From chemistry-request@server.ccl.net Wed Jul 5 02:52:20 2000 Received: from wacx73.chemie.uni-wuerzburg.de (root@wacx73.chemie.uni-wuerzburg.de [132.187.24.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA29023 for ; Wed, 5 Jul 2000 02:52:20 -0400 Received: (from munzar@localhost) by wacx73.chemie.uni-wuerzburg.de (8.9.3/8.9.3) id IAA03759; Wed, 5 Jul 2000 08:52:11 +0200 From: Marketa Ludmilla Munzarova Message-Id: <200007050652.IAA03759@wacx73.chemie.uni-wuerzburg.de> Subject: Mulliken pop. analysis of MOs To: chemistry@ccl.net Date: Wed, 5 Jul 2000 08:52:11 +0200 (CEST) CC: munzar@wacx73.chemie.uni-wuerzburg.de X-Mailer: ELM [version 2.4ME+ PL60 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear computational chemists, I am interested in analyzing the composition of optimized molecular orbitals from a Gaussian98 output. The MO coefficients can be found easily, but I would like to perform a Mulliken population analysis ot the optimized MOs. However, the IOPs in link 601 do offer only Mulliken analysis of the _total_ electron density. It seems to me that the only possibility to get MOs analyzed is to code the Mulliken analysis myself, using optimized MO coefficients and the overlap matrix. But maybe there is still an IOP option in the Gaussian which does this automatically? Thank you in advance for your help, Marketa Munzarova --------- Marketa Ludmila Munzarova Faculty of Science, Masaryk University Brno e-mail: ludmila@chemi.muni.cz -------- From chemistry-request@server.ccl.net Wed Jul 5 08:19:47 2000 Received: from vytautas.vdu.lt (mail@vytautas.vdu.lt [193.219.38.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA31190 for ; Wed, 5 Jul 2000 08:19:45 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 139o9E-0003cv-00; Wed, 05 Jul 2000 14:19:24 +0200 Received: from vaidila.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id OAA18756 for ; Wed, 5 Jul 2000 14:19:24 +0200 (GMT) Message-ID: <3963A64B.3F25AC8A@vaidila.vdu.lt> Date: Wed, 05 Jul 2000 14:19:08 -0700 From: "art'" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 CC: chemistry@ccl.net Subject: G94 Cube file References: <200007050652.IAA03759@wacx73.chemie.uni-wuerzburg.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, CCLers, There is lack of formation about CUBE in the help of Gaussian. These are files with data of MO or density information in 3D lattice. What kind of soft can visualise Cube files? How they should be interpreted or analized? Any information concerning that is wellcome. I will summurise A.Ziemys *Vytautas Magnus Universitu Ins. of Biochemistry Dept. of Biology Lab. of Enzymatic chemistry Vileikos 8 Mokslininku 12 LT-3035, Kaunas Vilnius Lithuania Lithuania From chemistry-request@server.ccl.net Wed Jul 5 10:30:49 2000 Received: from Kitten.mcs.net (Kitten.mcs.com [192.160.127.90] (may be forged)) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA31681 for ; Wed, 5 Jul 2000 10:30:49 -0400 Received: from oemcomputer (P62-Chi-Dial-4.pool.mcs.net [205.253.224.254]) by Kitten.mcs.net (8.9.3/8.9.3) with SMTP id JAA88619; Wed, 5 Jul 2000 09:30:36 -0500 (CDT) (envelope-from rone@mcs.net) Message-ID: <000a01bfe68c$702a6620$fee0fdcd@oemcomputer> From: "Rebecca Rone" To: , "Richard Gee" Subject: Re: CCL:Charmm Date: Wed, 5 Jul 2000 09:22:22 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Dear Richard, Look around to see if you have access to MSI's QUANTA. QUANTA will let you build a number of polymers including all the file types you named. You may need to use the 3D editor to modify the monomeric unit for the fluoropolymer but that should be straight forward. If memory serves it is then possible to embed the new monomeric unit in the selection files that come up in the polymer builder toolkit. If you need some advice feel free to contact me. Dr. Rebecca Rone Rone Biotechnology Consulting www.mcs.net/~rone -----Original Message----- From: Richard Gee To: chemistry@ccl.net Date: Friday, June 30, 2000 6:37 PM Subject: CCL:Charmm >Dear all, > >I recently decided to use Charmm to do MD on fluoropolymers, and can >find no information, examples, etc. on using Charmm for such a >purpose. Does anyone out there use Charmm for synthetic polymer >simulations? If so, any references, databases, websites, etc. would >be appreciated. In fact, if anyone could send "rtf", "prm", etc type >files, for synthetic polymer residues, I would be grateful! > >Best regards, > > >________________________________________________________________________ >Richard Gee >Chemistry and Materials Science Directorate >Lawrence Livermore National Laboratory >University of California >7000 East Avenue, MS L-268 >Livermore, CA, USA 94551 >Phone: (925) 423-1177 >Fax: (925) 422-6810 >email: gee10@llnl.gov >________________________________________________________________________ > >-= 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 Wed Jul 5 03:01:02 2000 Received: from gpo.munich.msi-eu.com (cam.msi-eu.com [192.190.183.254]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA29100 for ; Wed, 5 Jul 2000 03:01:00 -0400 Received: from woernitz.munich.msi-eu.com (woernitz.munich.msi-eu.com [172.29.64.178]) by gpo.munich.msi-eu.com (8.9.3/8.9.3/Debian/GNU) with ESMTP id IAA21763; Wed, 5 Jul 2000 08:58:49 +0200 Received: (from jxh@localhost) by woernitz.munich.msi-eu.com (8.8.8/8.8.8) id IAA20525; Wed, 5 Jul 2000 08:58:48 +0200 (MEST) From: "Joerg-Ruediger Hill" Message-Id: <10007050858.ZM20521@woernitz.munich.msi-eu.com> Date: Wed, 5 Jul 2000 08:58:47 +0200 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@ccl.net Subject: Re: CCL:Theta_0 values for polyatomics Cc: jxh@msi-eu.com Hi, > In the simple case of a diatomic molecule, we know that the internuclear > distance re (well depth) and r0 (zero-point corrected) differ slightly due > to the anharmonicity of the potential function. That's why r0 > re. But, > you can 'estimate' the difference r0 - re fairly easily. (One can easily > see the difference by just looking at the energy vs distance plot). > > In the most complex case of polyatomics, you have 3N-5 or 3N-6 degrees of > freedom. For the simpler case of a bent triatomic molecule as for example > H2O, you have a Theta_e angle that you calculate by minimizing the energy, > but an experimentalist should be measuring a Theta_0 value. Most of the > time, calculations compare their theta_e results with an experimental > theta number, whatever its subscript. I know the difference between > theta_e and theta_0 should be very small in most triatomics, but sometimes > an experiment may report both values, their difference being as much as 1 > degree. > > I want to find out how I can 'correct' a theta_e value I calculate in some > level of theory, to theta_0, by incorporating in some way (which one?) the > zero-point contributions. > > As one can see, this is a special case in a big problem which will be more > and more evident in the future, as calculations become more and more > accurate. To what degree of accuracy are experimental and theoretical > results comparable, since 'theory decides what is measurable', but on the > other hand we don't really measure EXACTLY the same thing? The differences between equilibrium structures as calculated by computational chemistry methods and "measured" structures are well understood and there is a strict theoretical framework for calculating them, although it is very expensive (you need third derivatives) and therefore not very widely done=2E As a starting point you might want to check out: J.-R. Hill, J. Sauer, and R. Ahlrichs Ab Initio Calculation of Nuclear Motion Corrections to the Geometries of Water, Methanol and Silanol Mol. Phys. 73(2) (1991), 335 - 348 and references therein. The entire theoretical derivation can be found in: M. Toyama and T. Oka and Y. Morino Effect of vibration and rotation on the internuclear distance J. Mol. Spectrosc. 13 (1964), 193 Hope this helps J=F6rg-R=FCdiger Hill ------------------------------------------------------------------------- Dr. Joerg-Ruediger Hill | Phone +49 89 61459-413 | The opinions expressed in Molecular Simulations | Fax +49 89 61459-400 | this message are my perso- Inselkammerstrasse 1 | E-mail jxh@msi-eu.com | nal opinions and no offi- D-82008 Unterhaching | | cal statements of Molecu- Germany | http://www.msi.com/ | lar Simulations Inc. ------------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Jul 5 09:07:42 2000 Received: from gensig.nibsc.ac.uk (gensig.nibsc.ac.uk [193.62.43.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA31386 for ; Wed, 5 Jul 2000 09:07:42 -0400 Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by gensig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id OAA68103 for ; Wed, 5 Jul 2000 14:07:25 +0100 (BST) Message-ID: <3963344E.A3AFF658@nibsc.ac.uk> Date: Wed, 05 Jul 2000 14:12:46 +0100 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: time averaged restraints Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL members Which of the commonly available simulation/refinement codes allow incorporation of the 'time averaged' restraints first suggested by Torda et al.? Reference: J Mol Biol (1990) vol 214,223-235. Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat. Torda AE, Scheek RM, van Gunsteren WF Best wishes Mark -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@server.ccl.net Wed Jul 5 10:33:06 2000 Received: from sun.rhrk.uni-kl.de (sun.rhrk.uni-kl.de [131.246.137.50]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA31724 for ; Wed, 5 Jul 2000 10:33:05 -0400 Received: from aixs1.rhrk.uni-kl.de ( exim@aixs1.rhrk.uni-kl.de [131.246.137.3] ) by sun.rhrk.uni-kl.de id aa06986 for ; 5 Jul 2000 16:32 MESZ Received: from aixd1.rhrk.uni-kl.de ([131.246.137.210] ident=exim) by aixs1.rhrk.uni-kl.de with esmtp (Exim 3.03 #2) id 139qDs-0007Rc-00 for CHEMISTRY@server.ccl.net; Wed, 05 Jul 2000 16:32:20 +0200 Received: from gerwalin by aixd1.rhrk.uni-kl.de with local (Exim 3.03 #2) id 139qDr-00082A-00 for CHEMISTRY@server.ccl.net; Wed, 05 Jul 2000 16:32:19 +0200 To: CHEMISTRY@server.ccl.net Subject: Must g98 be compiled with pgf77 Message-Id: From: Elmar Gerwalin Date: Wed, 05 Jul 2000 16:32:19 +0200 Here's a (short) summary of the about 20 answers I got: (I edited them a bit) The original questions were: ? Do I have to use the pgf77 compiler to install gaussian98 on a LINUX PC ? ? What happens after the trial period ? ( I don't want to buy a Fortran compiler, as there are free ones available and Gaussian itself was expensive enough ;-) ) ? What has to be done to use the g77 compiler (from my SuSE LINUX distribution) ? ---------- the answers: -------- Why pgf77? *(Gaussian themselves:) The only supported compiler on Linux for G98 is the PGF77 compiler. We made this choice because it gives good performance improvements over the public domain compiler at a moderate price. In terms of manpower and support we need to choose one and this compromise seems the best. *(Gaussian themselves again:) When we decided to switch to the PGI compilers, it was not a decision we made lightly. We found that performance was typically a factor of two or more better than gcc/g77. We weighed that performance gain against the need to buy a compiler, and decided that the benefits outweighed the costs. * (Gaussian ...:) You also have the option of getting a precompiled distribution. This is a viable option for many sites where they primarily wish to run the code as distributed and are not doing development. * It's far the best compiler for LINUX (much faster than g77 or f2c) What happens after the evaluation period ? (members of the Portland group(pg): please ignore this part ;-) Old versions of the pgf77: * Dont worry. Install the PGI compilers and G98 will run OK even after the license expires Actual evaluation version:( Version 3.1 of pgf77 ) * different from earlier trial versions executables compiled with it cease to work after the trial period, unfortunately. * The compiled binaries will fail after the trial period! * executables are deleted after the trial period So why not using another f77 compiler ? * Problems are the files mdutil.F and mdutil.c. There are a few changes .., depending on the revision of gaussian. * hand-edit the Makefile. I remember I once compiled g98 with g77, and for some reason I started from the Sun Makefile instead of the i386 Makefile. Then, you have to modify byteorder-specific things etc. You can get a flavour what has to be done if you compare the individual Makefiles coming along with g98.... --> So in summary, if you are a decent hacker, no problem. * No. It will compile quite happily with g77, with a few minor changes. * I did it and it worked for redhat 6.1 (changes in bsd/i386.make) What did I do ? I didn't test another compiler yet(!),although the executables were deleted after 14 days... I won't buy pgf77 therefore, I guess -------end of summary --------- Elmar From chemistry-request@server.ccl.net Wed Jul 5 11:33:55 2000 Received: from cuces.unisi.it (cuces.unisi.it [193.205.4.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA32172 for ; Wed, 5 Jul 2000 11:33:54 -0400 Received: from unisi.it (indy.ctf.unisi.it [192.167.123.180]) by unisi.it (PMDF V5.2-32 #31247) with ESMTP id <01JREZVO1KDC002220@unisi.it> for chemistry@ccl.net; Wed, 5 Jul 2000 17:33:40 MET Date: Wed, 05 Jul 2000 17:34:09 +0200 From: "Dr. Fabrizio Manetti" Subject: pi-stacking Sender: fabrizio@unisi.it To: chemistry@ccl.net Message-id: <39635571.A6B35AB4@unisi.it> MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.2 IP22) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: it Dear All, I would like to know if and how it is possible (by means of Macromodel/Batchmin package) to evaluate aromatic pi-pi effects and their impact on interactions between small ligands and macromolecules. Answers will be summarized. Thank you, Fabrizio ******************************** Dr. Fabrizio Manetti Dip. Farmaco Chimico Tecnologico Universita' degli Studi di Siena Via Aldo Moro I-53100 Siena, Italy Phone: ++39 0577 234307 Fax: ++39 0577 234333 ******************************** From chemistry-request@server.ccl.net Wed Jul 5 12:44:48 2000 Received: from gerwazy.chem.uni.wroc.pl (gerwazy.chem.uni.wroc.pl [156.17.103.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA32519 for ; Wed, 5 Jul 2000 12:44:46 -0400 Received: from wchuwr.chem.uni.wroc.pl ([156.17.103.1]) by gerwazy.chem.uni.wroc.pl (8.8.8+Sun/8.8.8) with ESMTP id SAA12882 for ; Wed, 5 Jul 2000 18:55:00 +0200 (MET DST) Received: from WCHUWR/SpoolDir by wchuwr.chem.uni.wroc.pl (Mercury 1.44); 5 Jul 00 18:48:23 MET Received: from SpoolDir by WCHUWR (Mercury 1.44); 5 Jul 00 18:48:07 MET From: "Adrian Radomir Jaszewski" Organization: University of Wroclaw (Chemistry) To: chemistry@server.ccl.net Date: Wed, 5 Jul 2000 18:48:07 MET Subject: compiler for Gaussian98 on Linux/AMDAthlon system Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Message-ID: Dear CCL'ers What compiler do I have to use to install gaussian98 on a LINUX PC with AMD Athlon 800MHz processor? I know that Gaussian recommends the PGF77 compiler for Linux/Pentium systems but I have some problems with a correct complitation/instalation of G98 on my Athlon machine using a trial verison of this compiler. What has to be done to use the g77 compiler (Red Hat Linux distribution)? Adrian =============================================== Adrian R. Jaszewski Faculty of Chemistry UNIVERSITY OF WROCLAW 14 Joliot-Curie St. 50-383 Wroclaw Poland e-mail: adrian@wchuwr.chem.uni.wroc.pl ================================================ From chemistry-request@server.ccl.net Wed Jul 5 14:50:01 2000 Received: from wacx73.chemie.uni-wuerzburg.de (root@wacx73.chemie.uni-wuerzburg.de [132.187.24.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA00297 for ; Wed, 5 Jul 2000 14:50:00 -0400 Received: (from munzar@localhost) by wacx73.chemie.uni-wuerzburg.de (8.9.3/8.9.3) id UAA07780 for chemistry@ccl.net; Wed, 5 Jul 2000 20:50:00 +0200 From: Marketa Ludmila Munzarova Message-Id: <200007051850.UAA07780@wacx73.chemie.uni-wuerzburg.de> Subject: Mulliken PA of MOs: Answers To: chemistry@ccl.net Date: Wed, 5 Jul 2000 20:50:00 +0200 (CEST) X-Mailer: ELM [version 2.4ME+ PL60 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi CCLers, I am collecting here the answers which I got on my following question: ********************************************************************* Dear computational chemists, I am interested in analyzing the composition of optimized molecular orbitals from a Gaussian98 output. The MO coefficients can be found easily, but I would like to perform a Mulliken population analysis ot the optimized MOs. However, the IOPs in link 601 do offer only Mulliken analysis of the _total_ electron density. It seems to me that the only possibility to get MOs analyzed is to code the Mulliken analysis myself, using optimized MO coefficients and the overlap matrix. But maybe there is still an IOP option in the Gaussian which does this automatically? Thank you in advance for your help, Marketa --------- Marketa Ludmila Munzarova Faculty of Science, Masaryk University Brno e-mail: ludmila@chemi.muni.cz -------- ********************************************************************* ANSWER1: ********************************************************************* Return-Path: X-Sender: pis_diez@dalton.quimica.unlp.edu.ar Date: Wed, 05 Jul 2000 09:24:38 -0300 To: Marketa Ludmilla Munzarova Subject: Re: CCL:Mulliken pop. analysis of MOs Dear Ludmilla, I wrote a small set of subroutines to make the part of the MPA that g98 doesn't make. You have to request g98 to print the overlap matrix and the coeffs of the MO-LCAO expansion and prepare two files from them. During runtime you must answer some trivial question (# of atoms, #of basis, ie order of the matrix, and # of MOs in which you are interested. That's because I didn't include any parser in my routines). It works well, it gives the MO population in terms of the AOs and in terms of the atoms. This info complements well the overlap population part that g98 does. If you are interested in that program please let me know and I'll send it to you as soon as I make some changes (Titles are in Spanish!!) an include a well-documented example. Regards, Reinaldo ********************************************************************* ANSWER2: ********************************************************************* Return-Path: Date: Thu, 6 Jul 2000 00:05:20 +0930 To: Marketa Ludmilla Munzarova Subject: Re: CCL:Mulliken pop. analysis of MOs Return-Receipt-To: b_duke@quoll.ntu.edu.au Hi, Do you mean you want to do a Mulliken analysis of each occupied orbital? That is - for MO i define P(k,l,i) = 2*C(k,i)*C(l,i)*S(k,l) and then take sum over k of P(k,l,i) to give g(l,i) and then perhaps to sum g(l,i) over all orbitals l on atom A. I coded this myself - I think it is l601. I may be able to let you have this but I am not at home in Australia at present. I am in England. My code also sum the g(l,i) terms over all orbitals of the same angular momentum quantum number as I am looking for mixing in so called core orbitals between say d orbitals on one atom and s orbitals on a neighbour. Regards, Brian. -- Associate Professor Brian Salter-Duke (Brian Duke) Chemistry, Faculty of Science, IT and Education, Northern Territory University, Darwin, NT 0909, Australia. Phone (61) (0)8-89466702 e-mail: b_duke@lacebark.ntu.edu.au or b_duke@quoll.ntu.edu.au ****************************************************************** From chemistry-request@server.ccl.net Wed Jul 5 15:30:42 2000 Received: from terra.ifi.unicamp.br (terra.ifi.unicamp.br [143.106.6.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA00493 for ; Wed, 5 Jul 2000 15:30:38 -0400 Received: from ifi.unicamp.br (lua [143.106.6.13]) by terra.ifi.unicamp.br (8.9.3/8.9.3) with ESMTP id QAA03202 for ; Wed, 5 Jul 2000 16:28:34 -0300 (BSC) Received: (from daemon@localhost) by ifi.unicamp.br (8.9.3/8.9.3) id QAA27433 for ; Wed, 5 Jul 2000 16:28:30 -0300 (BSC) Received: from sala18.ifi.unicamp.br(143.106.72.138), claiming to be "pasteur" via SMTP by lua.ifi.unicamp.br, id smtpdAAAa006g.; Wed Jul 5 16:28:23 2000 From: "Scheila" To: Subject: atomic units to electric field Date: Wed, 5 Jul 2000 16:21:53 -0300 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dears CClers, In the new version of the hyperchem program it is possible to apply an electric field to a molecule and perform geometry optimization considering this field. The electric field units considered in the software is atomic units. Could someone help-me converting this atomic units to a more familiar units of electric field, that is V/m or N/C? Thanks Scheila Braga IFGW - DFA - UNICAMP Campinas - Brasil scheila@ifi,unicamp.br From chemistry-request@server.ccl.net Wed Jul 5 16:52:27 2000 Received: from Mercury.acs.unt.edu (mercury.acs.unt.edu [129.120.220.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA00943 for ; Wed, 5 Jul 2000 16:52:26 -0400 Received: from jove.acs.unt.edu (10759@jove.acs.unt.edu [129.120.220.41]) by Mercury.acs.unt.edu (8.8.8/8.8.8) with ESMTP id PAA06368 for ; Wed, 5 Jul 2000 15:52:10 -0500 (CDT) Received: from localhost (tdp0006@localhost) by jove.acs.unt.edu (8.8.8/8.8.8) with ESMTP id PAA17916 for ; Wed, 5 Jul 2000 15:52:09 -0500 (CDT) Date: Wed, 5 Jul 2000 15:52:09 -0500 (CDT) From: TREVOR D POWER To: CHEMISTRY@ccl.net Subject: Re: CCL:atomic units to electric field In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Scheila, Divide the electric field (in V/m) by 5.1423 X 10^11 V/m to get atomic units. source: Szabo and Ostlund, Modern Quantum Chemistry, Dover Publications, INC. published in 1996, p. 42. Cheers, David Power Department of Chemistry University of North Texas NT Station, Box 305070 Denton, TX 76203-5070 tdp0006@unt.edu On Wed, 5 Jul 2000, Scheila wrote: > > > Dears CClers, > > > In the new version of the hyperchem program it is possible to apply an > electric field to a molecule and perform geometry optimization considering > this field. The electric field units considered in the software is atomic > units. > Could someone help-me converting this atomic units to a more familiar > units of electric field, that is V/m or N/C? > > Thanks > > Scheila Braga > > > IFGW - DFA - UNICAMP > Campinas - Brasil > scheila@ifi,unicamp.br > > > -= 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 Wed Jul 5 13:29:40 2000 Received: from genxy.com (mailhub.genxy.com [207.137.9.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA00006 for ; Wed, 5 Jul 2000 13:29:25 -0400 Received: from genxy.com (genxy5-50.genxy.com [172.20.5.50]) by genxy.com (8.9.1b+Sun/8.9.1) with ESMTP id KAA03945 for ; Wed, 5 Jul 2000 10:33:48 -0700 (PDT) Message-ID: <39636FA4.CF35D7C0@genxy.com> Date: Wed, 05 Jul 2000 10:25:56 -0700 From: Iraj Daizadeh X-Mailer: Mozilla 4.73 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: comutational precision: removing round-off errors. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello. If one takes 625 and divides this number by, lets say, 5 on a computer one may get one of two numbers that look like: 125.000000000000000001 and 124.4999999999999999 . Is this true? and, if so, how does one remove possible rounding errors produced when this occurs during lets say integration.... Thanks, Iraj Daizadeh, Ph.D. Patent Liaison Statistical Genomics Genset Corporation iraj.daizadeh@genxy.com From chemistry-request@server.ccl.net Wed Jul 5 18:17:47 2000 Received: from sungod.ccs.yorku.ca (sungod.ccs.yorku.ca [130.63.236.104]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA01268 for ; Wed, 5 Jul 2000 18:17:46 -0400 Received: from sunburn.ccs.yorku.ca (sunburn.ccs.yorku.ca [130.63.236.110]) by sungod.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id SAA21581; Wed, 5 Jul 2000 18:17:44 -0400 (EDT) Received: from localhost (serge@localhost) by sunburn.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id SAA28509; Wed, 5 Jul 2000 18:17:41 -0400 (EDT) X-Authentication-Warning: sunburn.ccs.yorku.ca: serge owned process doing -bs Date: Wed, 5 Jul 2000 18:17:37 -0400 (EDT) From: "S.I.Gorelsky" X-Sender: serge@sunburn.ccs.yorku.ca To: Marketa Ludmila Munzarova cc: chemistry@ccl.net Subject: Re: CCL:Mulliken PA of MOs: Answers In-Reply-To: <200007051850.UAA07780@wacx73.chemie.uni-wuerzburg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would like to mention my program (MOMIX) which does exactly what you want. It includes Mulliken population analysis (MPA), modified Mulliken population analysis (MMPA) (where the overlap is scaled - the method proposed by Stout and Politzer), and one more... It reads output files from Gaussian 98, HyperChem, e.t.c. The program is written as a MS-DOS or Windows application, and it is made as user-friendly as possible (at least, I think so :-) ). Sorry no UNIX version. Check the web site: http://www.chem.yorku.ca/grad/SG/momix.htm ----------------------------------------------------------------------- Serge On Wed, 5 Jul 2000, Marketa Ludmila Munzarova wrote: > Date: Wed, 5 Jul 2000 20:50:00 +0200 (CEST) > From: Marketa Ludmila Munzarova > To: chemistry@ccl.net > Subject: CCL:Mulliken PA of MOs: Answers > > Hi CCLers, > > I am collecting here the answers which I got on > my following question: > > ********************************************************************* > Dear computational chemists, > > I am interested in analyzing the composition of optimized > molecular orbitals from a Gaussian98 output. The MO coefficients > can be found easily, but I would like to perform a Mulliken > population analysis ot the optimized MOs. > However, the IOPs in link 601 do offer only Mulliken analysis of the > _total_ electron density. It seems to me that the only possibility > to get MOs analyzed is to code the Mulliken analysis myself, > using optimized MO coefficients and the overlap matrix. > But maybe there is still an IOP option in the Gaussian which does > this automatically? > > Thank you in advance for your help, Marketa > > --------- > Marketa Ludmila Munzarova > Faculty of Science, Masaryk University Brno > e-mail: ludmila@chemi.muni.cz > -------- > ********************************************************************* > > ANSWER1: > > ********************************************************************* > Return-Path: > X-Sender: pis_diez@dalton.quimica.unlp.edu.ar > Date: Wed, 05 Jul 2000 09:24:38 -0300 > To: Marketa Ludmilla Munzarova > Subject: Re: CCL:Mulliken pop. analysis of MOs > > Dear Ludmilla, > > I wrote a small set of subroutines to make the part of the MPA that g98 > doesn't make. You have to request g98 to print the overlap matrix and the > coeffs of the MO-LCAO expansion and prepare two files from them. > During runtime you must answer some trivial question (# of atoms, #of > basis, ie order of the matrix, and # of MOs in which you are interested. > That's because I didn't include any parser in my routines). > It works well, it gives the MO population in terms of the AOs and in > terms of the atoms. This info complements well the overlap population part > that g98 does. > If you are interested in that program please let me know and I'll send it > to you as soon as I make some changes (Titles are in Spanish!!) an include > a well-documented example. > Regards, > > Reinaldo > ********************************************************************* > > ANSWER2: > ********************************************************************* > Return-Path: > Date: Thu, 6 Jul 2000 00:05:20 +0930 > To: Marketa Ludmilla Munzarova > Subject: Re: CCL:Mulliken pop. analysis of MOs > Return-Receipt-To: b_duke@quoll.ntu.edu.au > > Hi, > > Do you mean you want to do a Mulliken analysis of each occupied orbital? > > That is - for MO i define P(k,l,i) = 2*C(k,i)*C(l,i)*S(k,l) > and then take sum over k of P(k,l,i) to give g(l,i) and then perhaps > to sum g(l,i) over all orbitals l on atom A. > > I coded this myself - I think it is l601. I may be able to let you have > this but I am not at home in Australia at present. I am in England. My code > also sum the g(l,i) terms over all orbitals of the same angular momentum > quantum number as I am looking for mixing in so called core orbitals between > say d orbitals on one atom and s orbitals on a neighbour. > > Regards, Brian. > > -- > Associate Professor Brian Salter-Duke (Brian Duke) > Chemistry, Faculty of Science, IT and Education, Northern Territory University, > Darwin, NT 0909, Australia. Phone (61) (0)8-89466702 > e-mail: b_duke@lacebark.ntu.edu.au or b_duke@quoll.ntu.edu.au > > ****************************************************************** > > > > > -= 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 > > > > > ________________________________________________________________ Sergey Gorelsky, M. Sc. Department of Chemistry, York University 4700 Keele St., Toronto, Ontario M3J 1P3, Canada tel.(416) 736-2100 ext#77720 and ext#70131 fax:(416) 736-5936 http://www.chem.yorku.ca/grad/SG/ ________________________________________________________________ From chemistry-request@server.ccl.net Wed Jul 5 19:22:07 2000 Received: from yakko.cimav.edu.mx (root@[207.248.161.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA01461 for ; Wed, 5 Jul 2000 19:21:54 -0400 Received: from glossman ([207.248.161.47]) by yakko.cimav.edu.mx (8.9.3/8.8.7) with SMTP id QAA23369 for ; Wed, 5 Jul 2000 16:30:02 -0600 Message-ID: <006f01bfe6df$d164c180$2fa1f8cf@cimav.edu.mx> From: "Dr. Daniel Glossman" To: "Computational Chemistry List" Subject: d-aug-cc-pVDZ for sulphur Date: Wed, 5 Jul 2000 17:19:14 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear netters: Where can I find the coefficients of the d-aug-cc-pVDZ basis set for sulphur? I have checked the EMSL data base but that basis set for sulphur is lacking. Thanks in advance. Daniel Glossman **************************************************************************** ******** Dr. Daniel Glossman Mitnik Centro de Investigación en Materiales Avanzados (CIMAV) Departamento de Polímeros Miguel de Cervantes 120 Complejo Industrial Chihuahua Chihuahua, Chih. 31109 Mexico Phone: (52) 14 391151 FAX: (52) 14 391112 E-mail: glossman@mail.cimav.edu.mx glossman@hotmail.com **************************************************************************** ********