From jpdognon@concerto.valrho.cea.fr Thu Sep 25 03:26:31 1997 Received: from nenuphar.saclay.cea.fr for jpdognon@concerto.valrho.cea.fr by www.ccl.net (8.8.3/950822.1) id DAA11763; Thu, 25 Sep 1997 03:13:50 -0400 (EDT) Received: from muguet.saclay.cea.fr by nenuphar.saclay.cea.fr (8.8.5/ CEANET-ROUTER-3.0) with ESMTP id JAA13034 for ; Thu, 25 Sep 1997 09:13:13 +0200 (MET DST) Received: from concerto.valrho.cea.fr by muguet.saclay.cea.fr (8.8.5/ CEANET-ROUTER-3.0) with SMTP id JAA11974 for ; Thu, 25 Sep 1997 09:13:12 +0200 (MET DST) Received: from 194.57.214.81 by concerto.valrho.cea.fr (SMI-8.6/CEANET.2.0.1) id JAA00296; Thu, 25 Sep 1997 09:17:59 +0200 Message-ID: <342A1E11.103F@concerto.valrho.cea.fr> Date: Thu, 25 Sep 1997 09:17:21 +0100 From: Dognon X-Mailer: Mozilla 3.01Gold [fr] (Macintosh; I; PPC) MIME-Version: 1.0 To: CCL Subject: point charges in gaussian94 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear colleagues, We search informations and differences between the use of keyword Massage and keyword Charge in Gaussian94. Does anyone have experience or references. Many thanks, ====================================== Jean-Pierre Dognon CEA, FRANCE email: jpdognon@concerto.valrho.cea.fr ====================================== From laaksone@csc.fi Thu Sep 25 03:48:29 1997 Received: from voxopm.minedu.fi for laaksone@csc.fi by www.ccl.net (8.8.3/950822.1) id CAA11674; Thu, 25 Sep 1997 02:34:49 -0400 (EDT) Received: from laaksonen.csc.fi (laaksonen.csc.fi [193.166.1.75]) by voxopm.minedu.fi (8.8.5/8.8.5/CSC/SGI-2.59) with SMTP id JAA27656 for ; Thu, 25 Sep 1997 09:34:44 +0300 (EET DST) Date: Thu, 25 Sep 1997 09:34:54 +0300 (GFT Daylight Time) From: Leif Laaksonen To: chemistry@www.ccl.net Subject: Updated version of the RTAM database available Message-ID: X-X-Sender: laaksone@laaksonen.csc.fi MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, An updated version (V4.0 September 25, 1997) of the Relativistic Theory of Atoms and Molecules (RTAM) bibliography database is searchable at the addresses: http://laaksonen.csc.fi/rtam/ and http://www.csc.fi/lul/rtam/ The database contains about 9000 references. The first URL is an experimental tcl driven search engine, while the second one is the old Unix glookbib based engine. Please try the both ones and please comment on any possible bugs or failures. Regards, -leif laaksonen ------------------------------------------------------------------- Center for Scientific Computing | Phone: 358 9 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 9 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi -------- URL: http://laaksonen.csc.fi/leif.laaksonen.html --------- From citra@syrres.com Thu Sep 25 09:26:34 1997 Received: from apollo.syrres.com for citra@syrres.com by www.ccl.net (8.8.3/950822.1) id IAA12965; Thu, 25 Sep 1997 08:42:31 -0400 (EDT) Received: from pc-citra.syrres.com ([204.168.121.167]) by apollo.syrres.com (Netscape Mail Server v2.0) with SMTP id AAA166 for ; Thu, 25 Sep 1997 08:41:40 -0400 X-Sender: citra@srcinet.syrres.com X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: citra@syrres.com (mario citra) Subject: Charges and dipole moments Date: Thu, 25 Sep 1997 08:41:40 -0400 Message-ID: <19970925124140173.AAA166@pc-citra.syrres.com> How are the default charges computed in MOPAC? I understand how the Mulliken charges are obtained, but I have never seen a reference to the default charges. I am assuming they are obtained by calculating the charge density from the localized MO's. Is this correct? Often Mulliken charges do not reproduce physical observables such as dipole moments accurately. Are there any references to alternative methods which calculate atomic charges and show good agreement with experimentally determined dipole moments? Thank you in advance. ********************************** * Regards, * * Mario J. Citra PhD * * Syracuse Research Corporation * * 6225 Running Ridge Road * * North Syracuse, New York 13212 * * * * phone 315-452-8406 * * email citra@syrres.com * ********************************** From hebant@ext.jussieu.fr Thu Sep 25 09:46:50 1997 Received: from shiva.jussieu.fr for hebant@ext.jussieu.fr by www.ccl.net (8.8.3/950822.1) id IAA12931; Thu, 25 Sep 1997 08:32:31 -0400 (EDT) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.8.7/jtpda-5.2) with ESMTP id OAA21077 for ; Thu, 25 Sep 1997 14:32:23 +0200 (METDST) Received: from [134.157.11.16] by idf.ext.jussieu.fr (8.8.5/jtpda-4.0) with ESMTP; Thu, 25 Sep 1997 14:32:21 +0200 (METDST) X-Sender: hebant@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 25 Sep 1997 10:32:32 +0100 To: CHEMISTRY@www.ccl.net From: Pascal HEBANT Subject: K2NO3 + : a black hole with G94 Content-Transfer-Encoding: 8bit Dear CCLers, I am performing calculations on K2NO3 + with G94 revision D.4 on a SGI Indy R4400. Here is one my input : %CHK=k2no3 #P HF/gen opt guess=core test scf=(maxcycle=500) ****************** 1 1 7 -0.00000010 0.00000014 -0.00000002 8 -0.74000007 1.28171770 -0.00000002 8 1.47999993 0.00000016 -0.00000002 8 -0.74000010 -1.28171750 -0.00000002 19 -0.00000010 0.00000014 1.85999999 19 -0.00000010 0.00000014 -1.85999989 K 0 LANL2DZ **** N 0 6-31G **** O 0 6-31G **** K 0 LANL2DZ **** --Link1-- %CHK=k2no3 # MP2/chkbas nosym Guess=Read opt freq geom=AllCheckpoint test scf=(maxcycle=500) And here is the distance matrix after the first geometry optimization : ---------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 N 0.000000 2 O 0.000000 0.000000 3 O 0.000000 0.000000 0.000000 4 O 0.000000 0.000000 0.000000 0.000000 5 K 0.000000 0.000000 0.000000 0.000000 0.000000 6 K 0.000000 0.000000 0.000000 0.000000 0.000000 6 6 K 0.000000 As you can see, all the atoms are superimposed... And, of course, there is an error and calculation stops. I try to perform runs at the DFT level (SVWN, B3LYP or B3PW91). I used the 3-21G Basis set for K. I used the geometry obtained with DMol as a starting point. And I always reach that final point after one or more geometry optimizations. Can anyone help me? Regards Pascal ***************************************************************************** Pascal HEBANT Laboratoire d'Electrochimie et de Chimie Analytique Ecole Nationale Superieure de Chimie de Paris 11 rue Pierre et Marie Curie 75005 Paris FRANCE tel:+33 - 01 44 27 66 94 fax: +33 - 01 44 27 67 50 http://alcyone.enscp.jussieu.fr/Pages/LECA/GP/Pascal.html ***************************************************************************** Ä From Eric.Vangrevelinghe@univ-orleans.fr Thu Sep 25 11:26:35 1997 Received: from centre.univ-orleans.fr for Eric.Vangrevelinghe@univ-orleans.fr by www.ccl.net (8.8.3/950822.1) id KAA13616; Thu, 25 Sep 1997 10:59:16 -0400 (EDT) Received: from univ-orleans.fr (tourmalet.univ-orleans.fr [193.49.95.21]) by mailhost.univ-orleans.fr (8.8.7/jtpda-5.2) with ESMTP id QAA23965 for ; Thu, 25 Sep 1997 16:59:38 +0200 (MET DST) Message-ID: <342A7C12.958FEAF7@univ-orleans.fr> Date: Thu, 25 Sep 1997 16:58:27 +0200 From: Eric Vangrevelinghe Organization: ICOA CNRS UPRESS-A-6005 X-Mailer: Mozilla 4.02 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Molecular Shape Descriptors Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL Members I am seeking sample source codes or algorithms that will enable me to calculate the following shape descriptors: - Radius of gyration - Characteristic ratio - Persistence length Any programming languages or pointers are welcome. Thanks in advance. Eric -- _____________________________________________________________ Eric VANGREVELINGHE --- PhD Student mailto:eric.vangrevelinghe@univ-orleans.fr http://web.univ-orleans.fr/ICOA ------------------------------------------------------------- I.C.O.A. Institut de Chimie Organique et Analytique CNRS UPRESS-A-6005 BP 6759 45067 ORLEANS Cedex 2 FRANCE tel: (33) 02 38 49 45 77 fax: (33) 02 38 41 72 81 _____________________________________________________________ From comartin@wicc.weizmann.ac.il Thu Sep 25 12:26:53 1997 Received: from winston.weizmann.ac.il for comartin@wicc.weizmann.ac.il by www.ccl.net (8.8.3/950822.1) id MAA13859; Thu, 25 Sep 1997 12:00:13 -0400 (EDT) Received: from localhost by winston.weizmann.ac.il; (5.65v3.2/1.1.8.2/28Jul95-1212AM) id AA03642; Thu, 25 Sep 1997 17:46:24 +0200 Date: Thu, 25 Sep 1997 17:46:23 +0200 (IST) From: "Jan M.L. Martin" X-Sender: comartin@winston.weizmann.ac.il To: mario citra Cc: chemistry@www.ccl.net Subject: Re: CCL:M:Charges and dipole moments In-Reply-To: <19970925124140173.AAA166@pc-citra.syrres.com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 25 Sep 1997, mario citra wrote: > > How are the default charges computed in MOPAC? I understand how the > Mulliken charges are obtained, but I have never seen a reference to the > default charges. I am assuming they are obtained by calculating the charge > density from the localized MO's. Is this correct? > > Often Mulliken charges do not reproduce physical observables such as dipole > moments accurately. Are there any references to alternative methods which > calculate atomic charges and show good agreement with experimentally > determined dipole moments? Thank you in advance. Some alternative charge distributions: * CHELPG (charges from electrostatic potentials): C. M. Breneman and K. B. Wiberg, {\it J. Comput. Chem.} {\bf 11}, 361 (1990); see also Chirlian and Francl, quoted there. This should be the best for getting dipole moments >from the partial charges close to the one obtained from the wave function. (Agreement with expt. cannot be any better than for the underlying wave function, except fortuitously.) Other methods include: * topological method: R. F. W. Bader, {\it Atoms in molecules: a quantum theory} (Oxford University Press, Oxford, 1990). The most "rigorous", but also the most computationally expensive * APT (atomic polar tensor): J. Cioslowski, {\it J. Am. Chem. Soc.} {\bf 111}, 8333 (1989). The only one that directly relates to an observable quantity (IR intensities). Very costly to do for JUST that, but get thrown in as a freebie with a frequency+intensities calculation, so if you need the latter anyhow... * natural population analysis: A. E. Reed, L. A. Curtiss, and F. Weinhold, Chem. Rev. 88, 899 (1988). COmputationally quite inexpensive and probably a good compromise. If you were to move on to ab initio and/or DFT methods, Mulliken is the most sensitive of the lot to the basis set and APT to electron correlation. For more details see e.g.: F. De Proft, J. M. L. Martin, and P. Geerlings, ``On the performance of density functional methods for describing atomic populations, dipole moments and infrared intensities'' Chemical Physics Letters 250, 393--401 (1996). P. Geerlings, F. De Proft, and J. M. L. Martin, ``Density-Functional Theory Concepts and Techniques for Studying Molecular Charge Distributions and Related Properties'', in Theoretical and Computational Chemistry, Vol. 4: Recent developments and applications of modern density functional theory (ed. J. Seminario), Elsevier, New York, 1996, pp. 773-809. Finally, a general review article: S. M. Bachrach, in {\it Reviews in Computational Chemistry, Volume V} (ed. K. B. Lipkowitz and D. B. Boyd) (VCH, New York, 1995). JM --------------------------------------------------------------------------- dr. Jan M.L. Martin Senior Lecturer, Computational Chemistry Department of Organic Chemistry/Kimmelman Building, Room 262 Weizmann Institute of Science/Rechovot 76100/ISRAEL FAX +972(8)9344142 Phone +972(8)9342533 E-mail comartin@wicc.weizmann.ac.il *** research group WWW home page http://theochem.weizmann.ac.il/ *** ---- kol ha-olam kulo gesher tzar me'od, v'ha-ikar lo l'hitfached k'lal --- From cramer@pollux.chem.umn.edu Thu Sep 25 16:26:40 1997 Received: from pollux.chem.umn.edu for cramer@pollux.chem.umn.edu by www.ccl.net (8.8.3/950822.1) id PAA15108; Thu, 25 Sep 1997 15:41:06 -0400 (EDT) Received: by pollux.chem.umn.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) for chemistry@www.ccl.net id OAA25207; Thu, 25 Sep 1997 14:41:02 -0500 From: cramer@pollux.chem.umn.edu (Christopher Cramer) Message-Id: <199709251941.OAA25207@pollux.chem.umn.edu> Subject: CCL:M:Charges and dipole moments (fwd) To: chemistry@www.ccl.net Date: Thu, 25 Sep 1997 14:41:01 -0500 (CDT) X-Mailer: ELM [version 2.4 PL25] Content-Type: text Re below discussion on charges: > > > > How are the default charges computed in MOPAC? I understand how the > > Mulliken charges are obtained, but I have never seen a reference to the > > default charges. I am assuming they are obtained by calculating the charge > > density from the localized MO's. Is this correct? > > > > Often Mulliken charges do not reproduce physical observables such as dipole > > moments accurately. Are there any references to alternative methods which > > calculate atomic charges and show good agreement with experimentally > > determined dipole moments? Thank you in advance. > Some alternative charge distributions: > > * CHELPG (charges from electrostatic potentials): C. M. Breneman and K. B. > Wiberg, {\it J. Comput. Chem.} {\bf 11}, 361 (1990); see also Chirlian and > Francl, quoted there. This should be the best for getting dipole moments > from the partial charges close to the one obtained from the wave function. > (Agreement with expt. cannot be any better than for the underlying wave > function, except fortuitously.) > Quite the contrary -- a charge model can do better than the underlying wave function if it is DESIGNED to do so (what we have coined a Class IV charge model). The CM1 charge model (reference Storer, J. W.; Giesen, D. J.; Cramer, C. J.; Truhlar, D. G. " Class IV Charge Models: A New Semiempirical Approach in Quantum Chemistry" J. Comput.-Aid. Mol. Des. 1995, 9, 87. available on the web at http://www.ibc.wustl.edu/jcamd/278/paper.html) is a mapping procedure that takes lower quality charges (e.g., semiempirical ZDO Mulliken) and converts them to very high-quality charges that reproduce experiimental dipole moments better than the expectation value of the dipole moment operator acting on the semiempirical wave function. CJC -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 cramer@pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer From fgonzale@lauca.usach.cl Thu Sep 25 17:26:40 1997 Received: from ralun.usach.cl for fgonzale@lauca.usach.cl by www.ccl.net (8.8.3/950822.1) id QAA15377; Thu, 25 Sep 1997 16:34:56 -0400 (EDT) Received: from lauca.usach.cl (root@Lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.8.5/8.8.5) with ESMTP id QAA01728 for ; Thu, 25 Sep 1997 16:35:38 -0400 (CST) Received: (from fgonzale@localhost) by lauca.usach.cl (8.6.12/8.6.12) id QAA03741; Thu, 25 Sep 1997 16:35:55 -0400 Date: Thu, 25 Sep 1997 16:35:53 -0400 (CST) From: Fdo Danilo Gonzalez Nilo To: chemistry@www.ccl.net Subject: MD on LINUX Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi All! I'm looking for any information about the Molecular Dymanics programs running on LINUX (Free or Commercial). I will summarize the answers Thanks a Lot!!! Fernando Danilo Gonzalez N. University of Santiago de Chile Faculty of Chemistry and Biology, Computational Chemistry Lab. Casilla 40, Correo 33, Santiago, Chile Fono: (562) 681 2575 Anexo:799 E-mail : fgonzale@lauca.usach.cl Fax : (562) 681 2108 URL : http://quimbio.usach.cl/~danilo/ **************************************************************************