B23289@mail.chem.tamu.edu> Date: Wed, 07 Feb 2001 21:53:38 +0000 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: zh-CN, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: ONIOM and gen cannot work together Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, everyone, Today, I tried ONIOM method to calculate a rather big system containing a Nickel atom. I used a modified lanl2dz basis set to Ni and 6-31++G** to all atoms in the directly coordinated groups. B3LYP was used for this part of the molecule. PM3 was used to those substituents on the ligands. The input file is listed below: #P ONIOM(B3LYP/gen:PM3) Pseudo=cards opt scf=(maxcycle=256) freq molecule specification Ni 0 S 3 1.00 0.7620000000D+01 -0.4082550000D+00 0.2294000000D+01 0.7455308000D+00 0.8760000000D+00 0.5325721000D+00 S 4 1.00 0.7620000000D+01 0.1872591000D+00 0.2294000000D+01 -0.3966964000D+00 0.8760000000D+00 -0.4954003000D+00 0.1153000000D+00 0.1084434000D+01 S 1 1.00 0.3960000000D-01 0.1000000000D+01 P 3 1.00 0.2366000000D+02 -0.4815580000D-01 0.2893000000D+01 0.6258473000D+00 0.9435000000D+00 0.4715158000D+00 P 4 1.00 0.2366000000D+02 0.7131470000D-02 0.2893000000D+01 -0.1089909500D+00 0.9435000000D+00 -0.4615260000D-01 0.8400000000D-01 0.8025519700D+00 P 1 1.00 0.2400000000D-01 0.1000000000D+01 D 4 1.00 0.4272000000D+02 0.3726990000D-01 0.1176000000D+02 0.1956103000D+00 0.3817000000D+01 0.4561273000D+00 0.1169000000D+01 0.5621587000D+00 D 1 1.00 0.2836000000D+00 0.1000000000D+01 **** 2 3 4 5 6 7 8 9 10 6-31++G** **** Ni 0 lanl2dz But, this job could not work properly and the following error message was printed in the output file. Standard basis: VSTO-3G (5D, 7F) =============================================================================== ==================================================== PSEUDOPOTENTIAL PARAMETERS =============================================================================== ==================================================== CENTER ATOMIC VALENCE ANGULAR POWER COORDINATES NUMBER NUMBER ELECTRONS MOMENTUM OF R EXPONENT COE FFICIENT X Y Z =============================================================================== ==================================================== WANTED AN INTEGER AS INPUT. FOUND AN END-OF-LINE FOR INPUT. STO-3G ? Error termination via Lnk1e in /usr/local/g98.a7//g98/l301.exe. Cannot G98 work properly when ONIOM and gen are used together? Any advices are prefered. Thanks in advance Yubo -- ============================================================ Dr. Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================