From chemistry-request@server.ccl.net Tue Feb 29 01:31:25 2000 Received: from dns.campus.mlsultan.ac.za ([196.13.103.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA22923; Tue, 29 Feb 2000 01:31:04 -0500 Received: from wpogate.mlsultan.ac.za (wpogate.campus.mlsultan.ac.za [196.13.102.11]) by dns.campus.mlsultan.ac.za (AIX4.2/UCB 8.7/8.7) with SMTP id HAA09636; Tue, 29 Feb 2000 07:53:15 +0200 (USAST) Received: from MLSTGW-Message_Server by wpogate.mlsultan.ac.za with Novell_GroupWise; Tue, 29 Feb 2000 08:16:36 +0200 Message-Id: X-Mailer: Novell GroupWise 5.5.2 Date: Tue, 29 Feb 2000 08:16:09 +0200 From: "Thishana Singh" To: , Subject: Bond length of HCl gas Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id BAA22924 Dear CClers Can anyone help me in locating a literature value for the bond length of HCl gas ? Where can I find this value ? Thank you Thishana Singh Lab Assistant Dept.Of Chemistry ML Sultan Technikon Durban South Africa email : singht@wpo.mlsultan.ac.za From chemistry-request@server.ccl.net Tue Feb 29 03:12:31 2000 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA23376 for ; Tue, 29 Feb 2000 03:12:30 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP for ; Tue, 29 Feb 2000 09:11:41 +0100 Message-ID: <000901bf828c$d310f740$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: References: <17633.000228@mnc.md> Subject: Re: CCL:Programm to add H to XRay data Date: Tue, 29 Feb 2000 09:13:12 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Dear Mike, Mol2mol can do it. See http://www.compuchem.com/mol2mol.htm > | Dear chemistry, > : > >. > > I received XRay data without H atoms coordinates. Is there a programm > to add H to XRay data? Binaries for DOS/Win or C/C++ sources are > perfect. > > Best regards, > Mike mailto:mike@mnc.md Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. L. Kossuth University, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 316666/2472 fax: (+36-52) 512914 > From chemistry-request@server.ccl.net Tue Feb 29 04:05:02 2000 Received: from century.fen.bilkent.edu.tr (century.fen.bilkent.edu.tr [139.179.97.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA23736 for ; Tue, 29 Feb 2000 04:04:58 -0500 Received: from pinar (pinar [139.179.97.99]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with ESMTP id LAA12054 for ; Tue, 29 Feb 2000 11:07:01 +0200 (EET) Date: Tue, 29 Feb 2000 11:05:34 +0200 (EET) From: Ulrike Salzner X-Sender: salzner@pinar To: ccl Subject: Beowulf Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII is there a reason why Beowulf clusters usually consist of 8x something nodes or can these clusters be built in any size, let's say 27? I need this information to justify the required funding for a proposal. Thanks in advance, Uli Salzner =================================================================== Dr. Ulrike Salzner Department of Chemistry Tel.: (312) 290-2122 Bilkent University Fax.: (312) 266-5097 06533 Bilkent, Ankara e-mail: salzner@fen.bilkent.edu.tr Turkey ==================================================================== From chemistry-request@server.ccl.net Tue Feb 29 04:34:28 2000 Received: from gensig.nibsc.ac.uk (gensig.nibsc.ac.uk [193.62.43.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA23897 for ; Tue, 29 Feb 2000 04:34:27 -0500 Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by gensig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id JAA83967 for ; Tue, 29 Feb 2000 09:33:56 GMT Message-ID: <38BB926C.8F8CE739@nibsc.ac.uk> Date: Tue, 29 Feb 2000 09:33:33 +0000 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: Re: CCL:Re:REPLY TO HOW TO FIND BONDS References: <200002281318.VAA20604@ms.dicp.ac.cn> <38BAB281.6C0D3662@trentu.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL On the subject of defining a bond: The 'Atoms in Molecules' methodology of Richard Bader provides an objective means to define atoms and bonds, thereby linking chemical intuition with quantum mechanics. Check out the site http://www.chemistry.mcmaster.ca/faculty/bader/aim/ it is very informative. elewars wrote: > Hello, > > So far as I know there is no "true definition" of a bond. At one level the concept is simple, at another level sophisticated. Given > the cartesian coordinates of a molecule, the simplest way to get the "bonds" is to draw a line between all pairs of nuclei within a > distance that experience or general agreement says is bonding; there are programs that will do this (e.g. Molwin, some versions of > Spartan). This shows you what the molecule looks like, which is sometimes all you want. > Of course bonds can be assigned from calculated bond order, determined by the coefficients of the basis functions in the occupied > MOs (e.g. Lo:wdin B.O., Meyer B.O., Mulliken B. O), or from an analysis of the calculated electron density: AIM analysis--atoms in > molecules (Bader analysis). > > EL > ===== > > li guo hui wrote: > > > Dear Netters: > > i would like to know what is the true definition of bond, this question can also be given in the following: > > given a file only including coordinates of atoms in molecule, there are not connectivities between atoms in molecule, just from > > this file how can i find the bonds or connectivities? using Van der walls radius or covalance radius of atoms or some results of > > population analysis from theoretical calcualtion? > > > > thank you > > > > > > Li Guo Hui > > State Key Laboratory of Molecular Reaction Dynamics > > Dalian Institute of Chemical Physics > > Liao Ning Province, P.R.China > > > > Mailing Address: > > Room 715 > > Xing Hai Third Street, 59 # > > Sha He Kou District > > Dalian, Liaoning Province > > P.R.China, 116023 > > > > -= 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 -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@server.ccl.net Tue Feb 29 05:22:18 2000 Received: from angelos.phc.chalmers.se (angelos.phc.chalmers.se [129.16.97.41]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA24190; Tue, 29 Feb 2000 05:22:17 -0500 Received: from fkrs2.phc.chalmers.se (fkrs2.phc.chalmers.se [129.16.97.48]) by angelos.phc.chalmers.se (8.9.3/8.9.3) with ESMTP id LAA20796; Tue, 29 Feb 2000 11:21:45 +0100 Received: (from svedung@localhost) by fkrs2.phc.chalmers.se (8.8.8/8.8.8) id LAA11090; Tue, 29 Feb 2000 11:21:43 +0100 Date: Tue, 29 Feb 2000 11:21:39 +0100 (MET) From: Harald Svedung To: Thishana Singh cc: chemistry@ccl.net, chemistry-request@ccl.net Subject: Re: CCL:Bond length of HCl gas In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Thishana Singh and all, The value of 1.27455 Angstrom can be found for the ground state in: Huber, Herzberg, 'Molecular Spectra and Molecular Structure 4, Constants of Diatomic Molecules', Van Nostrand N.Y. (1979) (i.e. spectroscopic data) :-) /Harald On Tue, 29 Feb 2000, Thishana Singh wrote: > Dear CClers > Can anyone help me in locating a literature value for the bond length of HCl > gas ? > Where can I find this value ? > Thank you > > Thishana Singh > Lab Assistant > Dept.Of Chemistry > ML Sultan Technikon > Durban > South Africa > email : singht@wpo.mlsultan.ac.za > > > -= 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 > > > > > Harald Svedung (Ph.Lic.) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone: +46-31-240897, +46-709223206 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden www.che.chalmers.se/~svedung/ From chemistry-request@server.ccl.net Tue Feb 29 05:41:09 2000 Received: from mail-c.bcc.ac.uk (mail-c.bcc.ac.uk [144.82.100.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA24304; Tue, 29 Feb 2000 05:41:09 -0500 Received: from socrates-a.ucl.ac.uk by mail-c.bcc.ac.uk with SMTP (Mailer); Tue, 29 Feb 2000 10:40:23 +0000 From: uccatvm Message-Id: <2617.200002291040@socrates-a.ucl.ac.uk> Subject: Re: CCL:Bond length of HCl gas To: singht@wpogate.mlsultan.ac.za (Thishana Singh) Date: Tue, 29 Feb 2000 10:40:35 +0000 (GMT) Cc: chemistry@ccl.net (chemistry), chemistry-request@ccl.net (chemistry-request) In-Reply-To: from "Thishana Singh" at Feb 29, 2000 10:40:01 AM X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Thishana, > Can anyone help me in locating a literature value for the bond length of HCl > gas ? > Where can I find this value ? If it is the bond length of HCl in the gas phase that you are interested in, you may have a look at: T. van Mourik and T.H. Dunning, Jr., Int. J. Quantum Chem. 76, 205 (2000). In this paper, we report spectroscopic constants (including equilibrium bond lengths, harmonic frequencies, and anharmonicity constants) of a few diatomic molecules, among them HCl. These have been calculated with several theoretical methods and the correlation consistent basis sets up to aug-cc-pV6Z. Best regards, Tanja -- ==================================================================== Tanja van Mourik phone University College London work: +44 (0)207-679-4665 Christopher Ingold Laboratories home: +44 (0)1895-259-312 20 Gordon Street e-mail London WC1H 0AJ work: T.vanMourik@ucl.ac.uk United Kingdom home: tanja@netcomuk.co.uk ==================================================================== From chemistry-request@server.ccl.net Tue Feb 29 07:08:16 2000 Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by server.ccl.net (8.8.7/8.8.7) with SMTP id HAA25615 for ; Tue, 29 Feb 2000 07:08:09 -0500 Received: by lgdx04.lg.ehu.es id AA28463; Tue, 29 Feb 2000 13:05:50 +0100 Message-Id: <200002291205.AA28463@lgdx04.lg.ehu.es> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Tue, 29 Feb 2000 13:09:55 +0100 Subject: Re: CCL:Bond length of HCl gas From: "Pablo Vitoria" To: Thishana Singh , chemistry@ccl.net Mime-Version: 1.0 X-Priority: 3 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Hi, The Chemistry Webbook at NIST (http://webbook.nist.gov) gives a value of 1.27455 for equilibrium distance of HCl. The reference seems to be: Rank, D.H.; Rao, B.S.; Wiggins, T.A., Molecular constants of HCl35, J. Mol. Spectrosc., 1965, 17, 122. Best regards Pablo ----------------------------------------- Pablo Vitoria Garcia Dpto. Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Aptdo. 644 E-48080 Spain Phone: +34 94 6012000 Ext. 5529 Fax: +34 94 4648500 ----------------------------------------- ---------- >From: "Thishana Singh" >To: , >Subject: CCL:Bond length of HCl gas >Date: mart., 29 febr 2000 07:16 > > Dear CClers > Can anyone help me in locating a literature value for the bond length of HCl > gas ? > Where can I find this value ? > Thank you > > Thishana Singh > Lab Assistant > Dept.Of Chemistry > ML Sultan Technikon > Durban > South Africa > email : singht@wpo.mlsultan.ac.za > > > -= 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 Tue Feb 29 07:17:17 2000 Received: from alpha.luc.ac.be (alpha.luc.ac.be [193.190.2.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA25698 for ; Tue, 29 Feb 2000 07:17:16 -0500 Received: from sbg-ts (sbg-ts.luc.ac.be [193.190.1.15]) by alpha.luc.ac.be (8.9.3/8.9.3) with SMTP id NAA30970 for ; Tue, 29 Feb 2000 13:16:47 +0100 (MET) Date: Tue, 29 Feb 2000 13:16:47 +0100 (MET) Message-Id: <200002291216.NAA30970@alpha.luc.ac.be> X-Sender: skwasnie@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: Weights of vectors in G98 Hi, Does anyone know how the weights in the eigenvectors are defined in the excited states when doing a CIS or TD single point calculation in gaussian98 ? Thanks in advance Serge _________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 011/268315 fax : 011/268301 email : sergiusz.kwasniewski@luc.ac.be _________________________________________________ From chemistry-request@server.ccl.net Tue Feb 29 02:08:35 2000 Received: from email.guomai.sh.cn (ilkrsvkorz@e4000.guomai.sh.cn [202.96.206.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA23098 for ; Tue, 29 Feb 2000 02:08:18 -0500 Received: from guomai.sh.cn ([202.101.13.142]) by email.guomai.sh.cn (Sun Internet Mail Server sims.3.5.1999.07.30.00.05.p8) with ESMTP id <0FQO002IBK17KI@email.guomai.sh.cn> for CHEMISTRY@ccl.net; Tue, 29 Feb 2000 15:12:54 +0800 (CST) Date: Tue, 29 Feb 2000 15:05:57 +0800 From: Yubo Fan Subject: Text file transfer between linux and dos To: CHEMISTRY@ccl.net Message-id: <38BB6FD2.90708C33@guomai.sh.cn> Organization: Fudan University MIME-version: 1.0 X-Mailer: Mozilla 4.6 [en] (Win98; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Hi, I have installed Windows 98 and RedHat Linux 6.1 on my PC. Usually I edit G98 input file on Windows 98. The problem is when I start Linux and mount the DOS partitions, I cannot copy the input files correctly. "^M" was added to the end of each lines. They cannot work by G98. I need some help. Is there a way to copy the files by ascii way (not binary way). Thanks in advance Y. Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From chemistry-request@server.ccl.net Tue Feb 29 08:25:49 2000 Received: from fb13n.uni-paderborn.de (fb13n.uni-paderborn.de [131.234.240.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA26170 for ; Tue, 29 Feb 2000 08:25:48 -0500 Received: from oc1 ([131.234.240.61]) by fb13n.uni-paderborn.de (Netscape Messaging Server 3.62) with ESMTP id 182 for ; Tue, 29 Feb 2000 14:19:43 +0100 From: "Gregor Fels" To: Date: Tue, 29 Feb 2000 14:25:46 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: logP data Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12) Message-ID: <20000229131943109.AAA247.182@oc1> We are looking for logP data tables that include structure files of any file format (rather than just drawings of chemical structures), in order to run a comparison of various logP software. Thanks in advance Gregor Fels Dr. Gregor Fels University of Paderborn Department of Chemistry Warburgerstr. 100 D-33098 Paderborn Germany Tel.: +49-5251-602181 Fax: +49-5251-603245 Web: http://oc30.uni-paderborn.de/~chemie/fachgebiete/oc/ak_fels/index_haupt.html From chemistry-request@server.ccl.net Tue Feb 29 09:11:49 2000 Received: from dns.campus.mlsultan.ac.za ([196.13.103.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA26489 for ; Tue, 29 Feb 2000 09:11:22 -0500 Received: from wpogate.mlsultan.ac.za (wpogate.campus.mlsultan.ac.za [196.13.102.11]) by dns.campus.mlsultan.ac.za (AIX4.2/UCB 8.7/8.7) with SMTP id PAA08902 for ; Tue, 29 Feb 2000 15:32:54 +0200 (USAST) Received: from MLSTGW-Message_Server by wpogate.mlsultan.ac.za with Novell_GroupWise; Tue, 29 Feb 2000 15:13:42 +0200 Message-Id: X-Mailer: Novell GroupWise 5.5.2 Date: Tue, 29 Feb 2000 15:13:13 +0200 From: "Thishana Singh" To: , " Subject: Re:Bond length of HCl gas Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id JAA26490 Dear CClers To everyone who responded to my question....THANK YOU....(-: Your references have been very helpful and very much appreciated. Best wishes Thishana Lab Assistant Dept.Of Chemistry ML Sultan Technikon Durban South Africa email : singht@wpo.mlsultan.ac.za From chemistry-request@server.ccl.net Tue Feb 29 09:53:42 2000 Received: from century.fen.bilkent.edu.tr (century.fen.bilkent.edu.tr [139.179.97.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA26772 for ; Tue, 29 Feb 2000 09:53:39 -0500 Received: from pinar (pinar [139.179.97.99]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with ESMTP id QAA20287 for ; Tue, 29 Feb 2000 16:55:41 +0200 (EET) Date: Tue, 29 Feb 2000 16:54:13 +0200 (EET) From: Ulrike Salzner X-Sender: salzner@pinar To: ccl Subject: Beowulf Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thanks to everyone for all the nice and interesting replies to my question. I also got interesting advice beyond the original question that will certainly help me in the future. Regarding the cluster size everybody agrees that there is no reason not to built clusters of any amount of nodes. The clusters should, however, not become too large since they would not be extremely efficient. The power of two sizes of many clusters are probably due to supercomputer architectures and digitalization of computer scientists minds. This tendency is enhanced by the availablity of switches with 4x or 8x something ports. Thanks, Uli Salzner =================================================================== Dr. Ulrike Salzner Department of Chemistry Tel.: (312) 290-2122 Bilkent University Fax.: (312) 266-5097 06533 Bilkent, Ankara e-mail: salzner@fen.bilkent.edu.tr Turkey ==================================================================== From chemistry-request@server.ccl.net Tue Feb 29 10:01:36 2000 Received: from mum.mans.eun.eg (mum.mans.eun.eg [193.227.50.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA26870 for ; Tue, 29 Feb 2000 10:01:35 -0500 Received: by mum.mans.eun.eg with Internet Mail Service (5.5.2650.21) id <1P5098QT>; Tue, 29 Feb 2000 17:02:08 +0200 Message-ID: <4EF2E03A9B67D2119E2E0000F8053499427391@mum.mans.eun.eg> From: Tarek Mamoun El-Gogary To: "'CHEMISTRY@ccl.net'" Subject: Force field Date: Tue, 29 Feb 2000 17:02:07 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain Dear Netters, Dose anyone know how to determine the molecular force field of a molecule if the force constants of the its internal coordinates are known? Any comment or answer will be appreciated. Dr Tarek El-Gogary Dept of Chem Fac. of Sci. 34517 Domyat Al-Gideda Egypt. email asmasomy@mum.mans.eun.eg From chemistry-request@server.ccl.net Tue Feb 29 10:17:21 2000 Received: from nitrous.kc.rr.com (nitrous.kc.rr.com [24.94.163.109]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA27008 for ; Tue, 29 Feb 2000 10:17:21 -0500 Received: from [24.31.248.2] (mkc-248-002.kc.rr.com [24.31.248.2]) by nitrous.kc.rr.com (8.9.3/8.9.3) with ESMTP id JAA03721 for ; Tue, 29 Feb 2000 09:12:36 -0600 (CST) User-Agent: Microsoft Outlook Express Macintosh Edition - 5.01 (1630) Date: Tue, 29 Feb 2000 09:16:20 -0600 Subject: SAM1 semiempirical method From: Andy Holder To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Colleagues, Several days ago the following questions were posed. Sorry it took me some time to respond. > In 1993 the Dewar group announced the development of the SAM1 ("semi ab > initio #1") method. > I know the basic principles behind it, but would like to know: > 1) What became of it? It does not seem to appear much in the literature. The SAM1 method is still under development in my Group at the University of Missouri-Kansas City. We are working on refining some additional parameters and have added some new computational algorithms (an improved CI (1) and a quadratically (to be published) convergent SCF procedure) to make the method tractable for open-shell transition metals. The references to the method currently extant in the literature are listed below. A major paper describing the full implementation and listing parameter values is in preparation. > 2) Did computational chemists conclude it is not much better than AM1, > and so let it fall into disuse? Actually, SAM1 performs better than AM1 in most cases for CHON and the halogens. We have parameters for Si, S, P that are better than AM1 as well, especially for hypervalent species. The TM parameters for Fe, Cu, and Zn are basically completed and others are underway. > 3) I think it is offered in AMPAC; does any other package have it? Currently Semichem's AMPAC is the only program in which it has been implemented, but we expect other vendors to put it in when the theoretical paper and parameters are published. References: ----------- (1) [CI paper] Liotard, D.L.; Holder, A.J. J. Chem. Inf. Comput. Sci. 1999, 39, 587. (2) [SAM1] Dewar, M. J. S.; Jie, C.; Yu, G. Tetrahedron 1993, 23, 5003. (3) [SAM1] Holder, A. J.; Dennington, R. D.; Jie, C. Tetrahedron 1994, 50, 627. (4) [SAM1] Holder, A. J.; Evleth, E. M. in Modeling the Hydrogen Bond; Smith, D. A.; American Chemical Society, Washington, DC, 1994; p 113. Regards, Andy Holder -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- UUUU UUU MMM MMKK KKKK CCCC | ANDREW J. HOLDER UU U MM MMK K CC CC | Assoc. Prof. of Comp./Org. Chemistry UU U MMM M MK KK CCC | Dept. of Chemistry UU U M MM MK KK CC CC | University of Missouri-Kansas City UUUUU MMM M MMKK KK CCCC | Kansas City, MO 64110 KK | holdera@umkc.edu K | (816) 235-2293, FAX (816) 235-6543 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@server.ccl.net Tue Feb 29 11:25:03 2000 Received: from server.theo.chemie.tu-muenchen.de (server.theo.chemie.tu-muenchen.de [129.187.122.65]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA27412 for ; Tue, 29 Feb 2000 11:25:02 -0500 Received: from localhost (krawczyk@localhost) by server.theo.chemie.tu-muenchen.de (8.9.3/8.9.3) with ESMTP id RAA29839; Tue, 29 Feb 2000 17:24:04 +0100 Date: Tue, 29 Feb 2000 17:24:04 +0100 (CET) From: Robert Krawczyk Reply-To: robert.krawczyk@gmx.de To: Yubo Fan cc: chemistry@ccl.net Subject: Re: CCL:Text file transfer between linux and dos In-Reply-To: <38BB6FD2.90708C33@guomai.sh.cn> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 29 Feb 2000, Yubo Fan wrote: > Hi, > > I have installed Windows 98 and RedHat Linux 6.1 on my PC. Usually I > edit G98 input file on Windows 98. The problem is when I start Linux and > mount the DOS partitions, I cannot copy the input files correctly. "^M" This is due to the different line end. On MS-DOS the line ands with a CR/LF-Pair, UNIX uses LF. You will need the freely available utilities dos2unix or you can use (X)Emacs to convert the line ends (query replace). Hope that helps... Robert > was added to the end of each lines. They cannot work by G98. > > I need some help. Is there a way to copy the files by ascii way (not > binary way). > > Thanks in advance > > Y. Fan > > -- > ============================================================= > Yubo Fan Email: yubofan@guomai.sh.cn > Organic Synthesis Lab > The Department of Chemistry > Fudan University Phone: 8621-65648139 > No. 220 Handan Road Fax: 8621-65641740 > Shanghai, 200433 > P. R. China > ============================================================= > > > > > > -= 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 > > > > > ----------------------------------------------- Robert P. Krawczyk Lehrstuhl fuer Theoretische Chemie TU Muenchen Lichtenbergstr. 4 85747 Garching Tel.: +49 89 289 - 13618 Fax.: +49 89 289 - 13622 e-mail: robert.krawczyk@gmx.de ----------------------------------------------- From chemistry-request@server.ccl.net Tue Feb 29 11:53:15 2000 Received: from sinamaica.ciens.luz.ve (sinamaica.ciens.luz.ve [150.185.192.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA27606 for ; Tue, 29 Feb 2000 11:53:12 -0500 From: javier@sinamaica.ciens.luz.ve Received: from localhost (javier@localhost) by sinamaica.ciens.luz.ve (8.9.3/8.9.3) with ESMTP id BAA04705 for ; Mon, 28 Feb 2000 01:47:22 -0400 Date: Mon, 28 Feb 2000 01:47:22 -0400 (VET) To: chemistry@ccl.net Subject: How to construct a basis set? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all CLL netters I am working around to construct a atomic basis set. Anyone has information about to construct it from the begining. With begining i means to start from the first gaussian function until obtain the complete basis. I don`t want to modify a basis. I have some question. How are contructed the basis set? Is there some method to construct it from cero? Where can i get information on how to construct a basis set? Thanks to all, I will make a summary of all responses. Javier Hernnadez javierh@sinamaica.ciens.luz.ve Lab. Quimica Inorganica Teorica Facultad de Ciencias La Universidad del Zulia Marcaibo-Venezuela From chemistry-request@server.ccl.net Tue Feb 29 12:29:42 2000 Received: from gensig.nibsc.ac.uk (gensig.nibsc.ac.uk [193.62.43.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA27832 for ; Tue, 29 Feb 2000 12:29:40 -0500 Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by gensig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id RAA08592 for ; Tue, 29 Feb 2000 17:28:56 GMT Message-ID: <38BC01C0.95A06A7A@nibsc.ac.uk> Date: Tue, 29 Feb 2000 17:28:32 +0000 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: Re: CCL:Text file transfer between linux and dos References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL Here is a short perl script (crlf.pl) that will fix this problem for you. The usage is: crlf.pl dosfile.txt > unixfile.txt Hope this helps Mark F ----quote--- #!/usr/local/bin/perl while (<>) { $a=$_; $a =~ s/[\012]//; $a =~ s/[\015]//; print "$a\n"; } ---unquote--- Robert Krawczyk wrote: > On Tue, 29 Feb 2000, Yubo Fan wrote: > > > Hi, > > > > I have installed Windows 98 and RedHat Linux 6.1 on my PC. Usually I > > edit G98 input file on Windows 98. The problem is when I start Linux and > > mount the DOS partitions, I cannot copy the input files correctly. "^M" > > This is due to the different line end. On MS-DOS the line ands with a > CR/LF-Pair, UNIX uses LF. You will need the freely available utilities > dos2unix or you can use (X)Emacs to convert the line ends (query replace). > > Hope that helps... > > Robert > > > was added to the end of each lines. They cannot work by G98. > > > > I need some help. Is there a way to copy the files by ascii way (not > > binary way). > > > > Thanks in advance > > > > Y. Fan > > > > -- > > ============================================================= > > Yubo Fan Email: yubofan@guomai.sh.cn > > Organic Synthesis Lab > > The Department of Chemistry > > Fudan University Phone: 8621-65648139 > > No. 220 Handan Road Fax: 8621-65641740 > > Shanghai, 200433 > > P. R. China > > ============================================================= > > > > > > > > > > > > > > > > > > > > > > ----------------------------------------------- > Robert P. Krawczyk > Lehrstuhl fuer Theoretische Chemie > TU Muenchen > Lichtenbergstr. 4 > 85747 Garching > > Tel.: +49 89 289 - 13618 > Fax.: +49 89 289 - 13622 > e-mail: robert.krawczyk@gmx.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 -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@server.ccl.net Tue Feb 29 12:48:22 2000 Received: from Lilly.com (inet.d48.lilly.com [40.33.1.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA28022 for ; Tue, 29 Feb 2000 12:48:22 -0500 Received: from LILLY.COM ([40.25.2.46]) by INET.D48.LILLY.COM (PMDF V5.2-31 #34229) with ESMTP id <01JMHATWOXF8004UQO@INET.D48.LILLY.COM> for chemistry@ccl.net; Tue, 29 Feb 2000 12:45:49 EST Received: from aammta1.d51.lilly.com (aammta1.d51.lilly.com [40.1.129.162]) by CLAVIN.D51.LILLY.COM (PMDF V5.2-31 #34229) with SMTP id <01JMHATVKN3I0048FL@CLAVIN.D51.LILLY.COM> for chemistry@ccl.net; Tue, 29 Feb 2000 12:45:48 -0500 (EST) Received: by aammta1.d51.lilly.com(Lotus SMTP MTA v4.6.6 Hotfix2 (917.1 10-15-1999)) id 05256894.00619266 ; Tue, 29 Feb 2000 12:45:44 -0500 Date: Tue, 29 Feb 2000 12:45:35 -0500 From: Richard W Harper Subject: Re: CCL:Text file transfer between linux and dos To: chemistry@ccl.net Message-id: <05256894.006190D4.00@aammta1.d51.lilly.com> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-disposition: inline X-Lotus-FromDomain: LILLY Try mounting the disk from which you are copying the file with the '-auto' option. This enables conversion of the text files to Linux format (strips the CR/LF's and replaces with linefeeds - \n). It only operates on text files, not binary files. Dick Harper rwharper@lilly.com Yubo Fan on 02/29/2000 02:05:57 AM To: CHEMISTRY@ccl.net cc: Subject: CCL:Text file transfer between linux and dos Hi, I have installed Windows 98 and RedHat Linux 6.1 on my PC. Usually I edit G98 input file on Windows 98. The problem is when I start Linux and mount the DOS partitions, I cannot copy the input files correctly. "^M" was added to the end of each lines. They cannot work by G98. I need some help. Is there a way to copy the files by ascii way (not binary way). Thanks in advance Y. Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= -= 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 Tue Feb 29 12:40:56 2000 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 MAA27956 for ; Tue, 29 Feb 2000 12:40:56 -0500 Received: from mailbox.syr.edu (syru33-131.syr.edu [128.230.33.131]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id MAA16517; Tue, 29 Feb 2000 12:40:08 -0500 (EST) Message-ID: <38BC042C.9C535DA1@mailbox.syr.edu> Date: Tue, 29 Feb 2000 12:38:52 -0500 From: "Martin L. Sage" X-Mailer: Mozilla 4.61 [en] (OS/2; I) X-Accept-Language: en MIME-Version: 1.0 To: Yubo Fan CC: CHEMISTRY@ccl.net Subject: Re: CCL:Text file transfer between linux and dos References: <38BB6FD2.90708C33@guomai.sh.cn> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Run the program dos2unix on each file. If you do not have that program do the following: tr -d \\015 < 'file name' > 'new file name' where 'file name' is the name of the file you have in the mounted DOS partition including path and 'new file name' is the name of the file including path where you want the file to reside for use in Linux. If you want it to stay where it was and keep the same name you must change the name in the 'tr' operation and use 'mv' to change it back to the original name. Yubo Fan wrote: > > Hi, > > I have installed Windows 98 and RedHat Linux 6.1 on my PC. Usually I > edit G98 input file on Windows 98. The problem is when I start Linux and > mount the DOS partitions, I cannot copy the input files correctly. "^M" > was added to the end of each lines. They cannot work by G98. > > I need some help. Is there a way to copy the files by ascii way (not > binary way). > > Thanks in advance > > Y. Fan > > -- > ============================================================= > Yubo Fan Email: yubofan@guomai.sh.cn > Organic Synthesis Lab > The Department of Chemistry > Fudan University Phone: 8621-65648139 > No. 220 Handan Road Fax: 8621-65641740 > Shanghai, 200433 > P. R. China > ============================================================= > > -= 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 Tue Feb 29 12:08:43 2000 Received: from sinamaica.ciens.luz.ve (sinamaica.ciens.luz.ve [150.185.192.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA27732 for ; Tue, 29 Feb 2000 12:08:04 -0500 Received: from localhost (nestor@localhost) by sinamaica.ciens.luz.ve (8.9.3/8.9.3) with ESMTP id CAA04765; Mon, 28 Feb 2000 02:03:38 -0400 Date: Mon, 28 Feb 2000 02:03:38 -0400 (VET) From: Nestor Cubillan To: Yubo Fan cc: CHEMISTRY@ccl.net Subject: Re: CCL:Text file transfer between linux and dos In-Reply-To: <38BB6FD2.90708C33@guomai.sh.cn> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > I have installed Windows 98 and RedHat Linux 6.1 on my PC. Usually I > edit G98 input file on Windows 98. The problem is when I start Linux and > mount the DOS partitions, I cannot copy the input files correctly. "^M" > was added to the end of each lines. this is a diference between text format. this problem is solve with a perl script. there is a script called d2u-u2d: http://www.ftls.org/en/examples/perl-tools/d2u-u2d.shtml They cannot work by G98. > I need some help. Is there a way to copy the files by ascii way (not > binary way). i edit my file with vi editor. best regards > > > > From chemistry-request@server.ccl.net Tue Feb 29 12:08:33 2000 Received: from sdnt1.Acadia-SD (mail.acadia-pharm.com [209.77.18.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA27734 for ; Tue, 29 Feb 2000 12:08:32 -0500 Received: by sdnt1 with Internet Mail Service (5.5.2650.21) id ; Tue, 29 Feb 2000 09:05:26 -0800 Message-ID: <15189A4705A8D31189B700805F85410B1D8022@sdnt1> From: Daniel Severance To: "CCL (E-mail)" Subject: Summary of people and methods for GPCR drug discovery Date: Tue, 29 Feb 2000 09:05:25 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Hi, Here is the promised summary - original title - GPCRs and other non-structural targets P.S. I'm always happy to hear from others (industry/academic) working on these problems! -------------------------------------------------------------------------- Daniel Severance wrote: > > Hi, > Does anyone have a summary of what research groups are working on > computational methods for dealing with things where no structures are known? > I.e., given the structures of a series of small molecules and their > activities, trying to infer something about what interactions must be > important? > Also, for those of you who may have hired people to work on these kinds > of problems - what background have you found is best (assuming they did > something different as a student). Thanks. > Feel free to e-mail me directly and I'll summarize to the list. > Dan > Hi Dan, There are quite a few groups that are modeling GPCRs, although the process involves quite a bit of manual effort in terms of validation and refinement. Here is a small list: Weinstein (Mt. Sinai medical) Perez (ETS d'Enginyers Industrials) Donnelly (University of Leeds) Juretic (University of Split) Deber (University of Toronto) Reynolds (University of Essex) Mosberg (University of Michigan) Ferguson (University of Minnesota) Teeter (Boston College) Hibert (Marion Merrell Dow) Sylte (University of Tromso) Jacobson (NIH) Reggio (Kennesaw Valley State University) Parrill (University of Memphis - we have several publications in press, but none yet in print. I would be happy to send you preprints if you are interested) The earlier people in the list are more involved in methods development, and the latter people are applications-oriented. The other part of your question, modeling an active site from ligands (in cases other than GPCRs), can be classified as pseudoreceptor modeling. I know that David Rogers, Colin McMartin, and David Walters have all published in this area. -Abby ____________________________________________ Abby L. Parrill (901)678-2638 Assistant Professor (901)678-3447 Department of Chemistry University of Memphis Memphis, TN 38152 aparrill@memphis.edu Computational Research on Materials Institute at The University of Memphis (CROMIUM) ___________________________________________________________________ In our group in Barcelona there are people working in homology modelling of GPCR's. We are also working in 3D-QSAR studies with our software MIPSIM ( http://www1.imim.es/mipsim) Take care Jordi -- Jordi Villa i Freixa jorgevil@usc.edu Department of Chemistry University of Southern California Los Angeles, CA, USA, 90089-1062 Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 ------------------------------------------------------------- From: Leonardo De Maria [leonardo@ucmb.ulb.ac.be] Sent: Thursday, February 17, 2000 12:12 AM To: Daniel Severance Subject: Re: CCL:GPCRs and other non-structural targets Hello Daniel, there is a person in our group working on GPCRs. His name is Cedrid Govaerts. You can reach him at : cedric@ucmb.ulb.ac.be Bye, Leonardo +--------------------------------------------------+ | Leonardo De Maria | | Unite Conformation de Macromolecules Biologiques | ! Universite Libre de Bruxelles | | Av. F.D. Roosevelt 50 - CP160/16 | | B-1050 Bruxelles | | Tel: 0032 2 6485200 - FAX 0032 2 6488954 | | e-mail: leonardo@ucmb.ulb.ac.be | | | | On leave of absence from Centro Internacional de | | Fisica, Bogota-COLOMBIA | +--------------------------------------------------+ Hi Dan, how are you? We are still working on that sort of thing here in Wollongong (Bremner, Griffith) and have just had two things published: Griffith, R., Bremner, J.B., Coban, B., 'Docking Derived Pharmacophores >from Models of Receptor-Ligand Complexes', Book Chapter in 'Pharmacophore Perception, Development, and Use in Drug Design', O. F. Guner (Ed.). International University Line, 2000, San Diego, pp: 385-408. Bremner, J.B., Griffith, R., Coban, B., Groenewoud., K.M., and Yates, B.F., 'Pharmacophore Development and Ligand Design for alpha1-Adrenoceptor Subtype Selective Antagonists', Biorg.Med.Chem., 2000, 8, 201-214. I would be extremely interested in hearing who else responds to you! Cheers Renate -- Dr. Renate Griffith Phone: +61 (0)2 4221 3516 Research Fellow Fax: +61 (0)2 4221 4287 Department of Chemistry Email: renate_griffith@uow.edu.au University of Wollongong Northfields Ave Wollongong, NSW 2522 Australia --------------------------------------------------------------- Dan, You're really asking about QSAR groups (Quantitative Structure-Activity Relationships). There are a relatively small number of groups in the world who develop new QSAR methods, there are many more who use these methods. However if you're hiring someone you need to get someone with experience as it is easy to fall into traps using these methods: eg finding chance correlations; overfitting the SAR model; overtraining if using a neural net; incorrectly validating; poor choose of molecular descriptors etc. I work in small group lead by Frank Burden at Monash University where we have found new robust ways to do this. Much of our recent work is published in J. Med. Chem., QSAR, and J. Chem. Inf. Comput. Sci. Other groups include Yvonne Martin's at Abbott, Martyn Ford/David Livingston at Uni of Portsmouth, people associated with Toshio Fujita at Kyoto Uni., Hanch/Leo's people at Pomona College. Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC 3169 http://www.csiro.au Australia http://www.molsci.csiro.au -------------------------------------------------------------------- Hi Dan, You might have a look at www.opioid.umn.edu and papers published by David M. Ferguson et al over the last few years. The recent issue (Feb. 2000) of J. Med. Chem. could be one starting point, if you are interested in opioid literature. -subramanian.g some of the other people who have contributed to the GPCR field are Gilda H. Loew, Henry I. Mosberg, H. Weinstein govindan subramanian [vaishnavi66@hotmail.com] ---------------------------------------------------------- From: wsteinmetz [wsteinmetz@POMONA.EDU] Groups who employ three-dimensional (3D) QSAR methods such as CoMFA (comparative molecular field analysis) require the structures for a set of molecules. In most cases the structures are generated using methods of molecular modeling, either via quantum mechanics or molecular mechanics. Hence, run a search of the literature using CoMFA as your keyword and you will generate a list of groups. ------------------------------------------------------------------ ____________________________________________________ Daniel L. Severance Ph.D. Computational Chemistry ACADIA Pharmaceuticals 3911 Sorrento Valley Boulevard San Diego CA 92121-1402 USA phone (858) 558 2871 fax (858) 558 2872 dseverance@acadia-pharm.com www.acadia-pharm.com From chemistry-request@server.ccl.net Tue Feb 29 13:17:14 2000 Received: from mailsrv.engr.uconn.edu (mailsrv.engr.uconn.edu [137.99.21.179]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA28326 for ; Tue, 29 Feb 2000 13:17:13 -0500 Received: from engr.uconn.edu (IDENT:bhupen@camd [137.99.9.39]) by mailsrv.engr.uconn.edu (8.9.1a/8.9.1) with ESMTP id NAA03884 for ; Tue, 29 Feb 2000 13:19:19 -0500 (EST) Sender: bhupen@engr.uconn.edu Message-ID: <38BBEBBD.93CEBE07@engr.uconn.edu> Date: Tue, 29 Feb 2000 10:54:37 -0500 From: Bhupendra Wakankar Organization: University of Connecticut X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.5-15smp i686) X-Accept-Language: en MIME-Version: 1.0 To: CCL_posting Subject: NT parallel cluster Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, Hi. We have 6 computers in our lab (4 running on WINNT and 2 on RedHat 6.0). I use the Linux PC's for my computations while the 4 NT PC's stay relatively idle. All these PC's are fairly powerful (> 400MHz multiprocessor Pentiums) and thus have untapped number crunching power. I am wondering if it is possible to build a parallel cluster using these 4 NT PC's (and better still, using all 6 PC's). Almost all network of PC clusters that I read about on the web run under Linux. Is there any particular reason for not choosing NT (lack of parallel programs perhaps ?). I would also like to know if there are any DFT programs (parallel/single processor, free/commercial) running on Windows NT? Thanks in advance, Regards, Bhupendra From chemistry-request@server.ccl.net Tue Feb 29 13:32:32 2000 Received: from ml-firewall.ml.wpafb.af.mil (firewall-user@ml-firewall.ml.wpafb.af.mil [134.131.90.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA28484 for ; Tue, 29 Feb 2000 13:32:32 -0500 Received: by ml-firewall.ml.wpafb.af.mil; id NAA06077; Tue, 29 Feb 2000 13:31:55 -0500 (EST) Received: from riker.ml.wpafb.af.mil(134.131.35.6) by ml-firewall.ml.wpafb.af.mil via smap (V5.0) id xma005880; Tue, 29 Feb 00 13:31:16 -0500 Received: from Picard.ml.wpafb.af.mil (picard.ml.wpafb.af.mil [134.131.35.26]) by nsrhost.ml.wpafb.af.mil (8.8.6 (PHNE_14041)/8.8.6) with ESMTP id NAA29802 for ; Tue, 29 Feb 2000 13:31:15 -0500 (EST) Received: (from duanx@localhost) by Picard.ml.wpafb.af.mil id NAA21407; Tue, 29 Feb 2000 13:31:07 -0500 (EST) Date: Tue, 29 Feb 2000 13:31:04 -0500 (EST) From: "Xianofeng . Duan MLBP CON" To: chemistry@ccl.net Subject: mount zip/cdrom on linux? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: We set up a linux to run G98. Frequently we need to trasfer input and output files to zip disks. Since only root user has privilege to mount/unmount zip/cdrom, now the question is: Are there are any ways for a general user to do so without login to the root account? I asked the same question on a linux forum, but so far there are no answers. Thanks! **************************************** Xiaofeng Duan, Ph.D. AFRL/MLBP, Bldg. 654 2941 P St. Ste. 1 Wright-Patterson AFB, OH 45433 **************************************** From chemistry-request@server.ccl.net Tue Feb 29 11:59:07 2000 Received: from kasei.materials.ox.ac.uk (kasei.materials.ox.ac.uk [163.1.64.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA27664 for ; Tue, 29 Feb 2000 11:59:05 -0500 Received: from localhost (hfield@localhost) by kasei.materials.ox.ac.uk (8.9.3/8.9.3) with ESMTP id QAA03320 for ; Tue, 29 Feb 2000 16:57:14 GMT X-Authentication-Warning: kasei.materials.ox.ac.uk: hfield owned process doing -bs Date: Tue, 29 Feb 2000 16:57:14 +0000 (GMT) From: Andrew Horsfield X-Sender: hfield@kasei.materials.ox.ac.uk Reply-To: Andrew Horsfield To: Computational Chemistry List Subject: Lebedev integral meshes Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am interested in implementing the Lebedev integral meshes for integrals on the unit sphere. I have found the references to the journals in which the meshes are given, but cannot track down the journals themselves. Is there a table of points in some electronic format that someone can hand me? Cheers, Andrew +----------------------------------------------------+ Andrew Horsfield e-mail: horsfield@fecit.co.uk FECIT, 2 Longwalk Road, Stockley Park, Uxbridge, Middlesex UB11 1AB, United Kingdom. phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422 +----------------------------------------------------+ From chemistry-request@server.ccl.net Tue Feb 29 14:36:36 2000 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA29107 for ; Tue, 29 Feb 2000 14:36:35 -0500 Received: from hermes.scripps.edu (hermes.scripps.edu [137.131.200.6]) by relay1.scripps.edu (8.9.3/TSRI-3.1.0r) with ESMTP id LAA11220 for ; Tue, 29 Feb 2000 11:34:01 -0800 (PST) Received: from scripps.edu (bohr [137.131.252.68]) by hermes.scripps.edu (8.9.2/TSRI-3.0h) with ESMTP id LAA17144; Tue, 29 Feb 2000 11:33:58 -0800 (PST) Sender: ullmann@scripps.edu Message-ID: <38BC1F3F.F67CDBED@scripps.edu> Date: Tue, 29 Feb 2000 11:34:23 -0800 From: "G. Matthias Ullmann" X-Mailer: Mozilla 4.61 [en] (X11; U; Linux 2.0.36 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Math Problem: Polynomials and Matrices Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I have the following mathematical problem: Given is a polynomial in x: 0 = sum_{i=0}^{N} (-1)^i a_i x^i The roots of this polynomial {x_1 .... x_N} are all real. The question is: Is there an unambiguous way to find a symmetric matrix B that has the eigenvalues {x_1 ... x_N}, when the diagonal elements of B are known? A related problem is: Which unitary transformation transforms the diagonal matrix X (with the diagonal elements {x_1 ... x_N}) to a symmetric matrix B with known diagonal elements? Any help or hints what to look for is very much appreciated. Thank you in advance. Matthias -- ----------------------------------------- G. Matthias Ullmann Department of Molecular Biology The Scripps Research Institute 10550 N. Torrey Pines Rd., TPC-15 La Jolla, CA 92037 USA Phone: 858-784-8889 Fax: 858-784-8896 e-mail: ullmann@scripps.edu www: http://www.scripps.edu/~ullmann From chemistry-request@server.ccl.net Tue Feb 29 14:34:05 2000 Received: from Lilly.com (carltn.d48.lilly.com [40.33.1.27]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA29090 for ; Tue, 29 Feb 2000 14:34:04 -0500 Received: from LILLY.COM ([40.59.1.39]) by CARLTN.D48.LILLY.COM (PMDF V5.2-31 #34229) with ESMTP id <01JMHEDK5VI6004JQ1@CARLTN.D48.LILLY.COM> for chemistry@ccl.net; Tue, 29 Feb 2000 14:27:10 EST Received: from aammta1.d51.lilly.com (aammta1.d51.lilly.com [40.1.129.162]) by NEWMAN.D52.LILLY.COM (PMDF V5.2-31 #34229) with SMTP id <01JMHEIX9R920043K3@NEWMAN.D52.LILLY.COM> for chemistry@ccl.net; Tue, 29 Feb 2000 14:31:30 +0000 (GMT) Received: by aammta1.d51.lilly.com(Lotus SMTP MTA v4.6.6 Hotfix2 (917.1 10-15-1999)) id 05256894.006B3F82 ; Tue, 29 Feb 2000 14:31:26 -0500 Date: Tue, 29 Feb 2000 14:31:16 -0500 From: Richard W Harper Subject: CCL:mount zip/cdrom on linux? To: chemistry@ccl.net Message-id: <05256894.006B3E60.00@aammta1.d51.lilly.com> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii Content-disposition: inline X-Lotus-FromDomain: LILLY If the file entry in the '/etc/fstab' file (which lists devices to be mounted) with the 'user' option, then ordinary users can mount and unmount the device. Otherwise, SU privileges are required. Of course you have to pursuade someone with superuser privileges to edit the file. Dick Harper rwharper@lilly.com ---------------------- Forwarded by Richard W Harper/AM/LLY on 02/29/2000 02:28 PM --------------------------- "Xianofeng . Duan MLBP CON" on 02/29/2000 01:31:04 PM To: chemistry@ccl.net cc: Subject: CCL:mount zip/cdrom on linux? Dear CCLers: We set up a linux to run G98. Frequently we need to trasfer input and output files to zip disks. Since only root user has privilege to mount/unmount zip/cdrom, now the question is: Are there are any ways for a general user to do so without login to the root account? I asked the same question on a linux forum, but so far there are no answers. Thanks! **************************************** Xiaofeng Duan, Ph.D. AFRL/MLBP, Bldg. 654 2941 P St. Ste. 1 Wright-Patterson AFB, OH 45433 **************************************** -= 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 Tue Feb 29 14:33:52 2000 Received: from ice.lanl.gov (ice.lanl.gov [128.165.22.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA29084 for ; Tue, 29 Feb 2000 14:33:51 -0500 Received: from localhost (localhost [[UNIX: localhost]]) by ice.lanl.gov (8.9.3/8.9.3) id MAA26831; Tue, 29 Feb 2000 12:33:13 -0700 From: Matt Challacombe Reply-To: MChalla@T12.LANL.Gov Organization: Group T-12, Theoretical Chemistry and Molecular Physics To: "Xianofeng . Duan MLBP CON" , chemistry@ccl.net Subject: Re: CCL:mount zip/cdrom on linux? Date: Tue, 29 Feb 2000 12:27:43 -0700 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: In-Reply-To: MIME-Version: 1.0 Message-Id: <00022912331300.26760@ice> Content-Transfer-Encoding: 8bit Hi Xianofeng, In your /etc/fstab include a line like this: /dev/sdb1 /zip ext2 noauto,user 0 0 The user option allows the user to mount the disk. See the mount man page as well. -Matt +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ + Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ + + Los Alamos National Laboratory email: mchalla@t12.lanl.gov + + Theoretical Division vmail: (505) 698-4112 + + Group T-12, Mail Stop B268 phone: (505) 665-5905 + + Los Alamos, New Mexico 87545 fax: (505) 665-3909 + + + + "The secret to mountain biking is pretty simple. The slower you go + + the more likely it is you'll crash." -- Julie Furtado + +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ On Tue, 29 Feb 2000, Xianofeng . Duan MLBP CON wrote: > Dear CCLers: > We set up a linux to run G98. Frequently we need to trasfer input and > output files to zip disks. Since only root user has privilege to > mount/unmount zip/cdrom, now the question is: Are there are any ways for > a general user to do so without login to the root account? > I asked the same question on a linux forum, but so far there are no answers. > > Thanks! > > **************************************** > Xiaofeng Duan, Ph.D. > AFRL/MLBP, Bldg. 654 > 2941 P St. Ste. 1 > Wright-Patterson AFB, OH 45433 > **************************************** > > > -= 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 Tue Feb 29 16:02:53 2000 Received: from itbsdi1.kccd.cc.ca.us (root@itbsdi1.kccd.cc.ca.us [198.189.148.70]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA29820 for ; Tue, 29 Feb 2000 16:02:51 -0500 From: kvaughan@bc.cc.ca.us Received: from bc377 (host-243-140.bc.cc.ca.us [198.189.243.140]) by itbsdi1.kccd.cc.ca.us (8.9.0/8.9.0) with SMTP id MAA14871; Tue, 29 Feb 2000 12:48:29 -0800 (PST) Message-Id: <3.0.5.32.20000229125645.00b06980@pop.kern.cc.ca.us> X-Sender: kvaughan@pop.kern.cc.ca.us X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Tue, 29 Feb 2000 12:56:45 -0800 To: "Xianofeng . Duan MLBP CON" Subject: Re: CCL:mount zip/cdrom on linux? Cc: chemistry@ccl.net In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 01:31 PM 2/29/00 -0500, you wrote: >Dear CCLers: > We set up a linux to run G98. Frequently we need to trasfer input and >output files to zip disks. Since only root user has privilege to >mount/unmount zip/cdrom, now the question is: Are there are any ways for >a general user to do so without login to the root account? >I asked the same question on a linux forum, but so far there are no answers. I believe that you can add "users" and perhaps "auto" to the options part of the appropriate line in /etc/fstab. I'm uncertain, but the users might also have to be added to a certain group (disk or other?). I believe that "man fstab" may provide more information on this. Kenward ---------------------------------------------------- .'^~;,_ Dr. Kenward Vaughan ':,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| Bakersfield, CA 93305 / ', \ 661-395-4243 / o O \ kvaughan@bc.cc.ca.us (oOoOOoOo) ---========--- ???$$MM$$??? ---------------------------------------------------- From chemistry-request@server.ccl.net Tue Feb 29 16:51:26 2000 Received: from classic.chem.msu.su (classic.chem.msu.su [158.250.32.143]) by server.ccl.net (8.8.7/8.8.7) with SMTP id QAA30223 for ; Tue, 29 Feb 2000 16:51:24 -0500 Received: from ras21.icp.rssi.ru ( [194.85.223.62] ) by classic.chem.msu.su (Hethmon Brothers Smtpd) ; Wed, 1 Mar 2000 00:48:07 MSK-3MSD-4,3,5,0,7200,10,5,0,10800 Message-ID: <000c01bf82fe$d4bb9330$3edf55c2@alex> From: "Alex. A. Granovsky" To: "Bhupendra Wakankar" , "CCL_posting" References: <38BBEBBD.93CEBE07@engr.uconn.edu> Subject: Re: CCL:NT parallel cluster Date: Wed, 1 Mar 2000 00:49:17 +0300 Organization: MSU 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 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear Bhupendra Wakankar, You can use parallel version of the PC GAMESS to perform QC calculations on NT clusters. See the PC GAMESS homepages at MSU http://classic/gran/gamess/index.html http://quantum-2.chem.msu.ru/gran/gamess/index.html and at ISU http://www.msg.ameslab.gov/GAMESS/pcgamess.shtml Best regards Alex Granovsky From chemistry-request@server.ccl.net Tue Feb 29 17:43:11 2000 Received: from Post-Office.UH.EDU (Post-Office.UH.EDU [129.7.1.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA30604 for ; Tue, 29 Feb 2000 17:43:11 -0500 Received: from CS.UH.EDU (zeus.cs.uh.edu [129.7.192.1]) by Post-Office.UH.EDU (PMDF V5.2-32 #40812) with SMTP id <0FQP00AEWR2P8R@Post-Office.UH.EDU> for chemistry@ccl.net; Tue, 29 Feb 2000 16:42:25 -0600 (CST) Received: from blackbird.CS.UH.EDU by CS.UH.EDU (COSC/UH-zeus) id AA05134; Tue, 29 Feb 2000 16:42:26 -0600 (CST) Received: by blackbird.CS.UH.EDU (4.1/UH-4.1) id AA00223; Tue, 29 Feb 2000 16:43:06 -0600 (CST) Date: Tue, 29 Feb 2000 16:42:26 -0600 (CST) From: Zdenko Tomasic Subject: Re: CCL:Lebedev integral meshes In-reply-to: To: andrew.horsfield@materials.ox.ac.uk Cc: chemistry@ccl.net Reply-to: zdenko@CS.UH.EDU Message-id: <10002292242.AA05134@CS.UH.EDU> When I needed this, I managed to find out this much: refs: V.I. Lebedev 9th,11th,13th,15th,17th: [1] Zh. vychisl. Mat. mat. Fiz., [15],1,48-54 (1975) (russian) USSR Comput. Math. and Math. Phys. [16], 44-51 (1975) (eng.) 19th,23rd: [2] Zh. vychisl. Mat. mat. Fiz., [16],2,293-306 (1976) (russian) USSR Comput. Math. and Math. Phys. [16], 10-24 (1976) (eng.) 29th: [3] Sib. Matem. Zh. [18],132 (1977) (russian) Siberian Math. J. [18] (1977) (eng.) 35th: (russian PDE conference paper ed. Sobolev) ( my library could never find the right one, apparently there was a conference with the same title the same year but with a different editor) 41st,47th,53rd: (with A.L.Skorokhodov) [4] Ross. Akad. Nauk Dokl. [324],3, (1992) Russian Acad. Sci. Dokl. Math. [45], 3, 587-592 (1992) 59th: [5] Ross. Akad. Nauk Dokl. [338],4, (1994) Russian Acad. Sci. Dokl. Math. [50], 2, 283-286 (1995) Note that data contain errors and have limited(7-8 digits) working precision (as opposed to printed precision - 12-15 digits). Recalculation of solutions to nonlinear equations is not trivial. From chemistry-request@server.ccl.net Tue Feb 29 17:57:50 2000 Received: from chazin.structbio.vanderbilt.edu (root@chazin.structbio.Vanderbilt.Edu [160.129.248.64]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA30736 for ; Tue, 29 Feb 2000 17:57:50 -0500 Received: from structbio.vanderbilt.edu (IDENT:jsmith@chazin [160.129.248.64]) by chazin.structbio.vanderbilt.edu (8.9.3/8.9.3) with ESMTP id RAA01660 for ; Tue, 29 Feb 2000 17:03:15 -0600 Sender: jsmith@chazin.structbio.vanderbilt.edu Message-ID: <38BC5033.D1037C66@structbio.vanderbilt.edu> Date: Tue, 29 Feb 2000 17:03:15 -0600 From: Jarrod Smith Organization: Vanderbilt University X-Mailer: Mozilla 4.6 [en] (X11; I; Linux 2.2.5-22 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:mount zip/cdrom on linux? References: <3.0.5.32.20000229125645.00b06980@pop.kern.cc.ca.us> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit >mount/unmount zip/cdrom, now the question is: Are there are any ways for >a general user to do so without login to the root account? There is a GUI solution to this problem for your Zip drive: http://www.scripps.edu/~jsmith/jazip -- Jarrod A. Smith, Ph.D. Assistant Director, Center for Structural Biology Molecular Graphics and Computation jsmith@structbio.vanderbilt.edu From chemistry-request@server.ccl.net Tue Feb 29 16:23:01 2000 Received: from ns-mx.uiowa.edu (ns-mx.uiowa.edu [128.255.56.78]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA29950 for ; Tue, 29 Feb 2000 16:23:00 -0500 Received: from [128.255.72.43] (his.chem.uiowa.edu [128.255.72.43]) by ns-mx.uiowa.edu (8.9.3/8.9.1/ns-mx-1.7) with ESMTP id PAA33606 for ; Tue, 29 Feb 2000 15:22:25 -0600 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 29 Feb 2000 15:22:10 -0600 To: CHEMISTRY@ccl.net From: "Jan H. Jensen" Subject: 33rd Midwest Theoretical Chemistry Conference +++++++++++++++++++++++++++++++++++++++++++++ FIRST ANNOUNCEMENT 33rd Midwest Theoretical Chemistry Conference University of Iowa Iowa City, IA May 25-27, 2000 +++++++++++++++++++++++++++++++++++++++++++++ Please mark your calendar and plan to attend the 33rd Midwest Theoretical Chemistry Conference to be held May 25-27, 2000, at the University of Iowa and hosted by the Department of Chemistry. The conference covers all areas of theoretical and computational chemistry. Contributions are invited from all researchers, including undergraduate students, graduate students, postdocs, faculty, corporate scientists, and government researchers. A broad cross section of theoretical and computational topics is expected to be represented in both the oral and poster sessions. Traditionally, this meeting has served as a unique opportunity for students and postdocs to give short oral presentations on their current research. More information on the conference, including the registration form, can be obtained at the WWW site http://www.uiowa.edu/~mwtcc. I look forward to seeing you this May. Jan H. Jensen, Organizer =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jan H. Jensen Assistant Professor Department of Chemistry jan-jensen@uiowa.edu University of Iowa Phone:(319) 335-1108 Iowa City, IA 52242 FAX: (319) 335-1270 http://www.uiowa.edu/~chemdept/faculty/jensen/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@server.ccl.net Tue Feb 29 16:33:49 2000 Received: from wcse1.phy.cam.ac.uk (eximuser@wcse1.phy.cam.ac.uk [131.111.49.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA30069 for ; Tue, 29 Feb 2000 16:33:48 -0500 Received: from tcm2.phy.cam.ac.uk ([131.111.72.38] ident=mdt26) by wcse1.phy.cam.ac.uk with esmtp (Exim 2.05 #2) id 12PuGR-0000yX-00 for chemistry@ccl.net; Tue, 29 Feb 2000 21:33:07 +0000 Received: from mdt26 (helo=localhost) by tcm2.phy.cam.ac.uk with local-smtp (Exim 2.01 #1) for chemistry@ccl.net id 12PuGR-0006Yh-00; Tue, 29 Feb 2000 21:33:07 +0000 Date: Tue, 29 Feb 2000 21:33:07 +0000 (GMT) From: Michael Towler To: CCL Subject: QMC Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Quantum chemistry problem from a physics lab: I/we are looking for a package to generate ground and excited state wave functions for molecules to be used as trial wave functions in our quantum Monte Carlo code (extending our previous work on solids). Such a package needs to have the the following capabilities: (1) HF/DFT/CIS (CIS being the tricky but essential one to find). (2) Freeform input pseudopotentials. We have very specific pseudos tabulated on a grid for use in our QMC program. These neeed to be expanded in a basis set of Gaussians times powers of r for use in quantum chemistry packages. Because we need very accurate expansions, we require as few restrictions as possible on (a) the range of powers of r and (b) on the maximum number of basis functions in the expansion. (3) It needs to be fast and available for parallel platforms. In the latter case we have access to a Hitachi SR2201, a 64 CPU (R12000) SGI Origin 2000 and a Cray T3E. We need to do some very big CIS calculations which are beyond the reach of workstations. (4) not outrageously expensive ($$) (5) clearly documented output for conversion into format appropriate for hungry QMC code. Accessible source code would also be nice, but I guess we can do without it. We've been using Gaussian94 to do the above up to now, but it has severe limitations in the area of general ECPs i.e. acknowledged bugs and/or array size limitations which prevent us expanding the pseudos sufficiently accurately.. Gaussian98 appears to have corrected these problems to some extent but for reasons of either non-existence or lack of money it is not available on the parallel machines accessible to us. I don't mean any of the above as a criticism of the otherwise lovely Gaussian package - but these are genuine problems that I can't see a practical way around at the moment. I'll summarize any replies. Thanks, Mike PS: If anyone has a piece of code to perform an expansion of an arbitrary pseudopotential in a basis of gaussians times powers of r, and is prepared to share its secrets with me, I'd be interested to compare it with my own attempt.. ;-) ------------------------------------------------------------------------- Dr. Mike Towler (mdt26@phy.cam.ac.uk) Theory of Condensed Matter (Rm 524) Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK Tel. +44-(0)1223-337459 Fax. +44-(0)1223-337356 ----------------WWW: http://www.tcm.phy.cam.ac.uk/~mdt26/ --------------- From chemistry-request@server.ccl.net Tue Feb 29 22:11:35 2000 Received: from mail2.panix.com (mail2.panix.com [166.84.0.213]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA31955 for ; Tue, 29 Feb 2000 22:11:35 -0500 From: kynn@panix.com Received: from panix3.panix.com (panix3.panix.com [166.84.0.228]) by mail2.panix.com (Postfix) with ESMTP id 4FA80156C9; Tue, 29 Feb 2000 22:10:55 -0500 (EST) Received: (from kynn@localhost) by panix3.panix.com (8.8.8/8.7.1/PanixN1.0) id WAA20609; Tue, 29 Feb 2000 22:10:55 -0500 (EST) Date: Tue, 29 Feb 2000 22:10:55 -0500 (EST) Message-Id: <200003010310.WAA20609@panix3.panix.com> X-Authentication-Warning: panix3.panix.com: kynn set sender to kynn@panix.com using -f To: CHEMISTRY@ccl.net Subject: Yet another WHAM question... Dear CCL'ers: There's a line in Kumar et al.'s paper [1] on the WHAM method that makes no sense to me. It concerns the histogram's required dimensionality. Kumar considers a modified Hamiltonian of the form L ___ \ H = / \lambda_i V_i = V_0 + S --- i=0 That is, the Hamiltonian is a linear combination of L+1 terms with coefficients \lambda_i. Moreover, \lambda_0 is assumed to be identically 1, and the corresponding term V_0 to represent the unmodified Hamiltonian. The remaining terms V_i are restraining potentials, with coupling parameters \lambda_i. (I denote the sum of these last L terms by S; hence the potential energy becomes V_0 + S.) Furthermore, the authors assume that we are interested in determining the density of states as a function of a reaction coordinate \xi. In the appendix to the paper (p. 1020), they write: "When the restraining potential is a function of the coordinate \xi only the dimensionality of the histogram reduces from L + 2 to 2..." It's the "L + 2" that makes no sense to me. I don't see why, in this situation, the dimensionality of the histogram needs to be any larger than 3, even when L > 1. At most we need to histogram the values of V_0, S, and \xi. (If S is entirely a function of \xi, then, as the authors say, we can get away with only two dimensions, namely V_0 and \xi.) To histogram the values of each of the restraining potentials only increases the amount of data that must be collected without providing any obvious benefit (only the sum of these values enters in the WHAM equations). Besides, the restraining potentials are presumably of little intrinsic interest, since they are merely a technical trick to bias the sampling. If all this is true, what's the rationale for histogramming the values of the V_i (0 < i <= L)? Regards, Kynn Jones [1] Kumar, S. et al., J. Comp. Chem. 13(8):1011-1021, 1992