From chemistry-request@server.ccl.net Wed Sep 12 16:42:32 2001 Received: from mail.staff.site.ntu.edu.au ([138.80.69.54]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8CKgV325960 for ; Wed, 12 Sep 2001 16:42:31 -0400 Received: by mail.staff.site.ntu.edu.au with Internet Mail Service (5.5.2653.19) id ; Thu, 13 Sep 2001 06:12:29 +0930 Message-ID: From: Henry Pang To: "'chemistry@ccl.net'" Cc: "'thepangs@yahoogroups.com'" Subject: Alternant hydrocarbons and the film "My Fair Lady" Date: Thu, 13 Sep 2001 06:12:28 +0930 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hi CCL I am interested to find out if my impression CC is a super reductionist field is reasonable. The word "alternant" is found in CC books. Ira Levine (1983), Quantum Chemistry says, "An alternant hydrocarbon is a planar conjugated hydrocarbon in which the carbon atoms can be divided into a starred set and an unstarred set." My several general chemistry books do not mention alternant. I do not find any entry for "alternant hydrocarbon" in the Cambridge International Dictionary of English, Academic Press Dictionary of Science and Technology, but the Concise Oxford Dictionary says, "alternant is alternating, of alternating layers". I do not find any mention in books of cosmology, astronomy, physics, archaeology, anthropology, history, language, linguistics, law, medicine, surgery, politics, metal work, or mass media for example. I do have some idea; alternant is interesting in molecules such as cyclobutadiene, naphthalene, benzyl radical, azulene, cyclopentadienyl radical. I am looking for any discussion regarding what the word "alternant" means in plain English, which other people in the university and community might appreciate as human beings, even though not expert in CC. Please understand I am not being disrespectful or even facetious. Do you recall the award film "My Fair Lady"? Common flower girl Eliza Doolittle asks phonetics expert Professor Higgins to teach her to speak like a lady. Eliza becomes the belle of British society and the Prince takes her hand to lead her to the dance floor at the great Ball. Higgins takes all the credit. As he says, "I knew I could do it." He tells Eliza, but she replies in total defiance, "I do not understand anything you are saying to me. I am too ignorant!" I am not CC, but just an Australian medical doctor. I am just curious about CCL. Forgive me, but CCL seems like an intense activity looking the computer measurements and bond strengths of the Lego blocks put together by my children into interesting creations. CCL day in and day out, seems about finding better ways of computing the minute details of my children's Lego blocks? Questions - 1.Have you any material, which explains "alternant" in plain English for my children, so they might really understand what the animal is in real terms? 2.Have you ever heard of another word "Holism"? Could holism be of any interest to the super reductionist field of CC? Does it really matter to the world or our Universe in any case? (I am disgusted and very sad about New York and the Pentagon) Regards Dr Henry Pang (medical) Australia From chemistry-request@server.ccl.net Thu Sep 13 08:20:59 2001 Received: from luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8DCKw328076 for ; Thu, 13 Sep 2001 08:20:58 -0400 Received: from sbg-ts (localhost [127.0.0.1]) by luc.ac.be (8.9.3/8.9.3) with SMTP id OAA24995; Thu, 13 Sep 2001 14:20:51 +0200 (MET DST) Date: Thu, 13 Sep 2001 14:20:51 +0200 (MET DST) Message-Id: <200109131220.OAA24995@luc.ac.be> X-Sender: lucp1381@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: Henry Pang , chemistry@ccl.net From: sergiusz kwasniewski Subject: Re: CCL:Alternant hydrocarbons Hi, while I was in Exeter under the supervisory of Prof. Fowler, we used the alternant structures to explain certain things about fullerenes. I guess that if you would look for prof. Fowler's book on fullerenes it will certainly be explained for some part. A definition we used for it for my master's thesis goes like this: "An alternant is a bipartite structure that can be partitioned into two subsets of atoms, in a way that an atom of one subset is only surrounded by atoms of the other subset (starred and unstarred atoms)." You could also look into "Clar colouring" schemes like e.g. in reference: G. Brinkmann, P.W. Fowler, "Spiral coding of leapfrog polyhedra", J. Chem. Inf. Comput. Sci. (in press 1998) Hope this helps, Serge ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Thu Sep 13 09:41:02 2001 Received: from mail2.intermedia.net ([206.40.48.152]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8DDf2329945 for ; Thu, 13 Sep 2001 09:41:02 -0400 Received: from inaco.mentecolectiva.com (unverified [66.128.43.140]) by mail2.intermedia.net (Rockliffe SMTPRA 4.5.4) with ESMTP id for ; Thu, 13 Sep 2001 06:41:02 -0700 Message-Id: <5.1.0.14.0.20010913083609.009eb920@mail.mentecolectiva.com> X-Sender: esguerra%mentecolectiva.com@mail.mentecolectiva.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 13 Sep 2001 08:44:48 -0500 To: chemistry@ccl.net From: "Mauricio Esguerra N." Subject: Cluster Boards Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f8DDf2329946 Hello again, This time I would like to ask if any of you with experience building clusters could tell me if it's better to build a cluster using (for say a 6 node cluster) 3 dual motherboards or 6 single motherboards. I am specifically interested in knowing the price-performance relation between these two cases. Thanking your kind help, ################################################################ Mauricio Esguerra Neira Chemist Grupo de Química Teórica Universidad Nacional de Colombia email: esguerra@mentecolectiva.com tel: 57-1-3165000 ext18323 ################################################################ From chemistry-request@server.ccl.net Thu Sep 13 10:39:35 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8DEdZ330999 for ; Thu, 13 Sep 2001 10:39:35 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id KAA16956; Thu, 13 Sep 2001 10:39:23 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3BA0BEE4.B0E2B57F@cornell.edu> Date: Thu, 13 Sep 2001 10:12:53 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Re: CCL:Text vs. HTML formatted postings References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thomas Huber wrote: > Dear friends, > it seems to me, that recently the number of HTML formatted postings on > this list has increased. With the background of worm/virus resistant way > to view email is, at least for me, PINE. Unfortunatly it is not easy to > read HTML formatted emails with PINE. > It would be very kind to 'old-fashioned' guys like myself to avoid HTML > formatted postings. (Hint: In Netscape choose Edit/Preferences/Formatting > and choose 'send plain text'.) > Yours, > Thomas I'm wondering why an "old fashioned" guy would even know HOW to make postings in a non-HTML format using a program such as Netscape if the "old fashioned" guy isn't using Netscape? Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Thu Sep 13 10:42:31 2001 Received: from sungod.ccs.yorku.ca ([130.63.236.104]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8DEgU331054 for ; Thu, 13 Sep 2001 10:42:30 -0400 Received: from mountain.chem.yorku.ca (mountain.chem.yorku.ca [130.63.133.28]) by sungod.ccs.yorku.ca (8.9.3/8.9.3) with SMTP id KAA28847; Thu, 13 Sep 2001 10:42:23 -0400 (EDT) Date: Thu, 13 Sep 2001 10:43:52 -0400 (EDT) From: Rene Fournier X-Sender: renef@mountain.chem.yorku.ca To: Henry Pang cc: "'chemistry@ccl.net'" , "'thepangs@yahoogroups.com'" Subject: Re: CCL:Alternant hydrocarbons and the film "My Fair Lady" In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Dr Pang: To answer your question: >1.Have you any material, which explains "alternant" in plain English ... The word "alternant" shows up in matrix algebra. The "alternant" may be defined as the determinant of a Vandermonde matrix. The 3x3 Vandermonde matrices have this form: 1 a a^2 1 b b^2 1 c c^2 The determinant of this matrix, the ALTERNANT, is equal to (a-b)(b-c)(c-a) = (b-a)(c-b)(c-a) 4x4 Vandermonde matrices have this form: 1 a a^2 a^3 1 b b^2 b^3 1 c c^2 c^3 1 d d^2 d^3 The alternant for this matrix is the product (b-a)(c-a)(d-a)(c-b)(d-b)(d-c) etc... More generally, the product of all differences of a set of n numbers y_1, y_2, y_3, ... y_n is equal to the determinant of the corresponding n x n Vandermonde matrix (alternant) having elements y_1, y_2, y_3, ... y_n on the 2nd column. So for the general n x n case, the alternant is Product_for_all_pairs_i,j_(0 Hi CCL > > I am interested to find out if my impression CC is a super reductionist > field is reasonable. The word "alternant" is found in CC books. Ira Levine > (1983), Quantum Chemistry says, "An alternant hydrocarbon is a planar > conjugated hydrocarbon in which the carbon atoms can be divided into a > starred set and an unstarred set." > > My several general chemistry books do not mention alternant. I do not find > any entry for "alternant hydrocarbon" in the Cambridge International > Dictionary of English, Academic Press Dictionary of Science and Technology, > but the Concise Oxford Dictionary says, "alternant is alternating, of > alternating layers". I do not find any mention in books of cosmology, > astronomy, physics, archaeology, anthropology, history, language, > linguistics, law, medicine, surgery, politics, metal work, or mass media for > example. > > I do have some idea; alternant is interesting in molecules such as > cyclobutadiene, naphthalene, benzyl radical, azulene, cyclopentadienyl > radical. I am looking for any discussion regarding what the word "alternant" > means in plain English, which other people in the university and community > might appreciate as human beings, even though not expert in CC. > > Please understand I am not being disrespectful or even facetious. Do you > recall the award film "My Fair Lady"? Common flower girl Eliza Doolittle > asks phonetics expert Professor Higgins to teach her to speak like a lady. > Eliza becomes the belle of British society and the Prince takes her hand to > lead her to the dance floor at the great Ball. Higgins takes all the credit. > As he says, "I knew I could do it." He tells Eliza, but she replies in total > defiance, "I do not understand anything you are saying to me. I am too > ignorant!" > > I am not CC, but just an Australian medical doctor. I am just curious about > CCL. Forgive me, but CCL seems like an intense activity looking the computer > measurements and bond strengths of the Lego blocks put together by my > children into interesting creations. CCL day in and day out, seems about > finding better ways of computing the minute details of my children's Lego > blocks? > > Questions - > 1.Have you any material, which explains "alternant" in plain English for my > children, so they might really understand what the animal is in real terms? > 2.Have you ever heard of another word "Holism"? Could holism be of any > interest to the super reductionist field of CC? Does it really matter to the > world or our Universe in any case? > > (I am disgusted and very sad about New York and the Pentagon) > > Regards > Dr Henry Pang (medical) > Australia > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Thu Sep 13 12:05:04 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8DG54332477 for ; Thu, 13 Sep 2001 12:05:04 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id MAA21241; Thu, 13 Sep 2001 12:05:03 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Thu, 13 Sep 2001 12:06:44 -0400 (Eastern Daylight Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GJL00JKRTW93T@lvlmail.unitedcatalysts.com>; Thu, 13 Sep 2001 10:07:22 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Thu, 13 Sep 2001 10:12:13 -0400 Content-return: allowed Date: Thu, 13 Sep 2001 10:12:03 -0400 From: "Shobe, Dave" Subject: RE: Alternant hydrocarbons and the film "My Fair Lady" To: "'Henry Pang'" , "'chemistry@ccl.net'" Cc: "'thepangs@yahoogroups.com'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAB1F6@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f8DG54332478 Guess what? Even mathematicians studying graph theory (roughly, the mathematics of line drawings, connectivity, and networks) do not use the word "alternant". Their term is "bipartite". Your definition of "alternant" or "bipartite" is missing an important point: either word means that the vertices/nodes/atoms can be divided into two sets (starred/unstarred or red/blue or whatever) with the property that no two "adjacent" vertices are in the same set. "Adjacent" means that there is a line/edge/bond between the two vertices/atoms. Especially when explaining to children, it might be good to have them, as an exercise, try to do this division into two sets for different graphs/pi-systems, e.g. naphthalene and azulene. They might even discover, on their own, the relationship between alternant-ness and odd cycles. Computational chemistry is more holistic than you might think. One of the problems in computing large molecules is that the wave function of the electrons extends across the entire molecule and even outside of it. If you put several molecules together, there is one wave function for the entire system. It is the job of the theoretical chemist (not quite the same as computational chemist, although there is a large overlap between the two professions) to come up with reductionistic explanations of quantum systems in terms of bonds, interatomic forces, etc. where these are appropriate. In many areas we're still finding new ways to put the "Legos" together. On the other hand, the world's synthetic chemists are indeed making complex and interesting structures from the building blocks. Some of them imitate natural structures, while others are abstract. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Henry Pang [mailto:henry.pang@ntu.edu.au] Sent: Wednesday, September 12, 2001 4:42 PM To: 'chemistry@ccl.net' Cc: 'thepangs@yahoogroups.com' Subject: CCL:Alternant hydrocarbons and the film "My Fair Lady" Hi CCL I am interested to find out if my impression CC is a super reductionist field is reasonable. The word "alternant" is found in CC books. Ira Levine (1983), Quantum Chemistry says, "An alternant hydrocarbon is a planar conjugated hydrocarbon in which the carbon atoms can be divided into a starred set and an unstarred set." My several general chemistry books do not mention alternant. I do not find any entry for "alternant hydrocarbon" in the Cambridge International Dictionary of English, Academic Press Dictionary of Science and Technology, but the Concise Oxford Dictionary says, "alternant is alternating, of alternating layers". I do not find any mention in books of cosmology, astronomy, physics, archaeology, anthropology, history, language, linguistics, law, medicine, surgery, politics, metal work, or mass media for example. I do have some idea; alternant is interesting in molecules such as cyclobutadiene, naphthalene, benzyl radical, azulene, cyclopentadienyl radical. I am looking for any discussion regarding what the word "alternant" means in plain English, which other people in the university and community might appreciate as human beings, even though not expert in CC. Please understand I am not being disrespectful or even facetious. Do you recall the award film "My Fair Lady"? Common flower girl Eliza Doolittle asks phonetics expert Professor Higgins to teach her to speak like a lady. Eliza becomes the belle of British society and the Prince takes her hand to lead her to the dance floor at the great Ball. Higgins takes all the credit. As he says, "I knew I could do it." He tells Eliza, but she replies in total defiance, "I do not understand anything you are saying to me. I am too ignorant!" I am not CC, but just an Australian medical doctor. I am just curious about CCL. Forgive me, but CCL seems like an intense activity looking the computer measurements and bond strengths of the Lego blocks put together by my children into interesting creations. CCL day in and day out, seems about finding better ways of computing the minute details of my children's Lego blocks? Questions - 1.Have you any material, which explains "alternant" in plain English for my children, so they might really understand what the animal is in real terms? 2.Have you ever heard of another word "Holism"? Could holism be of any interest to the super reductionist field of CC? Does it really matter to the world or our Universe in any case? (I am disgusted and very sad about New York and the Pentagon) Regards Dr Henry Pang (medical) Australia -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Sep 13 12:21:53 2001 Received: from relay1.scripps.edu ([137.131.200.29]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8DGLq332753 for ; Thu, 13 Sep 2001 12:21:53 -0400 Received: from gamow.scripps.edu (gamow.scripps.edu [137.131.252.67]) by relay1.scripps.edu (8.11.6/TSRI-4.0.1r) with ESMTP id f8DGLZc18694 for ; Thu, 13 Sep 2001 09:21:35 -0700 (PDT) Received: (from case@localhost) by gamow.scripps.edu (8.9.2/TSRI-3.0.1) id JAA160781 for chemistry@ccl.net; Thu, 13 Sep 2001 09:20:14 -0700 (PDT) Date: Thu, 13 Sep 2001 09:20:14 -0700 (PDT) From: David Case Message-Id: <200109131620.JAA160781@gamow.scripps.edu> To: chemistry@ccl.net Subject: Future status of the Amber molecular modeling programs The following comments are a general reply to many questions I have been asked about the future status of the Amber molecular modeling programs. We were all saddened by Peter Kollman's untimely death, but we definitely plan to keep the Amber program alive (as Peter certainly wanted). Here is some information: For several years, David Case (at The Scripps Research Institute in San Diego) has been in charge of preparing releases, overseeing details of the code tree, test suites, and documentation. This will continue. Contributions to Amber come from many places, including UCSF, and have not been dependent on any one person or research group. Amber has been released on a "two-year" cycle for some time. Amber6 was released in January, 2000, and plans are well along for a release of Amber7, with a target date of January, 2002. Some of the features we plan for Amber7 are listed below; all of these were well in the "pipeline" when Peter Kollman died. (1) New force fields for proteins and nucleic acids, including polarizabilities on atoms, and off-center ("lone-pair") charges to better handle the orientation dependence of hydrogen bonds. This is an area that Peter Kollman was working very hard on, and continued development and testing is being led by senior collaborators Piotr Cieplak and Jim Caldwell. (2) Codes and force fields to automatically treat (almost) any organic molecule. This "general organic" Amber force field and corresponding computer codes for generating atom types and Amber-compatible input files, should greatly facilitate the incorporation of co-factors and ligands into Amber-based simulations. The principal developer here is Junmei Wang. (3) A "second generation" of generalized Born and other continuum solvent models, for problems where full explicit solvent simulations are not practical. These will include support for free energy simulations, and advanced methods of handling titratable residues. (4) Continued general improvements in the core simulation technologies: better parallel performance; new QM/MM models (in the Roar package from Ken Merz' group at Penn State); improved free energy techniques (especially with PME); updates to the preparation and analysis programs; and so on. Please note that we cannot yet guarantee either the release date or the specific set of features that will be included in Amber7, but the development team is committed to continuing to provide the best program suite we can put together. Other features that are in development may also be ready in time to be included in the Amber7 release. Questions can be addressed to me, using the contact information below. -- ================================================================== David A. Case | e-mail: case@scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ================================================================== From chemistry-request@server.ccl.net Thu Sep 13 12:32:56 2001 Received: from mail1.ats.rochester.edu (IDENT:998@[128.151.224.31]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8DGWu300593 for ; Thu, 13 Sep 2001 12:32:56 -0400 Received: from localhost (weiz@localhost) by mail1.ats.rochester.edu (8.11.6/8.11.6) with ESMTP id f8DGXs1389038 for ; Thu, 13 Sep 2001 12:33:54 -0400 (EDT) Date: Thu, 13 Sep 2001 12:33:54 -0400 From: Wei Zhuang X-Sender: weiz@mail1.ats.rochester.edu To: chemistry@ccl.net Subject: unit convertion in MM3 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi,all: I am using MM3 force field now. but the parameters in MM3 is quite wield to me. for example,for angles, k is in mdyne*A/rad^2. but energy is in kcal/mol, do I need to do any conversion before I use the formula? like change k into N*m/degree^2 wei zhuang e-mail:weiz@mail.rochester.edu office phone:716-2750387 From chemistry-request@server.ccl.net Thu Sep 13 13:20:09 2001 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8DHK8301492 for ; Thu, 13 Sep 2001 13:20:08 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id NAA05550; Thu, 13 Sep 2001 13:08:30 -0400 (EDT) Date: Thu, 13 Sep 2001 13:08:29 -0400 From: Rick Venable To: "Dr. Richard L. Wood" cc: "chemistry@ccl.net" Subject: Re: CCL:Text vs. HTML formatted postings In-Reply-To: <3BA0BEE4.B0E2B57F@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I'd like to echo Thomas Huber sentiments-- please don't post to mailing lists with either HTML or RTF (rich text format); there are a wide variety of people using a number of different mail programs, and plain text is the most appropriate to use for this. Old-fashioned or not, one ought to have to control over one's mail program, and know how to send plain text. I also use pine to read CCL, and usually discard any postings that aren't in plain text. > Thomas Huber wrote: > > Dear friends, > > it seems to me, that recently the number of HTML formatted postings on > > this list has increased. With the background of worm/virus resistant way > > to view email is, at least for me, PINE. Unfortunatly it is not easy to > > read HTML formatted emails with PINE. > > It would be very kind to 'old-fashioned' guys like myself to avoid HTML > > formatted postings. (Hint: In Netscape choose Edit/Preferences/Formatting > > and choose 'send plain text'.) On Thu, 13 Sep 2001, Dr. Richard L. Wood wrote: > I'm wondering why an "old fashioned" guy would even know HOW to make > postings in a non-HTML format using a program such as Netscape if > the "old fashioned" guy isn't using Netscape? =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 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 Thu Sep 13 14:41:23 2001 Received: from web20509.mail.yahoo.com ([216.136.226.144]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f8DIfN302431 for ; Thu, 13 Sep 2001 14:41:23 -0400 Message-ID: <20010913184123.22221.qmail@web20509.mail.yahoo.com> Received: from [63.172.3.149] by web20509.mail.yahoo.com via HTTP; Thu, 13 Sep 2001 11:41:23 PDT Date: Thu, 13 Sep 2001 11:41:23 -0700 (PDT) From: Deepak Singh Subject: Re: CCL:Text vs. HTML formatted postings To: chemistry@ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi CCLers I am a regular HTML mail user, but I agree with Thomas Huber and Richard Venable that for mass mailing lists like CCL plain text is by far the most appropriate format. Deepak ===== ----------------------- Deepak Singh, Ph.D. GeneFormatics, Inc. email: mndoci@yahoo.com __________________________________________________ Terrorist Attacks on U.S. - How can you help? Donate cash, emergency relief information http://dailynews.yahoo.com/fc/US/Emergency_Information/ From chemistry-request@server.ccl.net Thu Sep 13 14:41:55 2001 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8DIft302460 for ; Thu, 13 Sep 2001 14:41:55 -0400 Received: from sun5.lrz-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP for chemistry@ccl.net; Thu, 13 Sep 2001 20:41:51 +0200 Received: from localhost (ui22204@localhost) by sun5.lrz-muenchen.de (8.8.8+Sun/8.8.8) with ESMTP id UAA09780 for ; Thu, 13 Sep 2001 20:41:50 +0200 (MET DST) X-Authentication-Warning: sun5.lrz-muenchen.de: ui22204 owned process doing -bs Date: Thu, 13 Sep 2001 20:41:49 +0200 (MET DST) From: Eugene Leitl X-X-Sender: To: Subject: Re: CCL:Cluster Boards (fwd) Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id f8DIft302464 ---------- Forwarded message ---------- Date: Thu, 13 Sep 2001 20:03:06 +0200 From: Jakob Østergaard To: Eugene Leitl Subject: Re: CCL:Cluster Boards (fwd) On Thu, Sep 13, 2001 at 05:59:42PM +0200, Eugene Leitl wrote: ... > Hello again, > > > This time I would like to ask if any of you with experience building > clusters could tell me if it's better to build a cluster using (for say a 6 > node cluster) 3 dual motherboards or 6 single motherboards. I am > specifically interested in knowing the price-performance relation between > these two cases. You get added flexibility on dual boards, wrt. memory. Duals have been my choice for a long time - but the "real world" (the strange big room with the blue ceiling) has made me recommend UP machines lately. If you put in 1 GB RAM per CPU, with dual boards you will have the option of using 2 GB RAM with one CPU, leaving the other CPU idle. This can be useful, for some. The past two cluster projects I've been involved with, ended up choosing single processor (AMD) machines. For these reasons: 1) The Athlon is/was the most economical (price/performance) processor available - if we wanted single processor systems it would be AMD. 2) At the first cluster, the dual athlon was not yet available, and at the second cluster it was still "bleeding edge". The alternative is dual PIII 1GHz. Since the customers would run "mostly" one particular workload, we decided not to spend the extra money on getting the previously mentioned flexibility. When I get some experience with dual athlons, I may seriously consider using them in a cluster later. As I see it, there are three options: 1) UP Athlon - cheap, simple, reliable (with proper motherboard!) 2) SMP Athlon - not significantly more expensive, added flexibility, but I have no clue about it's stability. 3) SMP PIII - simple, reliable, but you need more machines for the same (theoretical) performance. PIII and PIV are pretty much out of the picture as I see it, unless you are using heavily SSE2 based software, in which case the PIV could, maybe, be worth looking into. Two single athlons are about the same cost as a dual PIII (give and take some), and you simply cannot buy a dual PIII of "comparable performance" unless your code will only run on two CPUs anyway and is communications intensive (communications-bound on a network). My uncertainty about the stability of dual athlons is the primary reason why I do not just recommend a dual. I have dual Pentium, PPro, PII and PIII systems working for me daily - maybe an Athlon will join the flock some day :) -- ................................................................ : jakob@unthought.net : And I see the elder races, : :.........................: putrid forms of man : : Jakob Østergaard : See him rise and claim the earth, : : OZ9ABN : his downfall is at hand. : :.........................:............{Konkhra}...............: From chemistry-request@server.ccl.net Thu Sep 13 16:35:03 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8DKZ3304925 for ; Thu, 13 Sep 2001 16:35:03 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id QAA00420; Thu, 13 Sep 2001 16:35:02 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3BA11240.119E2EF6@cornell.edu> Date: Thu, 13 Sep 2001 16:08:32 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Re: CCL:unit convertion in MM3 References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Wei Zhuang wrote: > hi,all: > > I am using MM3 force field now. but the parameters in MM3 is quite wield > to me. > > for example,for angles, k is in mdyne*A/rad^2. but energy is in kcal/mol, > do I need to do any conversion before I use the formula? like change k > into N*m/degree^2 > I would think that whatever program uses the MM3 force field would have a routine to convert the energies into the "proper" units. Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Thu Sep 13 15:45:19 2001 Received: from mail.staff.site.ntu.edu.au ([138.80.69.54]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8DJjI303971 for ; Thu, 13 Sep 2001 15:45:19 -0400 Received: by mail.staff.site.ntu.edu.au with Internet Mail Service (5.5.2653.19) id ; Fri, 14 Sep 2001 05:15:17 +0930 Message-ID: From: Henry Pang To: "'chemistry@ccl.net'" Subject: Alternant hydrocarbons and Holism? Date: Fri, 14 Sep 2001 05:15:17 +0930 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hi CCL Thank you for many responses on alternant hydrocarbons. I was too scared to stress my real intent. I merely used alternants to get through CCL filters. Forgive me but I referred to my children and Lego building blocks to say I think CC would benefit from a bit of holism instead of a total a narrow reductionism. CC appears to only focus on the properties and bonds of children's Lego blocks. CCL day in and day out is entirely about asking everyone for new and better methods of playing with Lego blocks. I am an Australian medical doctor studying Masters computational chemistry. My prime interest in CC is to link atoms and molecules to the Big Picture of the real world. I worry about the dependence of CC on approximations applied to everything in vision. I cannot solve the Schrodinger equation. Can you? Should I feel concerned when the whole edifice of CC is based only on approximations? I ponder is there an important reason for this forced position? Does CC really believe that one day, with more funding, it will reach Absolute Truth (whatever that might really be) in real terms? I like to dream with my children about our Universe, about origins of everything, about our planet earth, inanimate and animate things not least new human babies when I am in Labour Ward. I appreciate CC is about 'rigorous science' but with respect, I believe CC would be even greater, if there was space for a wider link to the real world. Do tell me where to find CC applications in my professional field of health and medical care. I think it could be wonderful and rewarding in many dimensions, if CCL could see its way to stimulate interest in 'holism', as a respected component in CC. Dictionary for the word Holism - "Holism noun [U] The belief that anything natural is in some way connected to everything else and that each thing, such as a person, is a whole which is more important than the parts that make it up. More and more people are taking holism seriously because they find materialism unsatisfying." Cambridge Dictionaries Online http://dictionary.cambridge.org/define.asp?key=holism*1+0 God Bless America Dr Henry Pang (medical) Australia From chemistry-request@server.ccl.net Thu Sep 13 15:59:08 2001 Received: from web14301.mail.yahoo.com ([216.136.173.77]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f8DJx8304182 for ; Thu, 13 Sep 2001 15:59:08 -0400 Message-ID: <20010913195905.589.qmail@web14301.mail.yahoo.com> Received: from [199.89.163.143] by web14301.mail.yahoo.com via HTTP; Thu, 13 Sep 2001 12:59:05 PDT Date: Thu, 13 Sep 2001 12:59:05 -0700 (PDT) From: jaouad Subject: Chime Encryption To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL, I am developing a web page where i am using chime plugins like interface for drawing structure and store thems in a database, but my data get encrypted when i submit my form to linux server, do some one know how to play around this problem. thanks jeb __________________________________________________ Terrorist Attacks on U.S. - How can you help? Donate cash, emergency relief information http://dailynews.yahoo.com/fc/US/Emergency_Information/ From chemistry-request@server.ccl.net Thu Sep 13 23:49:51 2001 Received: from deakin.edu.au (root@[128.184.136.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8E3nn318552 for ; Thu, 13 Sep 2001 23:49:50 -0400 Received: from [128.184.88.189] (128-184-88-189.bcs.deakin.edu.au [128.184.88.189]) by deakin.edu.au (8.11.4/8.11.4) with ESMTP id f8E3niE22881; Fri, 14 Sep 2001 13:49:44 +1000 (EST) Mime-Version: 1.0 X-Sender: lim@128.184.136.2 Message-Id: In-Reply-To: References: Date: Fri, 14 Sep 2001 13:32:24 +1000 To: computational chemistry list From: "Kieran F Lim (Lim Pak Kwan)" Subject: Re: CCL:Alternant hydrocarbons and Holism? Cc: Henry Pang Content-Type: text/plain; charset="us-ascii" ; format="flowed" Henry: >there was space for a wider link to the real world. Do tell me where to find >CC applications in my professional field of health and medical care. see, for example, the book by (I think Oxford Press) entitled Molecular Orbital Calculations for Biological Systems. it discusses, inter alia, computational calculations of pharmaceutical and other biochemical systems. >dependence of CC on approximations applied to everything in vision. I cannot >solve the Schrodinger equation. Can you? Should I feel concerned when the >whole edifice of CC is based only on approximations? I ponder is there an >important reason for this forced position? Does CC really believe that one you state you are a medical practitioner. how do you treat your patients? - you measure a temperature by thermometer in the mouth, or the ear or forehead or some other accessible body part and then APPROXIMATE that to be the (core) "body" temperature! this is an approximation. yet i have never met a doctor who questions this procedure. - you measure the body "weight" (mass) of a patient -- usually with clothes on and then APPROXIMATE a correction for shoes, clothes, etc, or sometimes APPROXIMATE the correction to be zero! - when you ask your children to buy a kilogram of bananas, i assume they usually take a whole number of bananas that is APPROXIMATELY 1 kg. they don't take 5.475893... bananas weighing 1 kg, or do they? the whole of edifice science, engineering, technology, medicine and society is based on approximations. you are really asking a philosophical question, and should see (for example) journals on the philosophy of science -- info about some of which (eg Foundations of Chemistry) is occasionally posted on CCL. Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html also I note your NTU address. talk to your local computational chemist(s) at NTU (I know him, and know him to be an interesting person to talk to). Kieran ------------------------------------------------------------ Dr Kieran F Lim Biol. and Chemical Sciences (Lim Pak Kwan) Deakin University ph: + [61] (3) 5227-2146 Geelong VIC 3217 fax: + [61] (3) 5227-1040 AUSTRALIA mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim From chemistry-request@server.ccl.net Thu Sep 13 23:50:53 2001 Received: from popeye.latrobe.edu.au ([131.172.4.60]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f8E3op318610 for ; Thu, 13 Sep 2001 23:50:51 -0400 Received: from [131.172.148.97] (gln.chem.latrobe.edu.au [131.172.148.97]) by popeye.latrobe.edu.au (8.9.3/8.9.3) with ESMTP id NAA24700; Fri, 14 Sep 2001 13:50:48 +1000 (EST) Mime-Version: 1.0 X-Sender: chemgn@pop.latrobe.edu.au Message-Id: In-Reply-To: References: Date: Fri, 14 Sep 2001 13:51:44 +1000 To: Henry Pang From: "Graeme L. Nyberg" Subject: Re: CCL:Alternant hydrocarbons ... Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" Henry, You've received some responses, all of which are correct, but I have my doubts as to whether you're now much wiser. Here is a simple (I hope) explanation. The word 'alternate' is derived from 'alternating'. Alternate hydrocarbons have alternating single and double bonds - eg CH2=CH-CH=CH-CH=CH2, hexa-tri-ene. Note that you can 'star' alternate C's: * * * The term arose in the consideration of the electronic structure (bonding) of such molecules, which are all planar, and are termed 'conjugated', meaning that the electrons of the double-bond system (referred-to as the pi-electrons) interact throughout the entire molecule. This results in their properties being quite different from those of even their closest non-conjugated relatives, eg CH2=CH-CH2-CH2-CH=CH2. Here the pi-electrons in the two double bonds don't interact, the molecule is not conjugated, and the concept of 'alternate-ness' doesn't apply. The more interesting class of conjugated (and alternate/non-alternate) molecules are the aromatic compounds, based on the benzene 6-membered ring (which is both fully conjugated and cyclic). The classical structural formula for this has alternating single and double bonds, but in fact no individual bond is either single or double; rather, they're all one-and-a-half. The concept of alternate- ness arose in the theory/model which was developed to properly account for this. The commonly occurring aromatic molecules - eg naphthalene, anthracene,phenanthrene - can be thought of as being constructed from fused benzene rings, and are all alternates (since each ring has six carbons). Note that any even-membered ring will be an alternate, but that an odd-membered ring won't. Normal compounds with odd-membered rings won't, however, be fully conjugated [eg cyclo-penta-di-ene, (CH)4CH2, with an 'interrupting' CH2 group], so alternate-ness is not a concept which has been adopted into ordinary organic chemistry. Some of the related ions [eg the cyclopentadienyl anion, (CH)5-] are, though, fully conjugated, aromatic, and quite stable (and form complexes with metal cations). It is at this point that the concept of 'starring' atoms becomes useful. In an even-membered ring, every 'starred' carbon will have two unstarred carbons as neighbours (and vise versa), whereas in an odd-membered ring there will be two adjacent carbons which are either both starred or both unstarred (and so be a non-alternate). Full conjugation is thus not synomymous with being alternate. As well, there are a few compounds with fused odd-membered rings - eg azulene,which has fused five- and seven-membered rings. It is fully conjugated, with alternating single and double bonds (around the periphery), but is a non-alternate (because of the adjacent starred/unstarred carbons across the bridge). In contrast to naphthalene, its isomer, it isn't aromatic. Many of the properties of these molecules are thus accounted-for by their topologies. The class of alternates can in fact be subdivided into odd-alternates (eg benzene = 'cyclo-hexa-triene') and even-alternates (eg cyclo-octa-tetrene). The former is aromatic, but the latter (though cyclic and nominally still fully conjugated) is not. (The neutral molecule is in fact non-planar.) The theory/model accounts for this. Fascinating, isn't it?! Make you wish you'd carried on with chemistry instead of medicine?? ;-) Cheers, Graeme Nyberg.