From chemistry-request@server.ccl.net Fri May 17 03:02:14 2002 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4H72Dp26338 for ; Fri, 17 May 2002 03:02:14 -0400 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Fri, 17 May 2002 09:02:22 +0200 Message-ID: <002a01c1fd70$ca77d520$3b8506c1@cthulhu> From: "Tamas E. Gunda" To: , References: <3CE3D243.4070601@iqm.unicamp.br> Subject: Re: CCL:.mol file Date: Fri, 17 May 2002 09:02:21 +0200 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 A number of different molecule file types use the *.mol extension. You should know the structural type of the file ( what is the creator/parent program?), and search accordingly. Tamas Gunda ----- Original Message ----- From: "Milton Taidi Sonoda" To: Sent: Thursday, May 16, 2002 17:37 Subject: CCL:.mol file > Hi all > Does anybody know what molecular viewer for > linux/unix/FreeBSD system that suports .mol extension? > Thankx in advance > Milton Taidi Sonoda > > > -= 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 Fri May 17 05:20:36 2002 Received: from plum.csi.cam.ac.uk (IDENT:exim@[131.111.8.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4H9KZp30005 for ; Fri, 17 May 2002 05:20:35 -0400 Received: from ursus.ch.cam.ac.uk ([131.111.121.19] helo=ursus.cam.ac.uk) by plum.csi.cam.ac.uk with esmtp (Exim 4.04) id 178dub-0004gr-00 for chemistry@ccl.net; Fri, 17 May 2002 10:20:33 +0100 Message-Id: <4.3.2.7.0.20020516170308.00ba6d28@pop.hermes.cam.ac.uk> X-Sender: pm286@pop.hermes.cam.ac.uk X-Mailer: QUALCOMM Windows Eudora Version 4.3.2 Date: Thu, 16 May 2002 17:54:48 +0100 To: chemistry@ccl.net From: Peter Murray-Rust Subject: CML (Chemical Markup Language) Update Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed CML is an Open XML infrastructure which supports molecular information and is compliant with current W3C (World Wide Web Consortium) protocols and philosophy. CML is designed as an application-independent adapter for chemical information. This is to announce a number of new developments. (Much of the work is jointly with Henry Rzepa). (A) Specifications: The W3C released the XML Schema Recommendation last year and we have converted the current V1.0 DTD to a schema. This is still at a draft stage, but increases the power of the language while simplifying some of the syntax. W3C schemas are seen as the main way forward for most XML applications and will support a variety of powerful new tools like XML forms, XML query, etc. In addition we have developed a core XML language (STMML) for representing scientific data (such as data structures (arrays, matrices), many data types, scientific units, metadata, etc.). STMML is a core part of CML but can be re-used in other applications. (B) Programming: We have created A W3C DOM (Document Object Model) for CML. This forms an Open abstract data model (and API) for those writing molecular applications in XML (and other OO approaches such as UML). The CML DOM has been developed alongside the Life Sciences Research group specification for small molecules for the Object Management Group. We have also created SAX2-based modules for CML. These interfaces are available under Open Source license for any developers. (C). Data: We are working closely with the National Cancer Institute (NCI) who are converting their database to CML. (D) CML is now an integral part of several Open Source projects such as OpenBabel, JMOL, JChemPaint and XDrawChem (all on http://www.sourceforge.net) (E) A new resource has been set up at Source Forge, the Open Source repository. Project Page: http://cml.sourceforge.net; Downloads and CVS repository at http://www.sourceforge.net/projects/cml. There is much supporting material including examples and Java. Javascript, and XSLT toolkits. We have developed a C++ SAX2-like parser for OpenBabel: http://www.sourceforge.net/projects/openbabel (F) SELFML: The SELF project (Prof. Henry Kehiaian, Paris) has created an ontology for physicochemical data (especially properties of molecules and mixtures of molecules). SELFML is the XML incarnation of SELF and supports the data and the specifications (dictionary entries). SELFML interoperates with CML and can therefore support collections of molecular properties (catalogues, dictionaries, etc.) (G) CML is being extended to support reactions and computational chemistry. We are starting to convert codes (initially Open Source such as MOPAC and GROMACS) to read and write XML, and to develop the XML ontologies required. Offers of collaboration welcomed :-) Peter Murray-Rust -- Peter Murray-Rust, pm286 AT cam.ac.uk Unilever Centre for Molecular Informatics, Chemistry Department Lensfield Road, Cambridge, CB2 1EW, UK +44-1223-336-432 From chemistry-request@server.ccl.net Thu May 16 12:22:13 2002 Received: from cascara.uvic.ca (root@[142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4GGMDk25659 for ; Thu, 16 May 2002 12:22:13 -0400 Received: from dial142.entirety.ca (dial142.entirety.ca [204.244.140.142]) by cascara.uvic.ca (8.11.6/8.11.6) with SMTP id g4GGMBI209178 for ; Thu, 16 May 2002 09:22:11 -0700 From: Roy Jensen To: chemistry@ccl.net Subject: Maximum in PES scans... Date: Thu, 16 May 2002 09:23:39 -0700 Message-ID: References: In-Reply-To: X-Mailer: Forte Agent 1.91/32.564 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g4GGMDk25660 I need to clarify this email: In the _dissociation_ of a diatomic molecule, there is sometimes a maximum along the dissociation coordinate. I am observing this in a relaxed PES scan of a tetra-atomic dissociation. The dissociation goes to the proper, neutral fragments. The maximum, and all points beyond, have only one negative frequency, but I cannot rationalize the drop after the maximum. X X X X X XXXX X X XXX X X XXXX X X XXXXXXXXXXXXXXXXXXXXXXXXX (A+B) X X X X X X X X XXX (AB) Your help is appreciated! Roy Jensen From chemistry-request@server.ccl.net Fri May 17 04:28:29 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4H8STp29265 for ; Fri, 17 May 2002 04:28:29 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0GW800H5BXJJ8F@mailstudenti.unimi.it> for chemistry@ccl.net; Fri, 17 May 2002 10:14:07 +0200 (MEST) Received: from vega (vega.farma.unimi.it [159.149.79.32]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0GW800CTUXJKGY@smtp.unimi.it> for chemistry@ccl.net; Fri, 17 May 2002 10:14:08 +0200 (MEST) Date: Fri, 17 May 2002 10:14:29 +0200 From: Giulio Vistoli Subject: Re: CCL:Autodock mol2topdbqs error (fwd) To: "mer@chem.wayne.edu" , CCL Message-id: <008e01c1fd7a$de3c0f40$204f959f@farma.unimi.it.farma.unimi.it> Organization: Ist. Chimica Farmaceutica MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal References: Dear AutoDock users, Try our program VEGA (http://users.unimi.it/~ddl): indeed VEGA is able to convert a lot of file formats in pdbq format and it runs under several O.S. with or without graphical engine Best regards Giulio Vistoli -- Dr. Giulio Vistoli Ist. di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano (Italy) Tel. +39 02 503 17522 Fax +39 02 503 17565 E-Mail: giulio.vistoli@unimi.it WWW: http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Thu May 16 12:20:48 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4GGKmk25619 for ; Thu, 16 May 2002 12:20:48 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id MAA13036; Thu, 16 May 2002 12:12:53 -0400 (EDT) Date: Thu, 16 May 2002 12:12:52 -0400 From: Rick Venable To: =?gb2312?q?yong=20pei?= cc: chemistry@ccl.net Subject: Re: CCL:Can dynamics pressure of the MD simulation compared with surface tension? In-Reply-To: <20020516145109.76038.qmail@web15004.mail.bjs.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 16 May 2002, [gb2312] yong pei wrote: > I want to know the relation between the dynamics > pressure and the surface tension of liquid . It can be evaluated for systems with either planar interfaces or for a droplet; there's a brief description for droplets in the "Computer Simulation of Liquids" book by Allen & Tildesley (pp. 289-291). You can find info on the CHARMM implementation and application to planar interfaces (water/octane, bilayers) in the following refs: ZHANG YH, FELLER SE, BROOKS BR, et al. COMPUTER-SIMULATION OF LIQUID/LIQUID INTERFACES .1. THEORY AND APPLICATION TO OCTANE/WATER J CHEM PHYS 103 (23): 10252-10266 DEC 15 1995 FELLER SE, ZHANG YH, PASTOR RW COMPUTER-SIMULATION OF LIQUID/LIQUID INTERFACES .2. SURFACE-TENSION AREA DEPENDENCE OF A BILAYER AND MONOLAYER J CHEM PHYS 103 (23): 10267-10276 DEC 15 1995 FELLER SE, ZHANG YH, PASTOR RW, et al. CONSTANT-PRESSURE MOLECULAR-DYNAMICS SIMULATION - THE LANGEVIN PISTON METHOD J CHEM PHYS 103 (11): 4613-4621 SEP 15 1995 An oriented ensemble (planar interfaces in XY plane) termed NPAT can be used to evaluate the surface tension directly from the diagonal of the pressure tensor as gamma = ( Pzz - (Pxx+Pyy)/2 )/2 for a system constructed with 2 planar interfaces. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Fri May 17 10:17:27 2002 Received: from c2bapps9 ([193.113.154.18]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4HEHQp02195 for ; Fri, 17 May 2002 10:17:26 -0400 Received: from patriot (actually host host213-122-59-34.in-addr.btopenworld.com) by c2bapps9 with SMTP-CUST (XT-PP); Fri, 17 May 2002 15:16:24 +0100 From: "Roma Oakes" To: "ccl" Subject: G98 Symmetry Date: Fri, 17 May 2002 15:15:23 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal Dear all I am trying to do an optimisation of a porphyrin (saddle structure). I cannot get G98 to recognise any symmetry within the molecule, I have used iop(2/17=1). the start of the output file says 'This structure is nearly, but not quite of a higher symmetry. Consider Symm=Loose if the higher symmetry is desired.' Does anyone have any other ideas on how to get any symmetry? the z-matrix is C C 1 1.46489 C 2 1.36208 1 107.32765 C 3 1.46489 2 107.30074 1 -2.99998 0 N 4 1.32832 3 110.61997 2 3.51915 0 C 1 1.42742 2 125.68839 3 -167.99837 0 H 2 1.07684 1 127.17103 6 9.00166 0 H 3 1.07705 2 125.52414 1 -179.99996 0 C 4 1.42308 3 125.2264 2 -168. 0 N 9 2.48163 4 94.30135 3 158.00001 0 C 10 1.38065 9 28.06927 4 -159.99997 0 C 11 1.44489 10 105.1031 9 170.00003 0 C 12 1.36208 11 108.6117 10 -3.00002 0 C 10 1.38061 9 140.29226 4 -134.41775 0 H 12 1.07537 11 126.07408 10 -178.00007 0 H 13 1.07587 12 125.01971 11 -179.99998 0 C 6 3.66931 1 124.75715 2 140.00045 0 C 17 1.36208 6 31.57118 1 -160.00264 0 C 6 1.42307 1 119.33617 2 150.00126 0 N 19 1.38442 6 123.29996 1 17.23781 0 C 20 1.38459 19 112.36384 6 -170.30015 0 H 17 1.07623 6 156.33447 1 -146.00084 0 H 18 1.0741 17 125.00114 6 168.99902 0 C 21 2.42488 20 96.36629 19 -156.06457 0 N 24 1.38101 21 97.53312 20 0. 0 C 25 1.38927 24 107.71199 21 158.52506 0 C 26 1.46963 25 108.50462 24 5.18742 0 C 27 1.36208 26 107.50112 25 -0.15033 0 H 28 1.07681 27 125.43996 26 -176.66351 0 H 27 1.07483 26 127.21118 25 -179.72895 0 C 26 1.41896 25 120.43101 24 159.13754 0 C 24 1.41284 21 31.35919 20 -157.86525 0 H 20 1.0138 19 123.28002 6 12.44419 0 H 10 1.01444 9 97.68685 4 29.99998 0 H 32 1.07 24 122.75667 21 -174.52872 0 H 6 1.07 1 119.90482 2 -26.00198 0 H 9 1.07 4 120.36706 3 -29.00001 0 H 31 1.07 26 117.36252 25 167.3077 0 Hope someone can help Regards Roma From chemistry-request@server.ccl.net Fri May 17 11:57:16 2002 Received: from brass.metals.hope.edu ([198.110.98.36]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4HFvGp04182 for ; Fri, 17 May 2002 11:57:16 -0400 Received: from hope.edu ([198.110.98.17]) by brass.metals.hope.edu (NAVGW 2.5.1.13) with SMTP id M2002051711561125595 for ; Fri, 17 May 2002 11:56:11 -0400 Received: from mrpink [198.110.99.151] (matthew.zwier@hope.edu) by hope.edu; Fri, 17 May 2002 11:56:29 -0400 X-WM-Posted-At: hope.edu; Fri, 17 May 02 11:56:29 -0400 From: "Matt Zwier" To: CHEMISTRY@ccl.net Date: Fri, 17 May 2002 11:57:15 -0400 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: G98: 64-bit file pointers on ia32 architectures Reply-to: matthew.zwier@hope.edu Message-ID: <3CE4F01B.19471.1D1F8816@localhost> Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12c) Hello all, Earlier in the week we ran into the infamous 2GB file limit with G98 on Linux (i686). I've searched the G98 site and the CCL archive, and while it's clear that the kernel and libc both support 64-bit file positions, it's much less clear how to get G98 to use them. Does this mean writing a replacement FORTRAN IO library? Or does it just mean setting some compile-time flag and rebuilding G98? Has anybody conquered this problem? Is there *any* way other than just splitting our rwf files, something that hasn't worked too well for us? Thanks bunches, Matt Zwier -- Matthew Zwier (matthew.zwier@hope.edu) Department of Chemistry Undergraduate Researcher Hope College, Holland, MI From chemistry-request@server.ccl.net Fri May 17 11:42:51 2002 Received: from goshen.rutgers.edu ([165.230.180.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4HFgpp03848 for ; Fri, 17 May 2002 11:42:51 -0400 Received: from eden.rutgers.edu (unknown [165.230.180.159]) by goshen.rutgers.edu (Postfix) with ESMTP id 0C9E0210F3 for ; Fri, 17 May 2002 11:40:23 -0400 (EDT) Received: from eden.rutgers.edu (pool2-192.envsci.rutgers.edu [165.230.172.192]) by eden.rutgers.edu (Postfix) with ESMTP id A23D9A29B7 for ; Fri, 17 May 2002 11:40:16 -0400 (EDT) Message-ID: <3CE526DB.5D19922@eden.rutgers.edu> Date: Fri, 17 May 2002 11:50:51 -0400 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary of Force Field construction Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thanks to everyone who replied: Fabien Fontaine: info is given at www.amber.ucsf.edu/amber/amber.html Jeff Nauss gave the following references: Hwang,M.-J. et al. 1994. JACS 116:2515-25. Cornell,W.D. et al. 1995. JACS: 117:5179-5197 Halgren,T.A. 1996. J.Comp. Chem. 17:490-519 MacKerell,A.D. Jr. et al. 1998. J. Phys. Chem B. 102:3586-3616 And the book by Andrew Leach-Molecular Modelling-Principles and Applications. Per-Ola Norrby has written or co-authored several papers and reviews: Coord. Chem. Rev. 2001.212:79-109 J.Comput. Chem.1998. 19:1146-1166 "Recipe for an organometallic force field" in Computational Organometallic Chemistry (ed. T. Cundari, Marcel Dekker NY,2001. pp 7-37) Dr. Norrby has a website:http://compchem.dfh.dk/PeO/ And recommended the following books Cramer:Essentials of Computational Chemistry. John Wiley,2001/2 (very recent) Jensen: Introduction to Computational Chemistry. John Wilet, 1999. Goodman: Chemical Applications of Molecular Modelling.1998.RCS. This information is greatly appreciated! Mary O'Connor,Ph.D. Rutgers University New Brunswick,NJ From chemistry-request@server.ccl.net Fri May 17 13:34:53 2002 Received: from web20006.mail.yahoo.com ([216.136.225.69]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4HHYrp05550 for ; Fri, 17 May 2002 13:34:53 -0400 Message-ID: <20020517173452.71896.qmail@web20006.mail.yahoo.com> Received: from [130.14.72.5] by web20006.mail.yahoo.com via HTTP; Fri, 17 May 2002 10:34:52 PDT Date: Fri, 17 May 2002 10:34:52 -0700 (PDT) From: S Bear Subject: Re: CCL:searching for chemical structures To: Rajarshi Guha , CHEMISTRY@ccl.net In-Reply-To: <200205161041.28154.rajarshi@presidency.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii ChemID operated by the National Library of Medicine http://chem.sis.nlm.nih.gov/chemidplus/ --- Rajarshi Guha wrote: > does anybody know of any free services where I can search > for a molecule > structure by name - apart form www.chemfinder.com? also see: http://www.chemexper.com/ccd/power/ http://www.sigma-aldrich.com/sacatalog.nsf/GenericSearch?OpenForm http://geocities.com/soaringbear/biomed/chem.html ===== Soaring Bear Ph.D. Research Pharmacologist Scientific advisor to the health professions soaringbear@yahoo.com soaringbear.com or http://www.geocities.com/soaringbear -- author of http://HERBMED.org acclaimed by Science & Brit Med J __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From chemistry-request@server.ccl.net Fri May 17 10:29:29 2002 Received: from math.fu-berlin.de ([160.45.40.10]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4HETTp02468 for ; Fri, 17 May 2002 10:29:29 -0400 Received: (qmail 27509 invoked by uid 9804); 17 May 2002 16:29:28 +0200 Received: from cognac.math.fu-berlin.de (160.45.41.44) by leibniz.math.fu-berlin.de with SMTP; 17 May 2002 16:29:26 +0200 Received: from localhost ([127.0.0.1] helo=math.fu-berlin.de ident=antony) by cognac.math.fu-berlin.de with esmtp (Exim 3.12 #1 (Debian)) id 178ijW-0006AS-00 for ; Fri, 17 May 2002 16:29:26 +0200 Sender: antony@ccl.net Message-ID: <3CE513C6.C0DDB77B@math.fu-berlin.de> Date: Fri, 17 May 2002 16:29:26 +0200 From: Jens Antony X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.6 i686) X-Accept-Language: en MIME-Version: 1.0 To: CCL post Subject: Normal mode scan Content-Type: text/plain; charset=iso-8859-15 Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS Perl-11 [27503] (NAI-uvscan@math.fu-berlin.de) Dear CCL, 1) How can I scan a potential energy surface along a vibrational normal mode with Gaussian or another molecular electronic structure program automatically ? 2) How can I increase the precision of the normal modes printed with Gaussian ? The answer to these questions are probably already in the CCL archive, but I cut not find them quickly. Thank you very much. Jens Antony -- Free University Berlin Institute for Mathematics II Arnimallee 2-6 D-14195 Berlin , Germany From chemistry-request@server.ccl.net Fri May 17 14:44:20 2002 Received: from ultra.chem.ucsb.edu ([128.111.114.119]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4HIiKp06754 for ; Fri, 17 May 2002 14:44:20 -0400 Received: from localhost (bushnell@localhost) by ultra.chem.ucsb.edu (8.12.3/8.12.3) with ESMTP id g4HIiH0O008217 for ; Fri, 17 May 2002 11:44:17 -0700 (PDT) Date: Fri, 17 May 2002 11:44:17 -0700 (PDT) From: John Bushnell To: chemistry@ccl.net Subject: RE: CCL:Maximum in PES scans... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-milter (http://amavis.org/) Hi, I would look at the change in bond distances between the four atoms for a clue. You would have to consider the mixing of higher (diabatic) states if this were in fact the dissociation of a diatomic molecule (which I guess it isn't actually). - John >Date: Thu, 16 May 2002 09:23:39 -0700 >From: Roy Jensen > >I need to clarify this email: > >In the _dissociation_ of a diatomic molecule, there is sometimes a >maximum along the dissociation coordinate. I am observing this in a >relaxed PES scan of a tetra-atomic dissociation. The dissociation goes ^^^^^^^^^^^^ >to the proper, neutral fragments. The maximum, and all points beyond, >have only one negative frequency, but I cannot rationalize the drop >after the maximum. > > X > X > X > X > X XXXX > X X XXX > X X XXXX > X X XXXXXXXXXXXXXXXXXXXXXXXXX (A+B) > X X > X X > X X > X X > XXX > (AB) > >Your help is appreciated! > > >Roy Jensen > -= 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 Fri May 17 15:48:50 2002 Received: from qtp.ufl.edu ([128.227.89.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4HJmop08078 for ; Fri, 17 May 2002 15:48:50 -0400 Received: from pc1 (dred7 [192.168.4.135]) by qtp.ufl.edu (8.9.1a/8.9.1/deumens) with SMTP id PAA13291; Fri, 17 May 2002 15:48:54 -0400 (EDT) Message-ID: <003a01c1fddc$e61a72d0$8704a8c0@qtp.ufl.edu> From: "Stefan Fau" To: "Jens Antony" Cc: "CCL - all" References: <3CE513C6.C0DDB77B@math.fu-berlin.de> Subject: Re: CCL:Normal mode scan Date: Fri, 17 May 2002 15:56:09 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-15" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Jens, you might try POLYRATE. It is a program (designed by Prof. Joel Bowman and others) to calculate vibrational frequencies and more by going beyond the harmonic oscillator approximation. Add the HPFREQ option to the FREQ command. You can find a very thorough documentation of G98 at: http://www.gaussian.com/techinfo.htm Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu University of Florida | (352) 392-6714 Quantum Theory Project 2341 NPB #92, P.O.Box 117200 Gainesville, FL 32611-7200 From chemistry-request@server.ccl.net Fri May 17 17:03:53 2002 Received: from netmaster.kds.com.ua ([194.44.106.42]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4HL3pp10127 for ; Fri, 17 May 2002 17:03:51 -0400 Received: from akhavr by netmaster.kds.com.ua with local (Exim 3.22 #1) id 178m7M-0001rK-00; Fri, 17 May 2002 21:06:16 +0300 To: "Matt Zwier" Cc: CHEMISTRY@ccl.net Subject: Re: G98: 64-bit file pointers on ia32 architectures References: <3CE4F01B.19471.1D1F8816@localhost> From: Andrey Khavryuchenko Organization: KDS Software Group X-Attribution: AVK Date: 17 May 2002 21:06:16 +0300 In-Reply-To: <3CE4F01B.19471.1D1F8816@localhost> Message-ID: Lines: 23 User-Agent: Gnus/5.0808 (Gnus v5.8.8) XEmacs/21.4 (Academic Rigor) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Matt, "MZ" == Matt Zwier wrote: MZ> Earlier in the week we ran into the infamous 2GB file limit with G98 MZ> on Linux (i686). I've searched the G98 site and the CCL archive, MZ> and while it's clear that the kernel and libc both support 64-bit file MZ> positions, it's much less clear how to get G98 to use them. Does MZ> this mean writing a replacement FORTRAN IO library? Or does it MZ> just mean setting some compile-time flag and rebuilding G98? Has MZ> anybody conquered this problem? Is there *any* way other than MZ> just splitting our rwf files, something that hasn't worked too well for MZ> us? Does G98 rebuild on recent Linux distribution helps? It should[1] work without any additional compile- or run-time flags. Footnotes: [1] but not necessary it would :) :( -- Andrey V Khavryuchenko http://www.kds.com.ua/ Offshore Software Development From chemistry-request@server.ccl.net Fri May 17 17:43:55 2002 Received: from zephyr.meteo.McGill.CA ([132.206.43.13]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4HLhtp10872 for ; Fri, 17 May 2002 17:43:55 -0400 Received: from kinetic.Meteo.McGill.CA by zephyr.meteo.McGill.CA (AIX 4.1/UCB 5.64/4.03) id AA07148; Fri, 17 May 2002 17:39:54 -0400 Date: Fri, 17 May 2002 17:43:46 -0400 From: Andrew Ryzhkov X-Mailer: The Bat! (v1.53d) Reply-To: Andrew Ryzhkov Organization: Dep. of Atm. & Oc. Sci. McGill Univ. X-Priority: 3 (Normal) Message-Id: <21275019617.20020517174346@zephyr.meteo.mcgill.ca> To: "Matt Zwier" Cc: CHEMISTRY@ccl.net Subject: Re: CCL:G98: 64-bit file pointers on ia32 architectures In-Reply-To: <3CE4F01B.19471.1D1F8816@localhost> References: <3CE4F01B.19471.1D1F8816@localhost> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello Matt, MZ> Earlier in the week we ran into the infamous 2GB file limit with G98 MZ> on Linux (i686). I've searched the G98 site and the CCL archive, MZ> and while it's clear that the kernel and libc both support 64-bit file MZ> positions, it's much less clear how to get G98 to use them. Does MZ> this mean writing a replacement FORTRAN IO library? Or does it MZ> just mean setting some compile-time flag and rebuilding G98? Has MZ> anybody conquered this problem? Is there *any* way other than MZ> just splitting our rwf files, something that hasn't worked too well for MZ> us? I think all people usually split files when use the 32-bit version of G98. There is another problem also, namely the 16Gb limit, which is more complex because indexes of arrays in G98 have INTEGER*4 type and can't address more than 8*2^32=16Gb data. The way, I guess, to avoid this problem is to recompile G98 after changing type of integer variables in sources. I think it should be no so difficult, just replace all INTEGER and INTEGER*4 to INTEGER*8. I don't know exactly whether the PGF compiler, usually used for compiling the G98, support such integer type, but I sure that it must. IFC, for example, can use INTEGER*8. So, to solve both these problems you should replace 32-bit integers to 64-bit one at least. Best regards, Andrew Dr. Andrei Ryjkov Departments of Chemistry, and Atmospheric and Oceanic Sciences, McGill University, 805 Sherbrooke St. West #808 Montreal, Quebec, CANADA, H3A 2K6. ---------------------------------------------------------------- E-mail: Andrew@Zephyr.Meteo.McGill.Ca Internet: http://RedAndr.tripod.com