From lavelle@mbi.ucla.edu Thu Jul 16 02:06:57 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 CAA04330 Thu, 16 Jul 1998 02:06:56 -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 XAA30474 for ; Wed, 15 Jul 1998 23:06:56 -0700 Received: from pc-ll.chem.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA03492; Wed, 15 Jul 1998 23:06:56 -0700 Message-Id: <9807160606.AA03492@ewald.mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0 Date: Wed, 15 Jul 1998 23:19:10 -0700 To: chemistry@www.ccl.net From: Laurence Lavelle Subject: RasMol 2.6 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi, I'm having some difficulty finding a copy of Raswin.hlp, the user manual file for RasMol 2.6 Anyone got a copy? Thanks Laurence From tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de Thu Jul 16 10:09:10 1998 Received: from mbp-sgi7.inet.dkfz-heidelberg.de (mbp-sgi7.inet.dkfz-heidelberg.de [193.174.59.125]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA06304 Thu, 16 Jul 1998 10:08:58 -0400 (EDT) Received: by mbp-sgi7.inet.dkfz-heidelberg.de (951211.SGI.8.6.12.PATCH1502/940406.SGI.AUTO) for chemistry@www.ccl.net id XAA09142; Thu, 16 Jul 1998 23:10:23 GMT From: "Emadeddin Tajkhorshid" Message-Id: <9807161610.ZM9140@mbp-sgi7.inet.dkfz-heidelberg.de> Date: Thu, 16 Jul 1998 16:10:14 -0700 Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net (Computational Chemistry List) Subject: Dipole moment of a charged species (Summary) Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Thank you very much for your replies. However, it is still not clear to me whether I can report the dipole moments of two charged species in a scientific paper or not. I mean, can I compare dipole moments of molecule_1 and molecule_2 (both negative ions, and the dipole moments are calculated after transforming the coordinate to a mass-weighted or charge-wieghted system) and can I say that the dipole moment of 1 is larger than 2, or if we align two molecules, the direction of the dipole vector with respect to the carbon chain is the opposite for molecule 1 as compared to the one in molecule 2. Since I would like to report these numbers in a scientific papers, I am a bit conservative. Perhaps I may pose the question in another way, asking: Do you know any paper where the dipole moments of the ionic species are compared and/or discussed? Or the people prefer not to discuss these numbers in their paper .... The Q and summary of replies: ******************************************************************************* Dear Colleagues I have calculated two molecules using gas phase calculations and a number of different solvent models. They are both negatively charged species. Now the question is whether and how we can compare the dipole moments between these molecules and among different solvent models. I mean, the values, and also the directions, calculated for the dipole moment of a charged species are completely dependent on the origin of the coordinates. With this regard, how are the dipole moments calculated in quantom chemical calculations (particularly, I am interested in the reported values in the output of the Gaussian94 or DMOL programs)? And (how) can we use them for further analysis of the results or it is better to look at other properties like the atomic charges? ****************************************************************************** From: Wayne Steinmetz Date: Tue Jul 14, 10:17am -0700 To: E.Tajkhorshid@DKFZ-Heidelberg.de Cc: Subject: Re: CCL:G:Dipole moment of a charged species Be very careful since the species to be compared possess net charge. It is a consequence of the principles of electricity and magnetism that the dipole moment is dependent on the choice of the origin when the molecule has net charge. In fact, the dipole moment can be made zero by choosing the origin of the charge distribution at the center of the charge. The value of the dipole moment is independent of the origin when the molecule has no net charge. ***************************************************************************** From: liang@wavefun.com Date: Tue Jul 14, 10:35am -0700 To: E.Tajkhorshid@dkfz-heidelberg.de Cc: liang@wavefun.com Subject: Re: CCL:G:Dipole moment of a charged species Dear Emad, For an N point charge system of total charge Q, the dipole moment is D = sum_i [ x_i * q_i ] where x and q are position vector and charge on point i. By translating to the center of geometry, X = (1/N) sum_i [ x_i ] one obtains D = sum_i [ (x_i - X) * q_i ] + X * sum_i [ q_i ] = D0 + X*Q D0 is a value that is independent of the positions of the point charge and therefore may be used for comparison purposes. For a continuous charge distribution, substitute an integral for the sum. Regards, Liang *************************************************************************** From: Doug Fox Date: Tue Jul 14, 12:19pm -0400 To: uunet.uu.net!uunet!DKFZ-Heidelberg.de!E.Tajkhorshid%lorentzian.com Cc: Subject: Re: CCL:G:Dipole moment of a charged species Emad, The dipole moment of a charge species includes a contribution from the separation of charge and the center of nuclear charge. Thus one approach is to compare dipoles with the origin at the center of charge to zero this contribution. In Gaussian this is the origin for the standard orientation and the orientation used in multipole report in the log file, not in the archive entry or if you use NoSymm. I don't know what DMOL reports but it should be fairly simple to correct one to the other. **************************************************************************** From: John McKelvey Date: Tue Jul 14, 2:06pm -0700 To: E.Tajkhorshid@dkfz-heidelberg.de Cc: Subject: Re: CCL:G:Dipole moment of a charged species Emad, I like using the charge-reference-coordinate as being the neutral molecule valence-electron-weighted (x,y,z) point in space. It puts the emphasis on where the meaningful chemistry is. Mass-weighted systems might also be useful, but there could be a significant shift, for example, if a H or F atom were replaced by, say, Iodine. Regards, John McKelvey NCSA *********************************************************************** From: Preston J. MacDougall Date: Tue Jul 14, 1:42pm -0700 To: E.Tajkhorshid@DKFZ-Heidelberg.de Cc: Subject: atomic first moments Dr. Tajkhorshid, You are correct that the dipole moment of a charged species is origin dependent. Packages must select origins anyway, so the computed dipole moment must be taken for what it is worth. You can assign first moments to the consituent atoms in a molecule or ion, whether there are partial charges on them or not (see J. Chem. Phys., vol. 87, p. 1142 (1987)). The first moment of an atom is also origin dependent, but is naturally chosen as the nucleus. I am not sure, but I believe that these first moments can be calculated from a G94 wavefunction using the AIMPAC option. If not, the AIMPAC software can be downloaded off of the internet at http://www.chemistry.mcmaster.ca/aimpac/ Hope this helps in your research, Dr. Preston J. MacDougall NASA-ASEE-Stanford Summer Faculty Fellow MS T27-A, NASA Ames Research Center Moffett Field, CA 94035 ************************************************************************** -- Emad ********************************************************************* E. Tajkhorshid German Cancer Research Center; DKFZ Tel: +49 6221 42 2340 Dept. Molecular Biophysics (H0200) FAX: +49 6221 42 2333 P.O.Box 101949 69009 Heidelberg, Germany Email: E.Tajkhorshid@DKFZ-Heidelberg.de ********************************************************************* * "Never express yourself more clearly than you think." -Niels Bohr * ********************************************************************* From csm@insc.net Thu Jul 16 10:11:32 1998 Received: from unix2.insc.net (unix2.insc.net [209.4.50.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA06370 Thu, 16 Jul 1998 10:11:31 -0400 (EDT) From: csm@insc.net Received: from sales-1 (ppp-mia88.insc.net [209.4.50.88]) by unix2.insc.net (8.8.5/8.8.5) with SMTP id KAA15167; Thu, 16 Jul 1998 10:09:50 -0400 Message-Id: <199807161409.KAA15167@unix2.insc.net> To: chemistry@www.ccl.net Date: Thu, 16 Jul 1998 09:43:33 -0500 Subject: Opportunity !! MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Would you buy a NEW product that offers you BIG PROFITS ?? Click here http://www.microsidecorp.com/equal.htm and win a free FX2000 The Ultimate Flight Control Stick Microside Corp. http://www.microsidecorp.net This message was sent through BR-MAIL (http://www.net2010.com/br-mail) From lnorris@kiwi.acns.nwu.edu Thu Jul 16 12:49:14 1998 Received: from kiwi.acns.nwu.edu (lnorris@kiwi.acns.nwu.edu [129.105.39.103]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA08586 Thu, 16 Jul 1998 12:49:14 -0400 (EDT) Received: (from lnorris@localhost) by kiwi.acns.nwu.edu (8.8.6/8.7.1) id LAA29962 for CHEMISTRY@www.ccl.net; Thu, 16 Jul 1998 11:49:13 -0500 (CDT) From: Lawrence Norris Message-Id: <199807161649.LAA29962@kiwi.acns.nwu.edu> Subject: Parallel Amber To: CHEMISTRY@www.ccl.net Date: Thu, 16 Jul 1998 11:49:13 -0500 (CDT) X-Mailer: ELM [version 2.4 PL25] Content-Type: text I want to implement AMBER 4.1 on an IBM SMP machine using IBM's version of MPI and AIX4.2. Has anyone done this before? I'd be interested in your tips, cautions, frustrations, etc. etc. and most importantly any changes you had to make in the Makefiles. Thanks -- Lawrence S. Norris ________________________________________________________________________ Departments of Biomedical Engineering |http://www.chem.nwu.edu/~lnorris/ and Chemistry |e-mail address: "lnorris@nwu.edu" Northwestern University |Phone: 847-491-5635 2145 Sheridan |Phone2: 773-975-7153 Evanston, IL 60208 |Fax: 847-491-4928 |anony. ftp site: ftp.chem.nwu.edu | cd pub/incoming/lnorris ------------------------------------------------------------------------ From nowak@chemie.uni-halle.de Wed Jul 15 10:37:11 1998 Received: from mailsrv.rz.fh-merseburg.de (mailsrv.rz.fh-merseburg.de [149.205.19.100]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA21626 Wed, 15 Jul 1998 10:37:03 -0400 (EDT) Received: from localhost (nowak@localhost) by mailsrv.rz.fh-merseburg.de (8.8.8/8.8.7) with SMTP id QAA25943; Wed, 15 Jul 1998 16:39:14 +0200 (METDST) X-Authentication-Warning: mailsrv.rz.fh-merseburg.de: nowak owned process doing -bs Date: Wed, 15 Jul 1998 16:39:14 +0200 (METDST) From: Thomas Nowak X-Sender: nowak@mailsrv.rz.fh-merseburg.de To: Alan Shusterman cc: chemistry@www.ccl.net Subject: CCL: SUMMERY Energy analysis? In-Reply-To: <5886887@isis.reed.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I want to thank all of you who gave me a reply... the orginal question was: ------------------------------------------------------------------------- Hi, I am looking for program for the analysis of the bond energy. I know there is one implementation of the Morokuma algorithm in ADF, so i looking for other implementations of this or similar algorithm which can be used with other quantum chemistry programs. It would be great, if we can do such analysis on DFT level. ------------------------------------------------------------------------- Alan.Shusterman@directory.reed.edu wrote: I would be interested in any answers that you receive. Thanks, Alan ----- Alan Shusterman Department of Chemistry Reed College Portland, OR www.reed.edu/~alan --------------------------------------------------------------------------- Dmitry Khoroshun wrote: Hello! GAMESS is also able of performing EDA. Sincerely, Dmitry Khoroshun dima@euch4e.chem.emory.edu -------------------------------------------------------------------------- Timm Lankau wrote: Sehr geehrter Herr Nowak, GAMESS US hat eine Implementation des Morokuma-Algorithmus - leider nur fuer RHF Rechnungen. Mit freundlichen Gruessen Timm Lankau ---------------------------------------------------------------------------- Andreas Ehlers wrote: Hallo Thomas, Prof. Frenking in Marburg hat etwas aehnliches, die CDA Analyse. Am besten informierst du dich bei ihm: Prof. Gernot Frenking Fachbereich Chemie Philipps-Universitaet Marburg Hans-Meerwein-Strasse D-35032 Marburg Germany Tel: (06421)285563 281535 (Sekr) FAX: (06421)282189 http://www.chemie.uni-marburg.de/~frenking/ mail: FRENKING@ps1515.chemie.uni-marburg.de Viel Erfolg, Andreas ---------------------------------------------------------------------------- Thanks to all Thomas Nowak Martin-Luther Universitaet Halle FB Chemie (Merseburg) IPC 06099 Halle email: nowak@chemie.uni-halle.de From tapas@risky3.thchem.siu.edu Thu Jul 16 17:07:07 1998 Received: from risky3.thchem.siu.edu (risky3.thchem.siu.edu [131.230.89.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA10405 Thu, 16 Jul 1998 17:07:05 -0400 (EDT) Received: (from tapas@localhost) by risky3.thchem.siu.edu (AIX4.2/UCB 8.7/8.7) id QAA23234; Thu, 16 Jul 1998 16:12:31 -0500 (CDT) Date: Thu, 16 Jul 1998 16:12:28 -0500 (CDT) From: Tapas Kar To: "Comp. Chem. List" Subject: MP of HBNH and H2BNH2 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII What is the melting point of HBNH and H2BNH2 ? -------------------------------------------- Tapas Kar, Ph. D Asst. Scientist Forestry Bldg 118 Department of Chemistry Southern Illinois University at Carbondale Illinois 62901-4409 Fax: (618) 453 6408 Tel: (618) 453 6433(Lab) 6485(Office) -------------------------------------------- From hxt10@po.cwru.edu Thu Jul 16 22:05:49 1998 Received: from babar.INS.CWRU.Edu (root@babar.INS.CWRU.Edu [129.22.8.213]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id WAA11639 Thu, 16 Jul 1998 22:05:49 -0400 (EDT) Received: from Silver.cwru.edu (dialin067.REMOTE.CWRU.Edu [129.22.220.67]) by babar.INS.CWRU.Edu with ESMTP (8.8.6+cwru/CWRU-3.3) id WAA24258; Thu, 16 Jul 1998 22:05:49 -0400 (EDT) (from hxt10@po.cwru.edu for ) Message-Id: <199807170205.WAA24258@babar.INS.CWRU.Edu> From: "Hui-Hsu (Gavin) Tsai" To: Subject: delicate workstation for ab initio calculations Date: Thu, 16 Jul 1998 22:05:35 -0500 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Computational Chemists: We consider to buy one delicate workstation to perform ab initio calculations (Becke3LYP/6-31G** level with geometry optimization and vibration calculations) of metalloporphyrins (at least 45 heavy atoms). I do not know what kind of workstations is excellent to do these calculations now because the computer techniques progress very fast. Has anyone comments or suggestions in purchasing the workstation to perform these large-scale calculations. Our budget is about $60000.00. Any comment, experience, and suggestion is welcomed. Thanks a lot. Gavin Tsai Case Western Reserve University