From jkl@ccl.net Thu Jul 29 02:55:13 1999 -0400 Return-Path: Received: from server.ccl.net (server.ccl.net [192.153.40.39]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id CAA04337 for ; Thu, 29 Jul 1999 02:55:12 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA04253 for ; Thu, 29 Jul 1999 03:00:06 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id IAA16697; Thu, 29 Jul 1999 08:54:59 +0200 From: Jochen Kuepper Reply-To: jochen@bacchus.pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: Gavin Tsai , CHEMISTRY Subject: Re: CCL:degenerate eigenvalue problem Date: Thu, 29 Jul 1999 08:52:31 +0200 X-Mailer: KMail [version 1.0.21] Content-Type: text/plain References: <001201bed87b$8ddcfe00$aec81681@cwru.edu> MIME-Version: 1.0 Message-Id: <99072908545802.14634@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by ccl.net id CAA04337 On Mit, 28 Jul 1999 Gavin Tsai wrote: > Is there any one can give me any suggestion or advice for the > degenerate = eigensystem? In case of a double degenerate eigenvalue, aren't any two linear combinations that span a two-dimensional vector-space eigenvectors of the system as well ? So how do ou know what "are" the correct eigenvalues ? -- Jochen Heinrich-Heine-Universität Düsseldorf jochen@uni-duesseldorf.de Institut für Physikalische Chemie I phone ++49-211-8113681 Universitätsstr. 26.43.02.29 fax ++49-211-8115195 40225 Düsseldorf, Germany www-public.rz.uni-duesseldorf.de/~jochen From jkl@ccl.net Thu Jul 29 03:41:10 1999 -0400 Return-Path: Received: from server.ccl.net (server.ccl.net [192.153.40.39]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id DAA04616 for ; Thu, 29 Jul 1999 03:41:09 -0400 (EDT) Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA04552 for ; Thu, 29 Jul 1999 03:46:03 -0400 Received: from ruppert.phys.chemie.tu-muenchen.de by mailrelay2.lrz-muenchen.de for @dfvgate.lrz-muenchen.de:chemistry@server.ccl.net; Thu, 29 Jul 1999 09:41:06 +0200 Received: from physik.tu-muenchen.de by ruppert.phys.chemie.tu-muenchen.de via ESMTP (940816.SGI.8.6.9/930416.SGI) for id JAA02074; Thu, 29 Jul 1999 09:41:01 +0200 Sender: tmehnert@physik.tu-muenchen.de Message-Id: <37A0058C.A7FD706F@physik.tu-muenchen.de> Date: Thu, 29 Jul 1999 09:41:01 +0200 From: Mehnert Thomas X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: force field Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi alltogether Can anyone recommend a force field program which is able to carry out calculations on molecules like Indole, Indene, Carbazole? Thanks in advance Thomas From jkl@ccl.net Thu Jul 29 05:09:26 1999 -0400 Return-Path: Received: from server.ccl.net (server.ccl.net [192.153.40.39]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id FAA05118 for ; Thu, 29 Jul 1999 05:09:25 -0400 (EDT) Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA05111 for ; Thu, 29 Jul 1999 05:11:34 -0400 Received: from ruppert.phys.chemie.tu-muenchen.de by mailrelay2.lrz-muenchen.de for @dfvgate.lrz-muenchen.de:chemistry@server.ccl.net; Thu, 29 Jul 1999 11:06:14 +0200 Received: from physik.tu-muenchen.de by ruppert.phys.chemie.tu-muenchen.de via ESMTP (940816.SGI.8.6.9/930416.SGI) for id LAA02290; Thu, 29 Jul 1999 11:06:13 +0200 Sender: tmehnert@physik.tu-muenchen.de Message-Id: <37A01984.DED60457@physik.tu-muenchen.de> Date: Thu, 29 Jul 1999 11:06:13 +0200 From: Mehnert Thomas X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: Clustering Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi alltogether, I investigate clusters normally consisting of two to three molecules. But sometimes generation of clusters works well and sometimes not depending on the molecules I use. I think the problem is the process of creation the clusters during the expansion in the nozzle which depends probably on the geometry of the nozzle. Does anyone have an idea with respect to this problem or does anybody know a reference referring to this? Thanks in advance Thomas From jkl@ccl.net Thu Jul 29 08:11:00 1999 -0400 Return-Path: Received: from server.ccl.net (server.ccl.net [192.153.40.39]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id IAA06684 for ; Thu, 29 Jul 1999 08:11:00 -0400 (EDT) Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA06923 for ; Thu, 29 Jul 1999 08:15:57 -0400 Received: from localhost (noronha@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id JAA54558 for ; Thu, 29 Jul 1999 09:10:41 -0300 Date: Thu, 29 Jul 1999 09:10:41 -0300 (BSC) From: antonio luiz oliveira de noronha To: chemistry@server.ccl.net Subject: MOPAC 2000 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi ccl'ers Does anyone know how to make contact with a MOPAC 2000 dealer? I already try the homeage of Fujitsu for MOPAC 2000 and the hp of the Schroedinger Inc too, send mails etc etc, and I don't receive a single response. Could anyone please give me a mail where they read my questions? Thanks Antonio Luiz Oliveira de Noronha - noronha@dedalus.lcc.ufmg.br Medicinal Chemistry of Organotin Compounds NEQUIM - Group of Studies in Medicinal Chemistry UFMG - Federal University of Minas Gerais - Brazil From jkl@ccl.net Thu Jul 29 09:53:48 1999 -0400 Return-Path: Received: from server.ccl.net (server.ccl.net [192.153.40.39]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id JAA08744 for ; Thu, 29 Jul 1999 09:53:48 -0400 (EDT) Received: from vanilla.ice.mpg.de (root@vanilla.ice.mpg.de [195.37.47.220]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA07470 for ; Thu, 29 Jul 1999 09:58:46 -0400 Received: from ice.mpg.de (relax.ice.mpg.de [195.37.47.89]) by vanilla.ice.mpg.de (8.8.7/8.8.7) with ESMTP id OAA24389; Thu, 29 Jul 1999 14:58:18 +0200 Message-ID: <37A05CE7.9B38DA5C@ice.mpg.de> Date: Thu, 29 Jul 1999 15:53:43 +0200 From: Christoph Steinbeck Reply-To: steinbeck@ice.mpg.de Organization: Max-Planck-Institute of Chemical Ecology X-Mailer: Mozilla 4.61 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@server.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU Subject: ANNOUNCE: JChemPaint 0.4 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I'd like to announce the release of JChemPaint v0.4 JChemPaint is a Java program for drawing 2D chemical structures like those found in most chemistry textbooks. Its GUI is based on the Swing tool kit. The program is developed as an Open Source Project and released under GNU General Public License. The code should be considered pre-alpha quality, but there are enough features implemented to get an idea about where the program development is heading. JChemPaint development is coordinated by Christoph Steinbeck and his Chemical Information group (http://www.ice.mpg.de/departments/ChemInf) at the Max Planck Instiutute of Chemical Ecology (http://www.ice.mpg.de). Version 0.4 now features one-click condensation of rings using predefined templates. The program currently supports: 1. A subset of the regular drawing features of commercial programs, as there are - drawing of single, double and triple bonds (no stereo descriptors yet). - deletion of bonds and atoms - one-click drawing of ring templates (3-8) - one-click attachment of rings to an atom or a bond (spiro attachment and ring condensation). 2. Loading and saving of structures as MDL Molfiles and in Chemical Markup Language (CML). 3. Automated Structure Layout, aka Structure Diagram Generation. More information as well as a download option can be found on http://www.ice.mpg.de/~stein/projects/JChemPaint/ People a sought to join the development of JChemPaint. JChemPaint is associated with the OpenScience project (www.openscience.org) and the 3D molecular viewer JMol (http://www.openscience.org/jmol/), both initiated by Dan Gezelter at Columbia University (http://www.chem.columbia.edu/~gezelter/). I'd be happy to get some feedback from people who have downloaded the program and got it up and running. Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/~stein) MPI of Chemical Ecology, Tatzendpromenade 1a, 07745 Jena, Germany Tel: +49(0)3641 643644 - Mobile: +49(0)177 8236510 - Fax: +49(0)3641 643665 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From jkl@ccl.net Thu Jul 29 10:15:01 1999 -0400 Return-Path: Received: from server.ccl.net (server.ccl.net [192.153.40.39]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id KAA09530 for ; Thu, 29 Jul 1999 10:15:00 -0400 (EDT) Received: from gatekeeper.bnfl.co.uk (gatekeeper.bnfl.co.uk [193.35.7.249]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA07609 for ; Thu, 29 Jul 1999 10:19:58 -0400 From: Scott.L.Owens@bnfl.com Received: by gatekeeper.bnfl.co.uk; id PAA14854; Thu, 29 Jul 1999 15:12:52 +0100 (BST) Received: from ant008-mailsweeper(10.128.8.60) by gatekeeper.bnfl.co.uk via smap (3.2) id xma014720; Thu, 29 Jul 99 15:12:22 +0100 Received: from ASN027.bnfl.com (unverified) by ANT008.SPR.BNFL.COM (Content Technologies SMTPRS 2.0.15) with ESMTP id for ; Thu, 29 Jul 1999 15:20:26 +0100 Received: from BNotesMTA1.sell.bnfl.com ([10.10.1.149]) by ASN027.bnfl.com (8.8.5/8.8.5) with SMTP id PAA17199 for ; Thu, 29 Jul 1999 15:14:02 +0100 (BST) Received: by BNotesMTA1.sell.bnfl.com(Lotus SMTP MTA v4.6.1 (569.2 2-6-1998)) id 002567BD.00539AE6 ; Thu, 29 Jul 1999 15:13:11 +0000 X-Lotus-FromDomain: BNFL To: CHEMISTRY@ccl.net Message-Id: <002567BD.0052B340.00@BNotesMTA1.sell.bnfl.com> Date: Thu, 29 Jul 1999 15:13:23 +0000 Subject: Mopac for 3D and heavier elements - summary MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Thanks to those of you who took the time to reply, summary is as follows The current and soon to be available (MOPAC2000) versions of MOPAC seem to work for periodic systems. As for heavier elements, the new version of MOPAC (MOPAC2000) is set up for inclusion of d-electrons, however in the next release there seem to be few elements parameterised, "It has Thiel's MNDO_d and also has Ag and Cu for AM1_d." I don't know if there are any other sources of parameters for MOPAC - if you know then please pass the information on. You can find out more about the new version of MOPAC on http://www.fujitsu.co.jp/hypertext/softinfo/product/indust/winmopac/mo pac2000/index_e.html There are also parameters for PM3 in Spartan which seem to cover a little bit more of the transition series. Dr. Scott Owens From jkl@ccl.net Thu Jul 29 11:35:41 1999 -0400 Return-Path: Received: from server.ccl.net (server.ccl.net [192.153.40.39]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id LAA12970 for ; Thu, 29 Jul 1999 11:35:40 -0400 (EDT) Received: from relay0.unizar.es (tozal.unizar.es [155.210.3.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA08144 for ; Thu, 29 Jul 1999 11:40:26 -0400 Received: from posta.unizar.es (posta.unizar.es [155.210.11.16]) by relay0.unizar.es (8.9.3/8.9.1) with ESMTP id RAA27502 for ; Thu, 29 Jul 1999 17:35:02 +0200 (MET DST) Received: from posta.unizar.es ([155.210.88.191]) by posta.unizar.es (8.9.1/8.8.5) with ESMTP id RAA25775 for ; Thu, 29 Jul 1999 17:35:04 +0200 (MET DST) Message-ID: <37A073BA.213DC7FE@posta.unizar.es> Date: Thu, 29 Jul 1999 17:31:06 +0200 From: Luis Salvatella =?iso-8859-1?Q?Ib=E1=F1ez?= X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Problems with B3LYP frequencies Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I have found some problems with the calculation of B3LYP frequencies. Thus, for the optimized LiH at B3LYP/3-21G level (internuclear distance = 1.6297 Angstroms), numerical computations indicate a positive frequency of 1398.9861 cm-1. Instead, analytical calculations yield an imaginary (negative) frequency of -1024.1595 cm-1. The analytical vibrational analysis of other structures optimized at B3LYP level by using different basis sets present very large numbers of imaginary (negative) frequencies. Can anybody explain these results? Thank you, LUIS SALVATELLA From jkl@ccl.net Thu Jul 29 12:05:05 1999 -0400 Return-Path: Received: from server.ccl.net (server.ccl.net [192.153.40.39]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id MAA13694 for ; Thu, 29 Jul 1999 12:05:04 -0400 (EDT) Received: from si.fi.ameslab.gov (si.fi.ameslab.gov [147.155.20.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA08670 for ; Thu, 29 Jul 1999 12:10:05 -0400 Received: (from pradipta@localhost) by si.fi.ameslab.gov (AIX4.2/UCB 8.7/8.7) id LAA34304 for chemistry@ccl.net; Thu, 29 Jul 1999 11:06:50 -0500 (CDT) From: Pradipta Bandyopadhyay Message-Id: <199907291606.LAA34304@si.fi.ameslab.gov> Subject: center of cavity in continuum! To: chemistry@ccl.net (CCL) Date: Thu, 29 Jul 1999 11:06:50 -0500 (CDT) X-Mailer: ELM [version 2.4 PL25] Content-Type: text Dear ccl-members, I have a question about the continuum method of solvation. Does it matter where I put my molecule inside the cavity? If I put the molecule ( dipole) in the center of the cavity and then put it away from the center, the dipole moment ( with respect to the origin) changes but the dipole moment of uncharged systems are independent of the origin. So is it really independent of the postion of the dipole? I want to know the answer for both quantum mechanical and classical treatment of the dipole(when the charge is zero). Can anyone tell me the answer for both quantum menchanical and classical cases? Thanks in advance. Pradipta -- ***************************************** * Dr. Pradipta Bandyopadhyay * * AMES LAB * * Department of Chemistry * * Iowa State Unievrsity * * Ames, IA 50011 * * USA * * e-mail: pradipta@si.fi.ameslab.gov * * Phone : 515-294-4604 (Lab) * * : 515-232-8067 (Residence) * * Fax : 515-294-0105 * * URL: http://www.msg.ameslab.gov/ * * Group/pradipta/index.html * ***************************************** ------------------------------------------------------------------------------ ...FOR AFTERWARDS A MAN FINDS PLEASURE IN HIS PAINS, WHEN HE HAS SUFFERED LONG AND WANDERED FAR. -- HOMER ------------------------------------------------------------------------------ From jkl@ccl.net Thu Jul 29 11:50:47 1999 -0400 Return-Path: Received: from server.ccl.net (server.ccl.net [192.153.40.39]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id LAA13316 for ; Thu, 29 Jul 1999 11:50:46 -0400 (EDT) Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA08309 for ; Thu, 29 Jul 1999 11:55:47 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id LAA13313 for ; Thu, 29 Jul 1999 11:50:41 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id RAA10865; Thu, 29 Jul 1999 17:49:59 +0200 From: Jochen Kuepper Reply-To: jochen@bacchus.pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: Gavin Tsai , CCL Subject: Re: double degenerate Date: Thu, 29 Jul 1999 17:41:14 +0200 X-Mailer: KMail [version 1.0.21] Content-Type: text/plain References: <000f01bed9cf$05125de0$aec81681@cwru.edu> MIME-Version: 1.0 Message-Id: <99072917495905.14634@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by ccl.net id LAA13316 I wrote: > >So how do you know what "are" the correct eigenvalues ? By correct I went back to your original question. This sounded like you weren't satisfied with the linear combinations you got ouf of NR-Jacobi. So I asked how you decide wether they are good in your sense. They are "correct" in a mathematical sense (if the implementation is correct, anyhow :-), aren't they ? On Don, 29 Jul 1999 Gavin Tsai wrote: > It is a good questions. I can not guarantee they are exactly correct. > But when compared with other calculations, the eigenvalues are very = > similar. > In my calculation, I just call the subroutine 'Jacobn' in the book = > "Numerical Recipes". > Do I need special routine to treat the double degenerate problem? I would say NO. But any two algorithms or even two different implementations of the same algorithm might give you different linear combinations of the eigenvectors. And they are all correct. Btw., Jacobi is a good algorithm for small matrices, but there are better algorithms for medium sized or large matrices. (Some people say Jacobi is good up to dim=10, probably dim=50 is usually ok, I would say.) And as someone stated before, NR routines are not the best in a sense of speed and robustness. They are simple though, as a pro. Probably you look at LAPACK to get a lot of good black-box matrix routines, check it out at netlib.org. -- Jochen Heinrich-Heine-Universität Düsseldorf jochen@uni-duesseldorf.de Institut für Physikalische Chemie I phone ++49-211-8113681 Universitätsstr. 26.43.02.29 fax ++49-211-8115195 40225 Düsseldorf, Germany www-public.rz.uni-duesseldorf.de/~jochen From chemistry-request@server.ccl.net Thu Jul 29 13:09:51 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA09550 for ; Thu, 29 Jul 1999 13:09:51 -0400 Received: from rock.helsinki.fi (rock.helsinki.fi [128.214.3.50]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id NAA15691 for ; Thu, 29 Jul 1999 13:04:47 -0400 (EDT) Received: from localhost (sundius@localhost) by rock.helsinki.fi (8.8.8/8.8.5) with ESMTP id UAA18180; Thu, 29 Jul 1999 20:04:44 +0300 (EET DST) Date: Thu, 29 Jul 1999 20:04:44 +0300 (EET DST) From: Tom Sundius X-Sender: sundius@rock.helsinki.fi To: Jochen Kuepper cc: Gavin Tsai , CCL Subject: Re: CCL:double degenerate In-Reply-To: <99072917495905.14634@bacchus.pc1.uni-duesseldorf.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 29 Jul 1999, Jochen Kuepper wrote: ... > > Btw., Jacobi is a good algorithm for small matrices, but there are better > algorithms for medium sized or large matrices. (Some people say Jacobi is > good up to dim=10, probably dim=50 is usually ok, I would say.) > And as someone stated before, NR routines are not the best in a sense of > speed and robustness. They are simple though, as a pro. > ... I once wrote a Jacobi routine in Fortran using the threshold method that worked quite well for even larger matrices. The good thing with the Jacobi method is that it always preserves orthogonality, but it is not a very fast method, especially for large matrices. If you want a faster method, you have to use the Householder method in combination with some other methods (look in NETLIB, e.g.). Of course Jacobi did not have access to a computer when he devised his method more than 100 years ago, he did his calculations by hand ;-) Regards, TS Tom Sundius University of Helsinki, Department of Physics phone +358-9-191 8339 P.O.Box 9, FIN-00014 Helsinki, Finland fax +358-9-191 8680 From chemistry-request@server.ccl.net Thu Jul 29 13:58:07 1999 Received: from voicenet.com (mail12.voicenet.com [207.103.0.6]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA10161 for ; Thu, 29 Jul 1999 13:58:07 -0400 Received: (qmail 29611 invoked from network); 29 Jul 1999 17:53:02 -0000 Received: from dialup0856-pri.voicenet.com (HELO billag.voicenet.com) (207.103.134.251) by mail12.voicenet.com with SMTP; 29 Jul 1999 17:53:02 -0000 Message-Id: <4.1.19990729132352.00a96260@popmail.voicenet.com> X-Sender: billag@popmail.voicenet.com X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Thu, 29 Jul 1999 13:52:46 -0400 To: noronha@dedalus.lcc.ufmg.br From: Bill Glauser Subject: CCL:MOPAC 2000 Cc: chemistry@server.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Antonio, We apologize for the difficulty that you encountered trying to contact a MOPAC 2000 dealer. We at Schrodinger, Inc. distribute and support MOPAC 2000 for North America only. But I can readily see how this could be confusing, since Schrodinger markets and sells all of our other software products (e.g., Jaguar, MacroModel) globally. We should have referred you to the appropriate distributor for your territory. In fact, a representative from Fujitsu will be contacting you shortly to provide the name of the local MOPAC 2000 distributor. We are very dedicated to customer support and apologize again for our error. Thanks and best regards, Bill ---- >Hi ccl'ers >Does anyone know how to make contact with a MOPAC 2000 dealer? >I already try the homeage of Fujitsu for MOPAC 2000 and the hp of the >Schroedinger Inc too, send mails etc etc, and I don't receive a single >response. >Could anyone please give me a mail where they read my questions? > >Thanks > >Antonio Luiz Oliveira de Noronha - noronha@dedalus.lcc.ufmg.br >Medicinal Chemistry of Organotin Compounds >NEQUIM - Group of Studies in Medicinal Chemistry >UFMG - Federal University of Minas Gerais - Brazil ---- William A. Glauser / Schrodinger, Inc. / 800-207-7482 / 610-869-0578 610-869-0577 (fax) / billg@schrodinger.com / http://www.schrodinger.com From chemistry-request@server.ccl.net Thu Jul 29 14:21:34 1999 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA10463 for ; Thu, 29 Jul 1999 14:21:33 -0400 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id OAA19987 for ; Thu, 29 Jul 1999 14:16:31 -0400 (EDT) Sender: desingh@mailbox.syr.edu Message-ID: <37A09BA5.535CBC41@syr.edu> Date: Thu, 29 Jul 1999 14:21:26 -0400 From: Deepak Singh Organization: Dept. of Chem & Biochem, Syracuse University X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: Computational Chemistry List Subject: GAMESS question Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everyone, I am rather new to using GAMESS and have a quick question regarding restart files. The GAMESS manual says that the IREST option is unreliable. In what way is it unreliable? Also, can one use IREST as well as NSTEP for OPTIMIZE calculations? I guess my main question is what is the best way to restart a GAMESS calculation (using OPTIMIZE). Thanks Deepak. -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Thu Jul 29 14:54:21 1999 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA10672 for ; Thu, 29 Jul 1999 14:54:21 -0400 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id OAA03046 for ; Thu, 29 Jul 1999 14:50:03 -0400 (EDT) Date: Thu, 29 Jul 1999 14:50:03 -0400 (EDT) From: Iraj Daizadeh To: chemistry@ccl.net Subject: pythonVSperl... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello. Perl seems to dominate the chem(bio)-informatical sciences these days. An example of such dominance is descibed on papers describing the BioPerl consortium http://bio.perl.org (see, e.g., an article in http://www.bitsjournal.com Bioperl:Standard perl modules for bioinformatics)... The question is why...why has python been neglected from its role in the informatics fields.... Your responses would be appreciated...Iraj. Iraj Daizadeh, Ph.D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@fas.harvard.edu WebPage: http://mcb.harvard.edu/gilbert/daizadeh From chemistry-request@server.ccl.net Thu Jul 29 15:01:36 1999 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA10750 for ; Thu, 29 Jul 1999 15:01:36 -0400 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id OAA03069 for ; Thu, 29 Jul 1999 14:57:17 -0400 (EDT) Date: Thu, 29 Jul 1999 14:57:17 -0400 (EDT) From: Iraj Daizadeh To: chemistry@ccl.net Subject: Large matrix diagonalization. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII For my phd dissertation, we spent quite some time diagonalizing SPARSE matrices of the order of 1000x1000 or so...The diagonalization process was performed by a routine called cboris (fortran code): cboris_(&n,&n,a,b,c,d,e,f,&ifail); It is included in the QCPE (255 I think) package for extended huckel calculations (i think it was written by someone in the hoffman group (theoretical group at cornell) This routine is not faster than the diagonalization packages that come with blas or something or that sort... Iraj. subroutine cboris(n,nd,a,b,c,d,e,f,ifail) implicit double precision(a-h,o-z) c dimension a(nd,nd),b(nd,nd),c(nd,nd),d(nd),e(nd),f(nd) c c ---------------------------------------------------------------------- c subroutine cboris solves the complex eigenvalue c problem c a*x=b*x*lambda c c where c a --- given matrix of order n c b --- given positive definite matrix of order n c x --- eigenvectors, column by column, c normalized to (bx,x)=i c lambda --- eigenvalues in increasing order c c matrices a and b should be given in c arrays a and b respectively in the following way c c diagonal elements in the diagonal c real parts of the lower triangle in the lower c triangle c imag parts of the lower triangle in the upper c triangle c c real parts of eigenvectors are stored in a, c imag parts in array c. array b is destroyed during c computation. it holds the lower triangle of the c choleski decomposition of matrix b (see c subroutine cchol). c c all matrices are of order n, declared in the c calling program with dimension nd which need c not to be equal to n. c c eigenvalues are stored in array d. arrays e c and f are used for intermediate results. c c ifail gets the following values c 0 --- computation finished succesfully c 1 --- b not positive definite c 2 --- qr algorithm does not converge Iraj Daizadeh, Ph.D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@fas.harvard.edu WebPage: http://mcb.harvard.edu/gilbert/daizadeh On Thu, 29 Jul 1999, Tom Sundius wrote: > On Thu, 29 Jul 1999, Jochen Kuepper wrote: > >... > > > > Btw., Jacobi is a good algorithm for small matrices, but there are better > > algorithms for medium sized or large matrices. (Some people say Jacobi is > > good up to dim=10, probably dim=50 is usually ok, I would say.) > > And as someone stated before, NR routines are not the best in a sense of > > speed and robustness. They are simple though, as a pro. > > > >... > > I once wrote a Jacobi routine in Fortran using the threshold method that > worked quite well for even larger matrices. The good thing with the > Jacobi method is that it always preserves orthogonality, but it is not > a very fast method, especially for large matrices. If you want a faster > method, you have to use the Householder method in combination with > some other methods (look in NETLIB, e.g.). > > Of course Jacobi did not have access to a computer when he devised his > method more than 100 years ago, he did his calculations by hand ;-) > > Regards, > > TS > > Tom Sundius > University of Helsinki, Department of Physics phone +358-9-191 8339 > P.O.Box 9, FIN-00014 Helsinki, Finland fax +358-9-191 8680 > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Jul 29 14:10:36 1999 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA10383 for ; Thu, 29 Jul 1999 14:10:36 -0400 Received: (from daemon@localhost) by bioc1.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id LAA03761 for <@bioc1.msi.com:CHEMISTRY@ccl.net>; Thu, 29 Jul 1999 11:06:14 -0700 (PDT) Received: from iris69.msi.com(146.202.3.69) by bioc1.msi.com via smap (V2.0) id xma003759; Thu, 29 Jul 99 11:06:12 -0700 Received: by iris69.msi.com (950413.SGI.8.6.12/930416.SGI) for CHEMISTRY@ccl.net id LAA19685; Thu, 29 Jul 1999 11:11:58 -0700 Date: Thu, 29 Jul 1999 11:11:58 -0700 From: tvd@msi.com (Ton van Daelen) Message-Id: <199907291811.LAA19685@iris69.msi.com> To: CHEMISTRY@ccl.net Subject: hashing algorithm Can anyone point me to an efficient hashing algorithm? I tried using SGI's hsearch. It works, but setting up the hash table gets really slow for tables >20,000 rows. Thanks - Ton Ton van Daelen, Ph.D. Product Manager Software Developer's Kit __o E: tvd@msi.com _`\<,_ Molecular Simulations Inc. P: -1-858-799-5329 (*)/ (*) 9685 Scranton Road F: -1-858-458-0136 /\/\/\/\/\/\ San Diego, CA 92121 W: http://www.msi.com The Cerius2 software developer's kit is now available free-of-charge Visit http://www.msi.com/support/sdk/ to sign up for a copy From chemistry-request@server.ccl.net Thu Jul 29 15:56:53 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA11301 for ; Thu, 29 Jul 1999 15:56:53 -0400 Received: from sp2n17.missouri.edu (sp2n17-t.missouri.edu [128.206.2.27]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id PAA24064 for ; Thu, 29 Jul 1999 15:51:47 -0400 (EDT) Received: from sp2n21.missouri.edu (sp2n21.missouri.edu [128.206.2.83]) by sp2n17.missouri.edu (8.9.0/8.9.0) with ESMTP id OAA65812 for ; Thu, 29 Jul 1999 14:51:28 -0500 Received: from localhost (c697999@localhost) by sp2n21.missouri.edu (8.9.0/8.9.0) with SMTP id OAA51090 for ; Thu, 29 Jul 1999 14:51:28 -0500 X-Authentication-Warning: sp2n21.missouri.edu: c697999 owned process doing -bs Date: Thu, 29 Jul 1999 14:51:28 -0500 (CDT) From: Raelene X-Sender: c697999@sp2n21.missouri.edu To: chemistry@www.ccl.net Subject: scaling factors... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Does anyone know what the scaling factors for Hartree-Fock and B3LYP calculations involving the LANL2DZ basis set are or where I could find them? Thanks. Raelene *********************************************************************** "Oh goody, my Niels Bohr swimsuit calender has finally arrived..." MST3K, The Movie *********************************************************************** A. R. Lawrence Plummer Group 125 Chemistry Bldg University of Missouri - Columbia Home: 573-445-7091 Work: 573-882-6077 E-mail: c697999@showme.missouri.edu