From chemistry-request@www.ccl.net Mon Sep 14 23:20:33 1998 Received: from theta1.ben2.ucla.edu (theta1.ben2.ucla.edu [164.67.131.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id XAA16894 Mon, 14 Sep 1998 23:20:33 -0400 (EDT) Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by theta1.ben2.ucla.edu (8.8.8/8.8.8) with SMTP id UAA21232; Mon, 14 Sep 1998 20:20:35 -0700 Received: from pc-ll.chem.ucla.edu by ewald.mbi.ucla.edu (5.65v4.0/1.1.10.5/13Sep98-1057PM) id AA01364; Mon, 14 Sep 1998 20:20:34 -0700 Message-Id: <9809150320.AA01364@ewald.mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Mon, 14 Sep 1998 20:29:33 -0700 To: chemistry@www.ccl.net From: Laurence Lavelle Subject: Amber 5 ported to NT? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Greetings, Anyone know if Amber 5 has been ported to NT? Laurence From chemistry-request@www.ccl.net Mon Sep 14 05:15:30 1998 Received: from org.chem.msu.su (org.chem.msu.su [158.250.32.94]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA11523 Mon, 14 Sep 1998 05:15:25 -0400 (EDT) Received: (from serge@localhost) by org.chem.msu.su (8.8.8/8.8.8) id NAA05779 for chemistry@www.ccl.net; Mon, 14 Sep 1998 13:14:35 +0400 (MSD) (envelope-from serge) Date: Mon, 14 Sep 1998 13:14:35 +0400 (MSD) From: "Serge A. Pisarev" Message-Id: <199809140914.NAA05779@org.chem.msu.su> To: chemistry@www.ccl.net Subject: PBE for conformations Lines: 13 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers Has anyone the experience in applying the Perdew group density functionals (PBE in particular) to the conformational analysis of organic molecules and their characteristics related to other functionals (BLYP, B3LYP, WVN etc) Thank you in advance. I'll summarize the answers, if any. Serge Serge A. Pisarev, QSAR and Computational Organic Chemistry Group, Chemistry Department, Moscow State University. Email: serge@org.chem.msu.su WWW: http://org.chem.msu.su/~serge From chemistry-request@www.ccl.net Mon Sep 14 08:48:14 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 IAA12331 Mon, 14 Sep 1998 08:48:13 -0400 (EDT) Received: from cockatoo.phy.bris.ac.uk (cockatoo.phy.bris.ac.uk [137.222.30.7]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id IAA06389 for ; Mon, 14 Sep 1998 08:48:02 -0400 (EDT) Received: by cockatoo.phy.bris.ac.uk id AA27708; Mon, 14 Sep 1998 13:47:32 -0400 Date: Mon, 14 Sep 1998 13:47:32 -0400 (EDT) From: Guido Germano X-Sender: guido@cockatoo.phy.bris.ac.uk Reply-To: Guido Germano To: chemistry@ccl.net Subject: Re: Gaussian 94 job Message-Id: Organization: Physics Department University of Bristol Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Sandra, not all neutral molecules a spin multiplicity of 1. Try to work out the possible multiplicities of your particular molecule and chose the one you prefer. Otherwise, simply go on by trial and error, starting with 3. Regards Dr. Guido Germano Research Assistant, University of Bristol, England Tel. +44-117-928 9000 ext. 8755, http://www.phy.bris.ac.uk/staff/germano_g.html From chemistry-request@www.ccl.net Mon Sep 14 10:01:42 1998 Received: from hermes.aston.ac.uk (hermes.aston.ac.uk [134.151.79.46]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA14329 Mon, 14 Sep 1998 10:01:41 -0400 (EDT) From: chaudash@aston.ac.uk Received: from pharm78100.aston.ac.uk (pharm7145.aston.ac.uk) [134.151.78.100] by hermes.aston.ac.uk with smtp (Exim 1.82 #3) id 0zIZD8-0004om-00; Mon, 14 Sep 1998 15:02:34 +0100 Comments: Authenticated sender is Organization: aston.ac.uk To: chemistry@www.ccl.net Date: Mon, 14 Sep 1998 15:03:38 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Hartree Fock enegy Reply-to: @aston.ac.uk Priority: normal X-mailer: Pegasus Mail for Windows (v2.54) Message-Id: Hi ccl'ers Could someone tell me /point me in the right direction as to where I can find a reference as to conversion of Hartree Fock energy to KJ/mol. A reference would also be much appreciated. Many thanks From chemistry-request@www.ccl.net Mon Sep 14 10:42:47 1998 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA18702 Mon, 14 Sep 1998 10:42:38 -0400 (EDT) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA12516; Mon, 14 Sep 98 07:41:18 -0700 Received: from unknown(146.202.7.50) by bioc1.msi.com via smap (V2.0) id xma012512; Mon, 14 Sep 98 07:41:15 -0700 Sender: osman@msi.com Message-Id: <35FD2B0B.7912F6BA@msi.com> Date: Mon, 14 Sep 1998 07:41:15 -0700 From: "Osman F. Guner" Organization: Molecular Simulations Inc. X-Mailer: Mozilla 4.05 [en] (X11; I; IRIX 6.2 IP22) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: Re: CCL:catalyst question References: <00022696.001444@am.pnu.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Please note that there is a Catalyst users listserver that helps Users of Catalyst exchange ideas, solutions, etc. To subscribe to the list, send a message to majordomo@msi.com with subscribe catalyst-l in the body of the message. Pil.H.Lee@am.pnu.com wrote: > > Hi, > > Does anyone know the address of MSI's program catalyst user group and/or the > program's technical support? > Thanks. > > > Pil H. Lee, Ph.D. > pil.h.lee@am.pnu.com > > > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- -- Osman F. Guner, Ph.D. Sr.Product Manager, Rational Drug Design Molecular Simulations, Inc. (619) 799-5341 osman@msi.com http://www.msi.com From chemistry-request@www.ccl.net Mon Sep 14 11:45:27 1998 Received: from mserv.rug.ac.be (mserv.rug.ac.be [157.193.40.37]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA25686 Mon, 14 Sep 1998 11:45:19 -0400 (EDT) Received: from hartree1.rug.ac.be (hartree1.rug.ac.be [157.193.91.8]) by mserv.rug.ac.be (8.9.0/8.9.0) with SMTP id RAA06884 for ; Mon, 14 Sep 1998 17:45:10 +0200 (MET DST) Received: by hartree1.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA06450; Mon, 14 Sep 1998 17:42:56 +0200 Date: Mon, 14 Sep 1998 17:42:55 +0200 (DFT) From: Patrick Bultinck To: CCL Subject: Charge differences between conformers Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear, I would like to hear your opinions on the relevance of charge differences on same atoms, but in different conformers. How big should charge difference be (I need not know exactly, but rather to get a feeling at it) to be considered relevant. For example, the difference in charge on an oxygen atom in two conformers. I have read material where NPA charge differences are considered relevantly different if they exceed 0.001. Anybody care to share an opinion, advice, experience (NPA, Mulliken, ...) ? Thanks, Patrick Bultinck Quantum Chemistry University of Ghent Belgium From chemistry-request@www.ccl.net Mon Sep 14 12:22:35 1998 Received: from toronto.acdlabs.com (root@toronto.acdlabs.com [207.176.233.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA29648 Mon, 14 Sep 1998 12:22:33 -0400 (EDT) Received: from xps05.acdlabs.com (victoria.acdlabs.com [207.176.233.34]) by toronto.acdlabs.com (8.8.5/8.7.3) with SMTP id MAA26102 for ; Mon, 14 Sep 1998 12:22:27 -0400 (EDT) Date: Mon, 14 Sep 1998 12:22:27 -0400 (EDT) Message-Id: <199809141622.MAA26102@toronto.acdlabs.com> X-Sender: victoria@mail.acdlabs.com (Unverified) X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: victoria@acdlabs.com (Victoria Barclay) Subject: Structure Drawing Applet available for download Advanced Chemistry Development, Inc. is making available a free downloadable structure drawing applet from its web-site. ACD Structure Drawing Applet (ACD/SDA) is a complete structure drawing, editing and visualization tool written in Java that can be incorporated into HTML documents. The applet can be used for composing substructure queries to databases and visualizing results. Unlike platform-dependent plugins or ActiveX controls, the applet runs in the same way on any hardware platform or operating system - the only requirement is a Java-compatible browser such as Netscape 2.0 or later or MS Internet Explorer 3.0 or later. ACD/SDA can be used to create true platform-independent Web applications ranging from electronic conferences to online database searches. ACD/SDA is featured in our other products, ACD/ILab and ACD/SLIMS. You can find out more information about the SDA, and access the download page from: http://www.acdlabs.com/products/java/sda/ From chemistry-request@www.ccl.net Mon Sep 14 12:29:50 1998 Received: from comsig.nibsc.ac.uk (comsig.nibsc.ac.uk [193.62.43.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA00400 Mon, 14 Sep 1998 12:29:49 -0400 (EDT) Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by comsig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id RAA09841 for ; Mon, 14 Sep 1998 17:29:12 +0100 (BST) Message-ID: <35FD4488.FE36B9FD@nibsc.ac.uk> Date: Mon, 14 Sep 1998 17:30:00 +0100 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Szabo and Ostlund book. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Comp. Chemists Does somebody have a copy of the FORTRAN source code, from the Ostlund and Szabo textbook, for performing a two electron STO SCF calculation ? I just want to study/compile/run it as an educational exercise. -- 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 01707 654753 FAX 01707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@www.ccl.net Mon Sep 14 14:25:30 1998 Received: from mailrelay2.pfizer.com (pfizergate2.pfizer.com [192.77.198.200]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id OAA06029 Mon, 14 Sep 1998 14:25:29 -0400 (EDT) Received: from giris3.pfizer.com by mailrelay2.pfizer.com (SMI-8.6/SMI-SVR4) id OAA16204; Mon, 14 Sep 1998 14:25:00 -0400 Received: (from wesselmd@localhost) by giris3.pfizer.com (8.8.7/8.8.7) id OAA25922 for chemistry@www.ccl.net; Mon, 14 Sep 1998 14:25:32 -0400 (EST) From: Matt Wessel Message-Id: <199809141825.OAA25922@giris3.pfizer.com> Subject: ACS Anaheim - PHYSICAL PROPERTY PREDICTION To: chemistry@www.ccl.net (ccl) Date: Mon, 14 Sep 1998 14:25:32 -0400 (EST) X-Mailer: ELM [version 2.4 PL24 ME5a] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit PHYSICAL PROPERTY ESTIMATION to be held at the American Chemical Society Meeting in Anaheim, CA March 21-25, 1999 Sponsored by the Division of Computers in Chemistry The estimation of physical properties (QSPR) such as aqueous solubility, boiling point, LogP, etc. has been a small but active area of research in computational chemistry. This symposium is intended to demonstrate new methods for property estimation and the application of existing methods to new properties and data sets. The due date for 150 word abstracts is November 18, 1998. I encourage the submission of electronic abstracts to me using the form at: http://www.acs.org/meetings/abstract/absdown.html Otherwise, abstracts can be submmitted to me directly at the address provided below. -- =========================================================== Matthew D. Wessel Phone: 860.715.5819 Research Scientist Fax: 860.441.4734 Computational Chemistry wesselmd@pfizer.com Exploratory Medicinal Sciences http://www.pfizer.com Central Research Division Pfizer Inc Eastern Point Road Groton, CT 06340 =========================================================== From chemistry-request@www.ccl.net Mon Sep 14 15:38:43 1998 Received: from deimos.cber.nih.gov (deimos.cber.nih.gov [128.231.52.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA06525 Mon, 14 Sep 1998 15:38:43 -0400 (EDT) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA296211698; Mon, 14 Sep 1998 15:34:58 -0400 Date: Mon, 14 Sep 1998 15:34:58 -0400 (EDT) From: Rick Venable To: Computational Chemistry List Subject: Re: CCL:Re: parallel md+mc In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sat, 12 Sep 1998, Guido Germano wrote: > Sorry, but you don't need to start your MD run from an *equilibrated* > configuration. You can use MD itself to reach equilibrium. So the > question should be: from which configuration start? There are two main > possibilities: construct a regular crystal-like arrangement and melt it > rising the temperature, or construct a random arrangement at lower > density and compress it gradually during the first steps of the run. > The first approach is easier and good enough for your case. It really depends on the system; for uncoupled LJ particles with no connectivity, I'd agree that MC equilibration is probably unnecessary. For many (bio)polymer systems, especially for more exploratory work where crystal and/or NMR structures aren't available, some form of evaluating model built configurations is probably essential, and MC is a reasonable tool to use. > On Wed, 9 Sep 1998, Matthias Hloucha wrote: > > One important task is to construct an equilibrated start configuration > > before starting the md runs. Do you think it is resonable to use Monte > > Carlo techniques to equilibrate very many simple particles? Are you aware > > of any existing code in this area? The book "Computer Simulations of Liquids" by MP Allen and DJ Tildesley should have what you need for this simple case of a LJ fluid; the program listings are online in a couple places (but, alas, not at the ftp site listed in the book). They are on MP Allen's web pages at http://toucan.phy.bris.ac.uk/AllenTildesley/home.html -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://www.erols.com/rvenable \/ |=| see http://www.fda.gov ) From chemistry-request@www.ccl.net Mon Sep 14 17:08:11 1998 Received: from karplus0.harvard.edu (tammy.harvard.edu [128.103.92.198]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA09471 Mon, 14 Sep 1998 17:08:11 -0400 (EDT) Received: from topanga.harvard.edu (topanga [128.103.92.179]) by karplus0.harvard.edu (8.8.2/8.8.2) with ESMTP id RAA09550; Mon, 14 Sep 1998 17:18:50 -0400 (EDT) Received: from localhost (qiang@localhost) by topanga.harvard.edu (8.8.2/8.8.2) with SMTP id QAA06659; Mon, 14 Sep 1998 16:54:23 -0400 (EDT) Date: Mon, 14 Sep 1998 16:54:22 -0400 (EDT) From: Qiang Cui To: CHEMISTRY@www.ccl.net Subject: Re: CCL:Multi-time scale integration. In-Reply-To: <9809131414.ZM3019@hamilton.math.missouri.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 13 Sep 1998, Don Steiger wrote: > > > In the literature on multi-time scale integration, a lot of importance is > placed > on time reversibility. Why this is so important is something that I have never > been able to figure out. If an integration algorithm is efficient and produces > a small global error then why is this not sufficient. If anybody can enlighten > me on this subject I would appreciate it. > Well, my guess is that the time-reversibility is not absolutely necc. if you go to higher order decomposition of the Liouville operator. For instance, take a look at the recent work of H. Ishida and A. Kidera, J. Chem. Phys. 109, 3276 (1998), Chem. Phys. Lett. 282, 115 (1998). > -- > Don Steiger > dons@hamilton.math.missouri.edu > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > > ___________________________________________________________________________ Qiang Cui Dept. of Chem. _ __..-;''`--/'/ /.',-`-. Harvard Univ. (`/' ` | \ \ \\ / / / / .-'/`,_ 12 Oxford St., /'`\ \ | \ | \| // // / -.,/_,'-, Cambridge, MA 02138 /<7' ; \ \ | ; ||/ /| | \/ |`-/,/-.,_,/') (617)-495-8997 / _.-, `,-\,__| _-| / \ \/|_/ | '-/.;.\' (617)-495-1775 `-` f/ ; / __/ \__ `/ |__/ | Fax: (617)-496-3204 `-' | -| =|\_ \ |-' | http://yuri.harvard.edu/~qiang __/ /_..-' ` ),' // ((__.-'((___..-'' \__.' 805 Mt. Auburn Street Apt. 35 Watertown, MA 02472 (617)-926-6027 __________________________________________________________________________ From chemistry-request@www.ccl.net Mon Sep 14 18:08:18 1998 Received: from jazz.ucc.uno.edu (jazz.ucc.uno.edu [137.30.1.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA09696 Mon, 14 Sep 1998 18:08:16 -0400 (EDT) Received: from slater (slater.chem.uno.edu) by jazz.ucc.uno.edu (PMDF V5.1-10 #D3119) with SMTP id <01J1SYLKRWC0922GKM@jazz.ucc.uno.edu> for CHEMISTRY@www.ccl.net; Mon, 14 Sep 1998 17:06:09 CST Date: Mon, 14 Sep 1998 17:04:10 -0500 From: Howard Alper Subject: Parameterization Sender: heacm@jazz.ucc.uno.edu To: CHEMISTRY@www.ccl.net Message-id: <35FD92DA.15FB@uno.edu> Organization: University of New Orleans MIME-version: 1.0 X-Mailer: Mozilla 3.0 (X11; U; AIX 1) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Hello, Sorry if this is a repeat, but as far as I could tell this message did not post when I originally sent it (due, likely, to floods in New Orelans!) Several weeks back I wrote about parameterization and units in simulation (still waiting for some replies...) Now I have some questions about parameterization to create forcefields for MD simulations. Specifically, I am interested in parameterizing Nitromethane. While any information regarding a set of parameters (bond, angle, torsion, out-of-plane,charges,van der Waals, etc) would be welcome, we are interested in generating the neccesary parameters, and in a form suitable for use in CHARMM. To this end I have several questions: 1) I need to derive, somehow, structural parameters and force constants for bond-stretching and angle-binding. The force constants should be in units of energy/(angstroms**2) and energy/(radian**2) (I have seen some force constants in old papers that give force constants in units of millidynes/angstroms, but I do not understand how that relates to the case of angle-bending constants...) I can perform an optimization and frequency calculation in Gaussian, for example, but >from what I can tell the resulting frequencies and force constants are for the normal modes of the molecule, not bonds and angles/etc. Does anyone know if Gaussian has any options to derive the type of force constants I require? Or, does anyone know of a post-Gaussian analysis program that would do the above? 2) I also need to derive van der Waals parameters. One person I asked said something on the order of "you can derive that from the interaction of two nitromethane molecules". To a parameterization novice, that is not very specific advice. Could anyone clarify what in detail needs to be done, provide references, describe how programs like Guassian might be used to get VDW parameters, etc? (If one calculates the interaction energy of two nitromethane molecules at verious distances and orientations, is not the total energy for a configuration the sum of coulombic and VDW terms? Does that mean the charges must first be derived?) Thanks in advance, Howard Alper -- Howard E. Alper, Ph.D. Dept. of Chemistry and The Advanced Materials Research Institute University of New Orleans New Orleans, LA 70148 504-280-7216 - Helping molecules find happiness for almost a 5th of a century. From chemistry-request@www.ccl.net Mon Sep 14 22:21:42 1998 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id WAA16728 Mon, 14 Sep 1998 22:21:33 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA01693; Tue, 15 Sep 98 10:19:46 -0700 Date: Tue, 15 Sep 1998 10:19:46 -0700 (PDT) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" Subject: Find free PC software! Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Can anyone tell me where I can find a free or cheap IR frequency calculation software, and a crystal building and graphics software. Thanks a lot! Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725 From chemistry-request@www.ccl.net Tue Sep 15 06:43:51 1998 Received: from cockatoo.phy.bris.ac.uk (cockatoo.phy.bris.ac.uk [137.222.30.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id GAA17930 Tue, 15 Sep 1998 06:43:50 -0400 (EDT) Received: by cockatoo.phy.bris.ac.uk id AA28899; Tue, 15 Sep 1998 11:43:33 -0400 Date: Tue, 15 Sep 1998 11:43:33 -0400 (EDT) From: Guido Germano X-Sender: guido@cockatoo.phy.bris.ac.uk Reply-To: Guido Germano To: Computational Chemistry List Subject: Multi-time scale integration. In-Reply-To: <199809150520.BAA17091@www.ccl.net> Message-Id: Organization: Physics Department University of Bristol Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > In the literature on multi-time scale integration, a lot of importance is > placed on time reversibility. Why this is so important is something > that I have never been able to figure out. If an integration > algorithm is efficient and produces a small global error then why is > this not sufficient. If anybody can enlighten me on this subject I > would appreciate it. > > -- > Don Steiger > dons@hamilton.math.missouri.edu Newton's equations are time-reversible, and Hamiltonian dynamics preserves phase space volume. Non-reversible integration schemes do not preserve volume in phase space and usually show also long-term energy drifts. The reasons for wanting time-reversibility are therefore eminently physical and not mathematical. A good reference is the book by Daan Frenkel and Berends Smit, "Understanding Molecular Simulation", Academic Press 1996. Regards Dr. Guido Germano Research Assistant in Theoretical Physics, University of Bristol, England Tel. +44-117-928 9000 ext. 8755, http://www.phy.bris.ac.uk/staff/germano_g.html From chemistry-request@www.ccl.net Tue Sep 15 09:04:52 1998 Received: from NPD1.NPD.UFPE.BR (npd1.npd.ufpe.br [150.161.6.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA18367 Tue, 15 Sep 1998 09:04:50 -0400 (EDT) Received: from rlongo1.dqf.ufpe.br ([150.161.5.18]) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with ESMTP id <01J1TXLDVRY8000WJV@NPD.UFPE.BR> for CHEMISTRY@www.ccl.net; Tue, 15 Sep 1998 09:48:33 GMT-3 Date: Tue, 15 Sep 1998 09:50:53 -0300 From: Ricardo Longo Subject: x-ray to cartesian To: CHEMISTRY@www.ccl.net Message-id: <35FE62AC.37EC64DF@npd.ufpe.br> MIME-version: 1.0 X-Mailer: Mozilla 4.01 [en] (Win95; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Priority: 3 (Normal) Dear Netters, Does anybody has a program that converts x-ray coordinates (symmetry + fractional coordinates of the unique atoms) into cartesian coordinates for the unit cell? I know that Ortep3 can plot the x-ray coordinates, but I cannot make to write up the cartesians of the unit cell. Thanks a lot. Ricardo Longo From chemistry-request@www.ccl.net Tue Sep 15 09:34:34 1998 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA18561 Tue, 15 Sep 1998 09:34:34 -0400 (EDT) Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.244.22]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id JAA20333 for ; Tue, 15 Sep 1998 09:34:35 -0400 Sender: richard@tc.cornell.edu Message-ID: <35FE6CEB.794B@tc.cornell.edu> Date: Tue, 15 Sep 1998 09:34:35 -0400 From: Richard Gillilan X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Re: CCL:Multi-time scale integration. References: <9809131414.ZM3019@hamilton.math.missouri.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Don Steiger wrote: > > In the literature on multi-time scale integration, a lot of importance is > placed > on time reversibility. Why this is so important is something that I have never > been able to figure out. If an integration algorithm is efficient and produces > a small global error then why is this not sufficient. If anybody can enlighten > me on this subject I would appreciate it. > My understanding is that some integrators have the additional property of being exact symplectic transformations of phase space from one time step to the next. Technically this means that phase-space volume and a hierarchy of other differential forms discovered by Poincare are exactly preserved under this transformation. If I'm not mistaken, this property also implies exact time reversibility. It has long been thought that the extraordinary long-time stability of Verlet's leapfrog algorithm was due to this property although I have not kept up with the literature enough to know if the connection has a formal basis. I believe there have been a number of numerical experiments in the literature in which high-order non-symplectic integrators are shown to blow up long before Verlet. Higher-order symplectic integrators seem to be implicit and so not as efficient unfortunately. There is a growing literature on this subject in Physics I think. Sorry, I can't seem to locate my few outdated refs on this topic, but I seem to recall some passing comments in a recent Klaus Schulten paper. Richard Gillilan Cornell Theory Center richard@tc.cornell.edu From chemistry-request@www.ccl.net Tue Sep 15 10:22:03 1998 Received: from crusher.cc.manhattan.edu (crusher.cc.manhattan.edu [149.61.10.20]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA19039 Tue, 15 Sep 1998 10:22:02 -0400 (EDT) Received: from europa.mc.manhattan.edu (europa.mc.manhattan.edu [149.61.74.6]) by crusher.cc.manhattan.edu (AIX4.2/UCB 8.7/8.7) with ESMTP id KAA22162 for ; Tue, 15 Sep 1998 10:00:03 -0400 (EDT) Received: from EUROPA/SpoolDir by europa.mc.manhattan.edu (Mercury 1.43); 15 Sep 98 10:16:12 -0500 Received: from SpoolDir by EUROPA (Mercury 1.43); 15 Sep 98 10:15:49 -0500 From: "Joseph Capitani" Organization: Manhattan College, Riverdale N.Y. To: chemistry@www.ccl.net Date: Tue, 15 Sep 1998 10:15:41 EST5EDT Subject: Allowed Spin Multiplicity of Transition States X-Confirm-Reading-To: "Joseph Capitani" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.52) Message-ID: <1C36121727D@europa.mc.manhattan.edu> Hello, We have been trying to calculate transition state energies and geometries for reactions that can be be summarized as AB + CD -----> { A---B---C---D} ----> AC + BD. AB is a known singlet, CD is a known triplet, AC is a known singlet and BD is a triplet. {A--B--C---D} is the T.S. and the reaction is not photochemical. My questions are: 1. What is/are the allowed spin(s) of the transition state? Are there general rules that govern the choice(s)? 2. Given the spin multiplicities of the reactants, are there general rules which fix the spins of the individual products? Any information would be greatly appreciated! Thanks, Joe Capitani From chemistry-request@www.ccl.net Tue Sep 15 11:31:00 1998 Received: from melba.fkem2.lth.se (melba.fkem2.lth.se [130.235.27.82]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA20626 Tue, 15 Sep 1998 11:30:59 -0400 (EDT) Received: from melba.fkem2.lth.se (melba.fkem2.lth.se [130.235.27.82]) by melba.fkem2.lth.se (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id RAA18037; Tue, 15 Sep 1998 17:25:35 +0200 Date: Tue, 15 Sep 1998 17:25:35 +0200 (CEST) From: Fernando Luis Barroso da Silva To: chemistry@www.ccl.net Subject: Some questions about MEAD Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear ALL, I would like some information about MEAD program: (a) Is there any "good" reference for MEAD software (Macroscopic Electrostatics with Atomic Detail, written by D. Bashford) ? (b) Is there an e-mailing list about MEAD ? (c) I also would be very grateful if somebody can tell me if MEAD works with the linearized Poisson-Boltzmann equation or the non-linearized form. If you have been working with this software, please, drop me a line. Thanks in advance for you attention and time. Best regards, Fernando. -- Fernando Luis Barroso da Silva Physical Chemistry II - Chemical Center POB 124 - Lund University Fax: +46 (46) 2224543 S-221 00 Lund, Sweden Phone: +46 (46) 2228241 (lab) E-mail: fernando@melba.fkem2.lth.se +46 (46) 2220381 (office) Fernando_Luis.Barroso_da_Silva@fkem2.lth.se http://www.fkem2.lth.se/personnel/fernando/dasilva.html http://idefix.ffclrp.usp.br/barroso/fernando.html From chemistry-request@www.ccl.net Tue Sep 15 12:22:58 1998 Received: from mailbox2.ucsd.edu (mailbox2.ucsd.edu [132.239.1.54]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA21256 Tue, 15 Sep 1998 12:22:58 -0400 (EDT) Received: from checfs2 (checfs2.ucsd.edu [132.239.73.6]) by mailbox2.ucsd.edu (8.8.8AS/8.6.9) with SMTP id JAA01054 for ; Tue, 15 Sep 1998 09:22:58 -0700 (PDT) Received: from [132.239.68.131] by checfs2 (SMI-8.6/UCSDPSEUDO.4) id JAA04285 for ; Tue, 15 Sep 1998 09:22:56 -0700 Message-Id: <199809151622.JAA04285@checfs2> Date: Tue, 15 Sep 1998 09:23:35 -0700 To: chemistry@www.ccl.net From: moto@ch.wani.osaka-u.ac.jp (Motohiro NAKANO) X-Sender: mnakano@checfs2.ucsd.edu Subject: Re: [Q] Dmol .outmol file MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.8r4-J15) Hello. I posted a following question two days ago. At 16:47 1998/09/13 -0700, Motohiro NAKANO wrote: >Dear CCL'ers, > >Hello. I have a question about the file format of .outmol files >generated by the MSI's Dmol program. > >Recently I tried to calculate a conjugate system by Dmol >in order to know pi- and sigma-electron population, respectively. >Dmol provided me a result of population analysis for each >irreducible representation. But when I summed up populations >on a specific atom over all irreducible representations, >it doesn't agree with the Mulliken atomic charge. > >Maybe I have a misunderstanding in reading the .outmol file. >You can read my .outmol file at > http://chehend1.ucsd.edu/~mnakano/c6br2o40.outmol >Any suggestion is welcome. Thank you. I found that the accumulated population over all irreducible representations should be divided by the number of equivalent atoms. Then it has same value with the Mulliken atomic charge. I thank to Steven D. Bennett at University of Delaware for his useful comment. -- Motohiro NAKANO 4124 Pacific Hall, UCSD 9500 Gilman Drive La Jolla, CA92093-0358 Phone 619-534-6085 (office) From chemistry-request@www.ccl.net Tue Sep 15 16:34:52 1998 Received: from dalton.dq.ufscar.br (dalton.dq.ufscar.br [200.136.224.67]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA23147 Tue, 15 Sep 1998 16:34:48 -0400 (EDT) Received: from lqt.dq.ufscar.br (dalton.dq.ufscar.br [200.136.224.67]) by dalton.dq.ufscar.br (8.8.8/8.8.8) with ESMTP id RAA22197 for ; Tue, 15 Sep 1998 17:34:18 -0300 (EST) (envelope-from garbujo@sertao.dq.ufscar.br) Sender: garbujo@sertao.dq.ufscar.br Message-ID: <35FECF4A.DC23BDC6@lqt.dq.ufscar.br> Date: Tue, 15 Sep 1998 17:34:18 -0300 From: Fabio Luiz Laurenti Garbujo Organization: LQT, DQ-UFSCar X-Mailer: Mozilla 4.5b1 [en] (X11; I; FreeBSD 2.2.6-RELEASE i386) X-Accept-Language: pt-BR MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: plot xyz Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Someone kwon a program (I prefer free ones) for FreeBSD unix who can do 3D graphics? Regards. Fabio garbujo@lqt.dq.ufscar.br