From assfeld@host23.lctn.u-nancy.fr Tue Jul 28 03:29:10 1998 Received: from host23.lctn.u-nancy.fr (host23.lctn.u-nancy.fr [192.54.210.30]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA25593 Tue, 28 Jul 1998 03:29:09 -0400 (EDT) From: assfeld@host23.lctn.u-nancy.fr Received: (from assfeld@localhost) by host23.lctn.u-nancy.fr (AIX4.2/UCB 8.7/8.7) id JAA13768 for CHEMISTRY@www.ccl.net; Tue, 28 Jul 1998 09:24:27 +0200 (DFT) Date: Tue, 28 Jul 1998 09:24:27 +0200 (DFT) Message-Id: <199807280724.JAA13768@host23.lctn.u-nancy.fr> To: CHEMISTRY@www.ccl.net Subject: Positives eigenvalues ? Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-MD5: 1cQivtnpJ5jsTc969TYwmw== Dears CCLers, I have a very basic question about quantum mechanics using finite basis set. 1) Let's start with the continuous form of the Hamiltonian (H). For simplicity, let's take the simple system, the Hydrogen atom. H = -(1/2)D + V, where D is the Laplacian, V the electrostatic potential (V = -1/r ; r : distance between the nucleus and the electron ) in atomic units. We have then the Schrodinger equation to solve : H Y = E Y where Y is the wave function of the system and E the energy associated to Y. There is an infinity of bound states solutions, called 1s, 2s, 2p ,.... All these solutions have an associated negative energy, which are accumulating under zero. [E = -(1/2)(Z^2/n^2)] However, when V is zero, the solutions of the Schrodinger equation form a continuum with positive energies. The essemble composed of the discrete negatives eigenvalues and the positive continuum is called the spectrum of the Hamiltonian. 2) Now let's use a basis set to solve the previous problem. All states Y can be written as a linear combination of the basis functions. Then, we use the variational principle (orthogonalisation + diagonalization) to find the best set of coefficient which gives the best (lower) energy. We are then focusing on the ground state. With any basis set of N functions, one finds only one negative eigenvalue (corresponding to the 1s state) and (N-1) positives eigenvalues. And now here is my question : (at least!) WHAT ARE THESE POSITIVES EIGENVALUES ? 1) Are they some values of the positive continuum of the spectrum ? I personally don't think so since V is not equal to zero. 2) Or do they correspond to other bound states that are so badly represented, because of the variationnal principle, that they are positives ? That is what I believe but have no proof. 3) Or are the zeros different in the two representations ? I don't think so because the zeroes mean the same : the atom is ionized. 4) Anything else ? I would be very gratefull if someone can point me some references dealing with this, or some textbook, or just teach me. Please reply to me directly, I will summarize to the list after. PS : I deliberatly choose the hydrogen atom since the Hamiltonian is the same as the Fockian, and people can perform calculations easily with any quantum chemical package with various basis set. ...Xav --------------------------------------------------------------------------- Ast. Pr. Xavier Assfeld assfeld@lctn.u-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.u-nancy.fr From hjj@dou.dk Tue Jul 28 05:28:02 1998 Received: from gamma.dou.dk (gamma.dou.dk [130.225.130.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA26085 Tue, 28 Jul 1998 05:28:01 -0400 (EDT) Received: from dou.dk (hjallese.chem.ou.dk [130.225.149.146]) by gamma.dou.dk (8.8.6/8.8.4) with ESMTP id LAA07348; Tue, 28 Jul 1998 11:27:56 +0200 (METDST) Message-ID: <35BD9A66.2ECD8436@dou.dk> Date: Tue, 28 Jul 1998 11:31:39 +0200 From: "Hans Joergen Aa. Jensen" Reply-To: hjj@dou.dk Organization: Department of Chemistry, Odense University X-Mailer: Mozilla 4.04 (Macintosh; I; PPC) MIME-Version: 1.0 To: assfeld@host23.lctn.u-nancy.fr CC: CHEMISTRY@www.ccl.net Subject: Re: CCL:Positives eigenvalues ? References: <199807280724.JAA13768@host23.lctn.u-nancy.fr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Xav, You don't explain how you get your positive eigenvalues. However, from what you write I would guess you have obtained them with an ROHF program, specifying just one electron. You see, the Fock matrix is NOT identical to the Hamiltonian matrix (bare nucleus matrix) for a one- electron system. The Hamiltonian matrix has as expected a number of negative eigenvalues corresponding to 1s, 2s, 2p, etc., the number and accuracy depending on the quality of the basis set. However, the Hamiltonian matrix correspond to the zero-electron Fock matrix, not the one-electron Fock matrix. The eigenvalue of the occupied orbital is identical to the value from the Hamiltonian matrix. The other eigenvalues, the virtual eigenvalues of the one-electron Fock matrix, correspond to approximate electron affinities (Koopmans' theorem), that is to forming the H- system. -- Hans Joergen. From dbuttar@hxsgi2.zeneca.com Tue Jul 28 06:46:46 1998 Received: from apsn03.zeneca.co.uk (apsn03.zeneca.co.uk [193.132.159.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA26277 Tue, 28 Jul 1998 06:46:45 -0400 (EDT) Received: by apsn03.zeneca.co.uk; id LAA07702; Tue, 28 Jul 1998 11:41:11 +0100 (BST) Received: from unknown(156.71.156.2) by apsn03.zeneca.co.uk via smap (3.2) id xma007567; Tue, 28 Jul 98 11:40:54 +0100 Received: from hxsgi2.ukhx.zeneca.com by gbzhp02.ukap.zeneca.com with ESMTP (1.40.112.8/16.2) id AA144060109; Tue, 28 Jul 1998 11:01:49 +0100 Received: by hxsgi2.ukhx.zeneca.com (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id LAA16340; Tue, 28 Jul 1998 11:00:33 +0100 From: "David Buttar" Message-Id: <9807281100.ZM16338@hxsgi2.ukhx.zeneca.com> Date: Tue, 28 Jul 1998 11:00:33 +0100 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Density Functional Codes Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii We are currently considering purchasing a code that will enable us to perform DFT calculations. I would like to ask if anyone has any comments on the following queries, [1]. Relative performance of Gaussian98, Cadpac, Unichem, ADF etc. [2]. The literature would indicate that the B3LYP functional is currently one of the most popular approaches to use, is this preferable to non-hybrid functionals such as BLYP. [3]. The suitability of the methods to study structures and binding energies of transition metal complexes and organic reaction profiles. Any thoughts or comments would be welcome, Thanks, David. -- ******************************************************************** Dr. David Buttar e-mail: dbuttar@hxsgi2.zeneca.com Zeneca Specialties Molecular Modelling Group Tel: (0161)-721-1673 Research Centre Hexagon House Fax: (0161)-721-2612 Blackley Manchester M9 8ZS U.K. ********************************************************************* From arloa@dqo.fcq.unc.edu.ar Tue Jul 28 08:25:08 1998 Received: from dqo.fcq.unc.edu.ar (arloa@dqo.fcq.unc.edu.ar [200.16.18.55]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA26751 Tue, 28 Jul 1998 08:25:06 -0400 (EDT) Received: from localhost (arloa@localhost) by dqo.fcq.unc.edu.ar (8.8.4/8.8.4) with SMTP id JAA00707 for ; Tue, 28 Jul 1998 09:25:16 -0300 Date: Tue, 28 Jul 1998 09:25:15 -0300 (ARST) From: Marcos Villarreal To: chemistry@www.ccl.net Subject: Hardware for modeling Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers. I am starting my PhD in Chemistry. I will study Lipid-Protein interaccion whit empiricals force fields. We have few computer resourses, so we are going to by one computer. We have aronud $ 3000 and the way I see, we have two alternatives: a) one single procesor Pentium 2 of 400 whit one disk of 9 Gb. b) two procesor Pentium 2 of 266 whit two disks of 4 Gb. Both whit 128 Mb RAM and RED HAT Linux. I will be the only one using this machine. Which one is the best for MM/MD. Thank you very much in advance. From Rissers-C@BATTELLE.ORG Tue Jul 28 08:46:00 1998 Received: from bclcl1.im.battelle.org (bclcl1.im.battelle.org [131.167.1.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA26942 Tue, 28 Jul 1998 08:45:59 -0400 (EDT) Received: from ns-pandora.im.battelle.org by BCLCL1 (PMDF V5.1-10 #14609) with ESMTP id <01IZXF55TTWMHUFUJJ@BCLCL1> for CHEMISTRY@www.ccl.net; Tue, 28 Jul 1998 08:46:11 EDT Received: by ns-pandora.im.battelle.org with Internet Mail Service (5.5.1960.3) id ; Tue, 28 Jul 1998 08:46:00 -0400 Content-return: allowed Date: Tue, 28 Jul 1998 08:45:59 -0400 From: "Risser, Steve" Subject: Positive eigenvalues To: "'CHEMISTRY@www.ccl.net'" Message-id: <5913080CA46DD111A98200A0C9960C10967C00@ns-bco-mse7.im.battelle.org> X-Mailer: Internet Mail Service (5.5.1960.3) Dear Xav That fact that you have positive and negative eigenvalues is simply a function of the Hamiltonian. As an example, think of the finite square well problem. There is a minimum of one, but possibly many, bound (negative energy) states associated with the well, but there is also an infinite number of unbound (positive energy) states also that are solutions. Any time you have an finite potential, there will be unbound solutions that exist. The question of how many of the bound and unbound states you can represent with a finite basis depends on the basis, not on the Hamiltonian. Steve ******************************************************** Dr Steven M. Risser Associate Professor, TAMU-Commerce Visiting Scientist at Battelle Memorial Institute ********************************************** From mn1@helix.nih.gov Tue Jul 28 11:34:48 1998 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA28852 Tue, 28 Jul 1998 11:34:47 -0400 (EDT) Received: (from mn1@localhost) by helix.nih.gov (8.8.5/8.8.5) id LAA27924; Tue, 28 Jul 1998 11:34:46 -0400 (EDT) Date: Tue, 28 Jul 1998 11:34:46 -0400 (EDT) From: "M. Nicklaus" Message-Id: <199807281534.LAA27924@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: Re: color printers Cc: mn1@helix.nih.gov On Mon, 27 Jul 1998 19:45:55, Themis Lazaridis wrote: > Can anybody recommend a color printer that works well for Acrobat PDF > documents with color? We have an HP color printer here but it doesn't > seem to be able to handle the large size of these jobs. We bought a QMS magicolor 2 EX color laser printer a few weeks ago. With 80 MB of RAM and a hard drive preinstalled, we've never seen it balk on any job we've thrown at it so far. This includes color output from Adobe Acrobat PDF documents (although I haven't checked how large those print jobs got). The printer comes with an Ethernet NIC preinstalled. We print to it >from Windows 3.11, Windows 95, MacOS, IRIX 5.3, IRIX 6.3 and 6.4, and probably a few more platforms that I forget now. Print quality is very good in color and black and white, with B&W (text) output being as good as on any B&W only laser printer. If you shop around, you should be able to get this printer for >US$4,300. Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 37 Convent Dr, MSC 4255 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute, & Center for Molecular Modeling, Ctr. for Information Technology, NIH ------------------------------------------------------------------------ From ccl@www.ccl.net Mon Jul 27 20:08:47 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA23131 Mon, 27 Jul 1998 20:08:46 -0400 (EDT) Received: from auric.chem.csiro.au (auric.chem.CSIRO.AU [138.194.44.10]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id UAA05594 for ; Mon, 27 Jul 1998 20:08:32 -0400 (EDT) Received: by auric.chem.csiro.au id AA05691 (5.67b/IDA-1.5 for chemistry@ccl.net); Tue, 28 Jul 1998 10:08:04 +1000 Received: from cpr-46107.chem.csiro.au(138.194.46.107), claiming to be "[138.194.46.107]" via SMTP by auric.chem.CSIRO.AU, id smtpd05688aaa; Tue Jul 28 00:07:58 1998 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 28 Jul 1998 10:07:51 +1000 To: CHMINF-L@LISTSERV.INDIANA.EDU, chemistry@ccl.net From: "Dr. Dave Winkler" Subject: Large database availability Dear Netters, I would like to acquire one or more large chemical structure databases for some research on developing new molecular representations for QSAR. I already have Maybridge, CSD and NCI. Is there a way of obtaining a 'chunk' of compounds in CAS (maybe a substantial fraction of the 18 million) which have been converted to 3D by Concord or similar, or at least are available in 2D or SMILES which I could convert? Databases indexed by CAS number would be most suitable but I would like to hear about any other options. Can anyone also advise on the AVAILABILITY of programs such as Marshall's DBMaker or similar which can generate hypothetical molecules. 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 From szarecka@sg3.pcy.kcl.ac.uk Tue Jul 28 09:16:35 1998 Return-Path: Received: from nitrogen.pcy.kcl.ac.uk (nitrogen.pcy.kcl.ac.uk [137.73.32.164]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA27128 Tue, 28 Jul 1998 09:16:31 -0400 (EDT) Received: from NITROGEN (localhost [127.0.0.1]) by nitrogen.pcy.kcl.ac.uk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id OAA15072 for ; Tue, 28 Jul 1998 14:16:31 +0100 Sender: szarecka@sg3.pcy.kcl.ac.uk Message-ID: <35BDCF2E.41C6@sg3.pcy.kcl.ac.uk> Date: Tue, 28 Jul 1998 14:16:31 +0100 From: Ms Szarecka X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: FField params for chlorine? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit My name is Agnieszka Szarecka. I'm a PhD student at Adam. Mickiewicz University in Poznan, Poland. Now I'm studying temporarily at King's Coll. London on MD simulation of crystallisation and using AMBER parameters. I'd like to simulate chloroform though and I need force fields parameters for chlorine-sp3 carbon bond, chlorine-sp3C-chlorine, chlorine-sp3C-hydrogen bond angles. And relevant non-bonded parameters as well. Maybe somebody has already come across this problem and knows the best values for the parameters? From calef1@llnl.gov Tue Jul 28 18:39:02 1998 Received: from popout.llnl.gov (popout.llnl.gov [128.115.18.67]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA02551 Tue, 28 Jul 1998 18:39:01 -0400 (EDT) Received: from calefnt (calefsnt.llnl.gov [128.115.232.92]) by popout.llnl.gov (8.8.5/LLNL-3.0.2) with SMTP id PAA14185; Tue, 28 Jul 1998 15:37:28 -0700 (PDT) Message-Id: <3.0.3.32.19980728154329.00957100@popout.llnl.gov> X-Sender: e130450@popout.llnl.gov X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Tue, 28 Jul 1998 15:43:29 -0700 To: amberLists , "APPLSPEC@uga.cc.uga.edu" , "CHEMCHAT@UAFSYSB.UARK.EDU" , "CHEMIG@LIST.NIH.GOV" , "CHEMISTRY@www.ccl.net" , "CHMINF-L@LISTSERV.INDIANA.EDU" , "ICS-L@UMDD.UMD.EDU" , "isisforum-l@mdli.com" , "listserver@ic.ac.uk" , "mailbase@mailbase.ac.uk" , "molecular-dynamics-news@mailbase.ac.uk" , "NATODATA@CC1.KULEUVEN.AC.BE" , "pdb-l@pdb.pdb.bnl.gov" From: Dan Calef Subject: West Coast Regional Meeting - LAST CHANCE (maybe...) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues, We are getting down to the wire on this.... The Northern California Section of the American Chemical Society and the Society for Applied Spectroscopy is hosting the 34th Western Regional ACS Meeting in San Francisco on October 29th through the 31st. We have been asked to organize a session, or perhaps two, on computational chemistry. Readers of the list who are interested in presenting a paper at the conference are urged to submit a title, soon, and an abstract shortly thereafter. This can include, for example, molecular dynamics of materials, MD of biomaterials, computational chemistry in support of combinatorial chemistry, and new methods. At the meeting two years ago, we had so many papers we split it into two sessions. Graduate students and post-docs are encouraged to submit papers. This is an excellent opportunity to present your work to a wider audience. Dan Calef Calef1@llnl.gov 925-422-7797 Mail Stop L-092 Larry Fried Fried1@llnl.gov 925-422-7796 Lawrence Livermore National Laboratory P.O. Box 808 Livermore CA 94550 From sshobana@mail.med.cornell.edu Tue Jul 28 19:21:24 1998 Received: from mail.med.cornell.edu (mail.med.cornell.edu [140.251.2.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA03145 Tue, 28 Jul 1998 19:21:23 -0400 (EDT) Received: from pc104181.med.cornell.edu (pc104181.med.cornell.edu [140.251.155.156]) by mail.med.cornell.edu (8.7.3/8.8.x/cumc1) with SMTP id TAA15114 for ; Tue, 28 Jul 1998 19:21:19 -0400 Message-Id: <199807282321.TAA15114@mail.med.cornell.edu> X-Sender: sshobana@mail.med.cornell.edu X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 28 Jul 1998 19:24:31 -0400 To: chemistry@www.ccl.net From: Shobana Sundaram Subject: Ester linkages Hello, Can anyone mail me CHARMM force field parameters for carbonyl carbon - ester oxygen - sp3carbon ? I want to simulate a peptide that has alternate peptide and ester linkages. Thanks. -shobana Shobana Sundaram Dept.of Physiology & Biophysics Cornell University Medical College New York, NY-10021