From owner-mailserv@www.ccl.net Tue Jan 28 18:30 EST 1997 Received: from wolfe.wimsey.com for resrch!janr@uucp.wimsey.com by www.ccl.net (8.8.3/950822.1) id SAA00028; Tue, 28 Jan 1997 18:30:11 -0500 (EST) Received: from resrch by wolfe.wimsey.com with uucp (Smail-3.2 #5) id m0vpMyd-000U2sC; Tue, 28 Jan 1997 15:30:07 -0800 (PST) Received: by molienergy.bc.ca (1.38.193.5/16.2) id AA01890; Tue, 28 Jan 1997 14:43:01 -0800 From: Jan Reimers Message-Id: <9701282243.AA01890@molienergy.bc.ca> Subject: Mulliken population analysis To: chemistry@www.ccl.net Date: Tue, 28 Jan 97 14:43:01 PST X-Mailer: ELM [version 2.3 PL10] Content-Type: text Douglas A. Smith asked: >The question: Can people please explain the concept of having a balanced >basis set and the dangers inherent in an unbalanced set? In particular, why >can I not simply use a large basis, including extra split valance functions, >polarization and diffuse functions, only on the atoms I need them on, and a >smaller, more compact basis set on the "unimportant" atoms to my chemical >question? This would certainly save time and resources during the calculation. In response, Per-Ola Norrby wrote: > I'll give it a try, and hopefully I can do it in chemists language >without loosing too much accuracy. > > The basic problem is that all basis sets are incomplete. There is >no way you can use a finite number of basis functions to describe the >electron density completely. You can get fairly close, but at a high cost. >Now, what happens to an atom with an incomplete basis? It has some >electron density that could be described better if it could use some >additional basis functions. Now, if there are unused basis functions on a >neighboring atom, there is always SOME way that a linear combination of >those can be used to stabilize the electron density on the original atom >further. Thus, the electron sharing between atoms is exaggerated and the >bonds look stronger than they actually are. This depends on how you determine the charge on each atom, and on how you determine bond strength. One must admit that adding more basis functions anywhere (lets ignore numerical presicion problems and near singular matricies for the moment) will give an improved approximation to the true (or HF) charge density. RFW Bader has shown us how to extract atomic charges and bond strengths (or bond orders) from the charge density. Using Baders definitions, these quantites (and many others) should improve as the approximation to the charge density improves. So one avoids the apparent paradox where augmenting the basis set decreases the quality of the answers you get. It should be no surprise that this works because Baders definitions of atomic charge and bond order are derived from the least action principle, as applied to a real physical quantity; the charge density. In fact Baders definitions, should really be called THE definitions. Things like Mulliken population analysis are hopelessly tied to the basis set, our approximation method for solving the SE. These numbers cannot possibly be considered "real physically observable quantities". If you modify your basis set, you can expect to get "funny" numbers from the population analysis. This is just a demonstration that the numbers are meaningless, nothing else! > Now, if all atoms have very few basis functions, there aren't too >many unused functions that can be used by the neighbors, so the errors >(basis set deficiency and superposition errors, BSDE and BSSE) partially >cancel. However, if one atom has a very small basis set and the neighbor >many diffuse and polarization functions, you may get into a situation where >a very substantial part of the electron density of the first atom is >described by basis functions on the second. If you try to do a Mulliken >analysis on such a system, you get weird results. The electron density in >that region will also most probably be skewed, causing all kinds of >distortions. Yes exactly, but I interepret this as a definiciency in the polulation analysis method, rather than as a basis set problem. > You CAN get away with things like this, if you are careful to do >only comparisons between very similar systems, where the effect stays >constant. Naturally, you can get away with ANYTHING as long as you fulfill >that requirement :-) Or better yet, just ask physically meaningful questions of the wave function and charge density. > Per-Ola Norrby +--------------------------------------+-------------------------------------+ | Jan N. Reimers, Research Scientist | Sorry, Don't have time to write the | | Moli Energy (1990) Ltd. B.C. Canada | usual clever stuff in this spot. | | janr@molienergy.bc.ca | | +--------------------------------------+-------------------------------------+ From jstewart@iti2.net Tue Jan 28 11:19:45 1997 Received: from cougar.iti2.net for jstewart@iti2.net by www.ccl.net (8.8.3/950822.1) id KAA22302; Tue, 28 Jan 1997 10:24:25 -0500 (EST) Received: from 171-29-106.ipt.aol.com (171-29-106.ipt.aol.com [152.171.29.106]) by cougar.iti2.net (8.7.6/8.7.3) with SMTP id IAA06896 for ; Tue, 28 Jan 1997 08:25:10 -0700 Message-Id: <3.0.16.19691231170000.3bef1628@iti2.net> X-Sender: jstewart@iti2.net (Unverified) X-Mailer: Windows Eudora Pro Version 3.0 (16) Date: Tue, 28 Jan 1997 08:24:05 -0700 To: CHEMISTRY@www.ccl.net From: "James J. P. Stewart" Subject: Putting New Parameters into MOPAC Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" When new parameters are added to the BLOCK DATA file in MOPAC, the source of the parameters should be supplied as well. MOPAC uses the presence of the reference as evidence for the parameters - specifically, the blank space at the start of the line. MOPAC93 is NOT designed to handle 'd' orbitals for any method. There is a single 'd' orbital element - Ti - but it is intended for use in demonstrating Russel-Saunders coupling only. That is, it is qualitative, not quantitative. Jimmy Stewart James J. P. Stewart ( @ @ ) .-------------oOOo----(_)----oOOo-------------------------------------. | Jimmy Stewart | E-mail | | Stewart Computational Chemistry | jstewart@fai.com (preferred) | | 15210 Paddington Circle | jstewart@iti2.net (local address) | | Colorado Springs CO 80921-2512 | MrMopac@aol.com (for fun) | | USA .ooo0 | Phone: (719) 488-9416 | | ( ) Oooo. | Fax: (719) 488-9758 | .--------------------\ (----( )-------------------------------------. \_) ) / (_/ From mn1@helix.nih.gov Tue Jan 28 13:23:19 1997 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id NAA24304; Tue, 28 Jan 1997 13:01:14 -0500 (EST) Received: (from mn1@localhost) by helix.nih.gov (8.8.4/8.8.4) id NAA09282; Tue, 28 Jan 1997 13:01:12 -0500 (EST) Date: Tue, 28 Jan 1997 13:01:12 -0500 (EST) From: "M. Nicklaus" Message-Id: <199701281801.NAA09282@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: G94: Problem with PES Scan in DFT Cc: mn1@helix.nih.gov Dear CCL'ers, I seem to be having a problem with a Potential Energy Surface (PES) scan in G94. I am running a relaxed PES scan on a nucleoside analog, trying to rotate the base. I am running this job at the DFT method/basis set B3LYP/6-31G(d). I'm using cartesian coordinates (a newzmat-generated input file with a Z-matrix didn't work previously), pre-optimized at the same level of theory from X-ray coordinates. For the first few conformations, everything seems to have proceeded nicely; i.e., the energy started out some 20 kcal/mol or so above the (presumed) global energy minimum, and then came down, during the partial optimization, to a reasonable value a few kcal/mol above the global min. With the current conformation, however, the job seems to be stuck, since for nearly 20 steps now, the energy has only been oscillating in a narrow band. Here's a grep of the output file (slightly modified through a filter --don't worry about the origin of the kcal/mol scale): SCF Done: E(RB+HF-LYP) = 6.587 kcal/mol ( -877.288353458 A.U.) after 12 cycles SCF Done: E(RB+HF-LYP) = 6.501 kcal/mol ( -877.288490683 A.U.) after 12 cycles SCF Done: E(RB+HF-LYP) = 6.470 kcal/mol ( -877.288539921 A.U.) after 11 cycles SCF Done: E(RB+HF-LYP) = 6.443 kcal/mol ( -877.288582731 A.U.) after 12 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288591742 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.439 kcal/mol ( -877.288590115 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288591793 A.U.) after 9 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288591832 A.U.) after 8 cycles SCF Done: E(RB+HF-LYP) = 6.440 kcal/mol ( -877.288588866 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288591957 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.439 kcal/mol ( -877.288590211 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288592040 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.440 kcal/mol ( -877.288588983 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288591984 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.440 kcal/mol ( -877.288588800 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288591901 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.439 kcal/mol ( -877.288589705 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288592037 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.440 kcal/mol ( -877.288588677 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288591887 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.439 kcal/mol ( -877.288589980 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.438 kcal/mol ( -877.288592074 A.U.) after 10 cycles SCF Done: E(RB+HF-LYP) = 6.440 kcal/mol ( -877.288588420 A.U.) after 10 cycles I'd hate to kill this job--which has already taken up ca. 20 CPU-days--if there'e any chance that it's going to converge at some reasonable time. So here are my questions: (a) Can anyone give me a hint as to what's going on here? Has anyone seen a similar behavior before? (b) Should I kill this job now, or wait a bit longer? How much longer? (c) If this is a known effect, is there anything I can do to avoid it? Marc ------------------------------------------------------------------------ Marc C. Nicklaus Lab. of Medicinal Chemistry e-mail: mn1@helix.nih.gov National Cancer Institute, NIH Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA WWW: http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM ------------------------------------------------------------------------ From chmigorn@leonis.nus.sg Thu Jan 30 02:19:44 1997 Received: from sable.nus.sg for chmigorn@leonis.nus.sg by www.ccl.net (8.8.3/950822.1) id BAA21333; Thu, 30 Jan 1997 01:27:12 -0500 (EST) Received: from leonis.nus.sg (chmigorn@leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.8.4/8.6.9) with ESMTP id OAA13565 for ; Thu, 30 Jan 1997 14:27:11 +0800 (SST) Received: (from chmigorn@localhost) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) id OAA32331 for chemistry@www.ccl.net; Thu, 30 Jan 1997 14:22:23 +0800 Date: Thu, 30 Jan 1997 14:22:23 +0800 From: Novak Igor Message-Id: <199701300622.OAA32331@leonis.nus.sg> To: chemistry@www.ccl.net Dear Netters, I wish to use ScatterPlot3D function in Mathematica software. However, when I try to run a test job (from Mathematica book on packages) I do not get a plot but only evaluated numbers. The test job is as follows: lpts=Table[{t Cos[t],t Sin[t],t},{t,0,4Pi,Pi/20}]; ScatterPlot3D[lpts] Can someone kindly point out the (obvious) mistake I am making? Regards, Dr I.Novak, Dept.of Chemistry, National University of Singapore e-mail: chmigorn@nus.sg From schiffer@h1tw0036.hoechst.com Thu Jan 30 04:19:48 1997 Received: from backup.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id DAA22723; Thu, 30 Jan 1997 03:48:17 -0500 (EST) Received: by backup.hoechst.com (SMI-8.6/SMI-SVR4) id JAA27661; Thu, 30 Jan 1997 09:46:31 +0100 Received: from unknown(134.81.79.248) by backup via smap (V1.3) id smaa27653; Thu Jan 30 09:45:53 1997 Received: from 134.81.76.36 by fra29.hiserv.de with SMTP (Microsoft Exchange Internet Mail Connector Version 4.0.994.63) id CNN9ZB3C; Thu, 30 Jan 1997 09:50:33 +0100 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id JAA01665; Thu, 30 Jan 1997 09:46:27 +0100 Message-ID: <32F05FE3.41C6@h1tw0036.hoechst.com> Date: Thu, 30 Jan 1997 09:46:27 +0100 From: "Dr. Heinz Schiffer" Organization: Hoechst Corporate Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Computational Chemistry List CC: her10531@argon.chem-tu-berlin.de Subject: dispersion interactions Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Roland Hertwig wrote : I am looking for information on dispersion interactions. Can anyone give me a hint on where to start reading? (Articles, reviews, monographs, etc) I give a list of a few papers, which I think are very important ( esp. 1-4 ) : (1) Reinhart Ahlrichs Convergence Properties of the Intermolecular Force Series (1/R-Expansion) Theoret. Chim. Acta 41, 7-15 (1976) (2) R. Ahlrichs, R. Penco, and G. Scoles Intermolecular Forces in Simple Systems Chem. Phys. 19 (1977) 119-130 (3) P. Claverie Elaboration of approximate formulas for the interactions between large molecules: applications in organic chemistry. Perspect. Quantum Chem. Biochem. 2 (1978) 69-305 (Intermolecular Interactions: From Diatomics to Biopolymers, Ed.: B. Pullman, John Wiley & Sons, New York, 1978) (4) Roberto Cambi, David Cappelletti, Giorgio Liuti, and Fernando Pirani Generalized correlations in terms of polarizability for van der Waals interaction potential parameter calculations J. Chem. Phys. 95 (1991) 1852-1861 (5) Bogumil Jeziorski, Robert Moszynski, Krzysztof Szalewicz Perturbation Theory Approach to Intermolecular Potential Energy Surfaces of van der Waals Complexes Chem. Rev. 94 (1994) 1887-1930 (6) Y. Andersson, D. C. Langreth, and B. I. Lundqvist van der Waals Interactions in Density-Functional Theory Phys. Rev. Lett. 76 (1996) 102-105 (7) Joerg-R. Hill Use of Test Particle Calculations for the Derivation of van der Waals Parameters Used in Force Fields J. Comput. Chem. 18 (1997) 211-220 (8) Evert Jan Meijer and Michiel Sprik A density-functional study of the intermolecular interactions of benzene J. Chem. Phys. 105 (1996) 8684-8689 Regards, Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main schiffer@msmwia.hoechst.com From cdac.ernet.in!sundar@parcom.ernet.in Thu Jan 30 04:29:04 1997 Received: from sangam.ncst.ernet.in for cdac.ernet.in!sundar@parcom.ernet.in by www.ccl.net (8.8.3/950822.1) id DAA22754; Thu, 30 Jan 1997 03:57:08 -0500 (EST) Received: (from root@localhost) by sangam.ncst.ernet.in (8.7.5) id OAA06674 for CHEMISTRY@www.ccl.net; Thu, 30 Jan 1997 14:32:23 +0530 (GMT+05:30) >Received: from parcom.UUCP by iucaa (4.1/SMI-4.1) id AA05608; Thu, 30 Jan 97 14:30:42+050 Received: from parcom by sangam.ncst.ernet.in; Thu, 30 Jan 1997 14:32 GMT Received: from parcom.UUCP by iucaa (4.1/SMI-4.1) id AA05608; Thu, 30 Jan 97 14:30:42+050 Received: by parcom.cdac.ernet.in (4.1/SMI-4.1) id AA08789; Thu Jan 30 14:08:29 1997 (GMT + 0530) Date: Thu, 30 Jan 1997 14:08:28 +0530 (IST) From: V Sundararajan To: CHEMISTRY@www.ccl.net Subject: CCL:Summary on Car-Parrinello codes Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Friends, A month back I asked for information on the availability of ab initio Molecular Dynamics code available on the internet. My question was: > Dear CCL friends, > I would greatly appreciate information regarding Car-Parrinello > code available in the public domain. I am interested in Silicon > cluster simulation having about 100 atoms. > I thank all those who responded for this. All the responses are summarised below for the benefit of others in the net. sundar ---------------------------------------------------------------------- V. Sundararajan, Applications group Centre for Development of Advanced Computing Pune University Campus, Pune 411 007 Phone: 352461/79/83/84 Ext 341/342 Direct 370098 Fax : +91 212 357551 e-mail: sundar@cdac.ernet.in ---------------------------------------------------------------------- Hello. I found one at the following url site: ftp: 141.14.129.9 file is /pub/physics/fhi93cp/fhi93cp.tar.Z I have compiled the source codes (fortran) and everything seems externally OK. Yet, as to bugs, or other problems concerning this code, I am in the dark. Good Luck. P.S. Please let me know of any other CP codes available. Thanks. Iraj. Hi, a summary would be nice and appreciated. Yours, Georg -- ============================================================================== Georg Schreckenbach Tel: (Canada)-403-220 8204 Department of Chemistry FAX: (Canada)-403-289 9488 University of Calgary Email: schrecke@zinc.chem.ucalgary.ca 2500 University Drive N.W., Calgary, Alberta, Canada, T2N 1N4 ============================================================================== Dear Sundar, The Fritz-Haber institute in Berlin offers a Car-Parinello code. Try at http://www/fhi-berlin.mpg.de/ . You will have to look around, but I am sure you will find it. Merethe PS. I guess it is more precise to call it an ab initio molecular dynamics code ******************************************************** Merethe Sjovoll * * Scientist * * Norsk Hydro a.s Research Center * * * * P.O.Box 2560 * HYDRO * N-3901 Porsgrunn, * RESEARCH * Norway * * * ((( * email: Merethe.Sjovoll@hre.hydro.com * (=====) * Phone:+47 35 56 48 97 * * Fax :+47 35 56 36 86 * * ******************************************************** > Dear Sir, Recently we get a public domain Car-Parrinello code from Francois Gygi called JEEP. You can find it at the following address : http://irrmawww.epfl.ch/fg/jeep/jeep.html Gygi'a address is : mailto:gygi@irrmasg6.epfl.ch (Francois Gygi) We didn't use JEEP yet, but a post-doc will arrive this year and probably use it. Therefore I would be grateful if you could please tell me about what you manage to do with it. My address is : maurel@ripault.cea.fr Good luck. Didier MATHIEU From: maurel From chpajt@bath.ac.uk Thu Jan 30 05:19:59 1997 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.8.3/950822.1) id EAA23156; Thu, 30 Jan 1997 04:52:18 -0500 (EST) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Thu, 30 Jan 1997 09:52:06 +0000 Date: Thu, 30 Jan 1997 09:51:57 +0000 (GMT) From: A J Turner To: Jan Reimers cc: chemistry@www.ccl.net Subject: Re: CCL:Mulliken population analysis In-Reply-To: <9701282243.AA01890@molienergy.bc.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! It would seem tha there is an argument for relating charge distribution in a 'real' property. In the case of macro-molecular systems this can be done by aproximating point charges to reproduce the gradients or force constants produced by an scf. As the gradients and force constants can then be confirmed by comparason to experiment - this would seem a logical approach. Best wishes Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- From slawek@alchmist.scs.uiuc.edu Thu Jan 30 05:21:41 1997 Received: from labrador.scs.uiuc.edu for slawek@alchmist.scs.uiuc.edu by www.ccl.net (8.8.3/950822.1) id EAA22924; Thu, 30 Jan 1997 04:25:27 -0500 (EST) Received: from piglet.scs.uiuc.edu (piglet.scs.uiuc.edu [130.126.227.130]) by labrador.scs.uiuc.edu (AIX4.2/UCB 8.7/8.7) with SMTP id DAA15922 for ; Thu, 30 Jan 1997 03:27:11 -0600 (CST) Received: by piglet.scs.uiuc.edu with Microsoft Mail id <01BC0E5D.3B0FCD50@piglet.scs.uiuc.edu>; Thu, 30 Jan 1997 03:25:24 -0600 Message-ID: <01BC0E5D.3B0FCD50@piglet.scs.uiuc.edu> From: Slawomir Janicki To: "'CCL'" Subject: A (silly) problem with G94 Date: Thu, 30 Jan 1997 03:25:22 -0600 Encoding: 33 TEXT I am trying to set up a G94 job with some geometry constrains. Here are first few lines from my input file: %chk=t_0deg.chk %int=t.int %d2e=t.d2e %rwf=t.rwf %mem=2000000 #p ub3pw91/6-31g* Opt=AddRedundant scf=direct However, G94 does not accept these keywords. Here is the relevant part of the output file: ********************************************** Gaussian 94: IBM-RS6000-G94RevB.3 30-May-1995 30-Jan-1997 ********************************************** %chk=t_0deg.chk %int=t.int %d2e=t.d2e %rwf=t.rwf %mem=2000000 --------------------------------------------- #p ub3pw91/6-31g* Opt=AddRedundant scf=direct --------------------------------------------- QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. #P UB3PW91/6-31G* OPT=ADDREDUNDANT SCF=D ' Last state="OPT1" TCursr= 4052 LCursr= 22 What is wrong about using AddRedundant? Isn't it a perfectly legitimate keyword? Slawek Janicki slawek@alchmist.scs.uiuc.edu From peon@medchem.dfh.dk Thu Jan 30 06:19:57 1997 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.8.3/950822.1) id FAA23629; Thu, 30 Jan 1997 05:46:52 -0500 (EST) Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.7.5/8.6) with SMTP id LAA12795; Thu, 30 Jan 1997 11:46:52 +0100 (MET) Received: from [130.225.177.59] (compmac2 [130.225.177.59]) by medchem.dfh.dk (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id MAA07959; Thu, 30 Jan 1997 12:03:36 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 30 Jan 1997 11:46:50 +0100 To: Slawomir Janicki From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:G:A (silly) problem with G94 Cc: chemistry@www.ccl.net > QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. > #P UB3PW91/6-31G* OPT=ADDREDUNDANT SCF=D > ' > Last state="OPT1" > TCursr= 4052 LCursr= 22 > >What is wrong about using AddRedundant? Isn't it a perfectly legitimate >keyword? Hi, I experienced EXACTLY the same problem. I guess it's a bug, but there's a very easy workaround: truncate it. I always use OPT=AddR , that works perfectly. Regards, Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, http://compchem.dfh.dk/ From FAU@ps1515.chemie.uni-marburg.de Thu Jan 30 07:20:10 1997 Received: from Mailer.Uni-Marburg.DE for FAU@ps1515.chemie.uni-marburg.de by www.ccl.net (8.8.3/950822.1) id GAA23842; Thu, 30 Jan 1997 06:45:41 -0500 (EST) Received: from ps1515.Chemie.Uni-Marburg.DE by Mailer.Uni-Marburg.DE (AIX 4.1/UCB 5.64/25.11.96) id AA27950; Thu, 30 Jan 1997 12:45:30 +0100 Received: from NWS_CHEMIE/MAILQ by ps1515.chemie.uni-marburg.de (Mercury 1.20); 30 Jan 97 12:47:13 GMT+2 Received: from MAILQ by NWS_CHEMIE (Mercury 1.20); 30 Jan 97 12:46:58 GMT+2 From: "Stefan Fau" To: chemistry@www.ccl.net Date: Thu, 30 Jan 1997 12:46:49 MDT Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: Mulliken population analysis Return-Receipt-To: "Stefan Fau" Priority: normal X-Mailer: Pegasus Mail for Windows (v2.01) Message-Id: <49A11067EA7@ps1515.chemie.uni-marburg.de> Hi, there is another method of determining atomic charges, the NBO analysis of Reed, Weinhold and coworkers. The results quite independent of the basis set. Furthermore, the NBO analysis gives bond orders and the best Lewis stucture for the molecule. The NLMO part gives information on (hyper)conjugation. Review: Reed, Curtiss and Weinhold: JCP 1988, 88, p.899 Stefan __________________________________________________________ Stefan Fau, fau@mailer.uni-marburg.de FB Chemie der Philipps-Universitaet Marburg, Hans-Meerwein-Str. D-35032 Marburg From harry@rsc.anu.edu.au Thu Jan 30 07:28:10 1997 Received: from anugpo.anu.edu.au for harry@rsc.anu.edu.au by www.ccl.net (8.8.3/950822.1) id HAA23898; Thu, 30 Jan 1997 07:00:34 -0500 (EST) Received: from rsc (rsc.anu.edu.au [150.203.35.129]) by anugpo.anu.edu.au (8.8.5/8.8.3) with SMTP id XAA12371; Thu, 30 Jan 1997 23:00:30 +1100 (EST) Received: from [150.203.148.139] by rsc (SMI-8.6/SMI-SVR4) id XAA29429; Thu, 30 Jan 1997 23:05:05 +1100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 30 Jan 1997 23:04:16 +1000 To: CHEMISTRY@www.ccl.net From: harry@rsc.anu.edu.au (Dr. Harold W. Schranz) Subject: CCL: ScatterPlot3D in Mathematica Cc: Harold.Schranz@anu.edu.au Dr I.Novak wrote: >Dear Netters, >I wish to use ScatterPlot3D function in Mathematica software. >However, when I try to run a test job (from Mathematica book on packages) >I do not get a plot but only evaluated numbers. >The test job is as follows: >lpts=Table[{t Cos[t],t Sin[t],t},{t,0,4Pi,Pi/20}]; >ScatterPlot3D[lpts] >Can someone kindly point out the (obvious) mistake I am making? >Regards, >Dr I.Novak, Dept.of Chemistry, National University of Singapore >e-mail: chmigorn@nus.sg Hi Dr. Novak, Possibly you have forgotten to actually load the package as many Mathematica packages are optional and have to be explicitly loaded e.g. via a command such as: Needs["Graphics`Graphics3D`"] then the ScatterPlot3D will become available and you can run the required test job: lpts=Table[{t Cos[t],t Sin[t],t},{t,0,4Pi,Pi/20}]; ScatterPlot3D[lpts] The following Mathematica session is illustrative: In[1]:= ?ScatterPlot3D Information::notfound: Symbol ScatterPlot3D not found. In[2]:= Needs["Graphics`Graphics3D`"] In[3]:= ?ScatterPlot3D ScatterPlot3D[{{x1, y1, z1}, ...}, (options)] plots points in three dimensions as a scatter plot. In[4]:= lpts=Table[{t Cos[t],t Sin[t],t},{t,0,4Pi,Pi/20}]; ScatterPlot3D[lpts] -Graphics3D- I hope that helps you out. Regards Harry. ------------------------------------------------------------------------------ Dr. Harold W. Schranz, Office Ph.: 61-6-249-3773 Research School of Chemistry, Dept. Ph.: 61-6-249-3637 Australian National University, Fax: 61-6-249-0750 Canberra, ACT 0200, Email: Harold.Schranz@anu.edu.au AUSTRALIA. WWW: http://porsche.anu.edu.au/HWS/hws.html RSC: http://porsche.anu.edu.au/Default.html ------------------------------------------------------------------------------ From schiffer@h1tw0036.hoechst.com Thu Jan 30 10:20:07 1997 Received: from backup.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id KAA25600; Thu, 30 Jan 1997 10:01:05 -0500 (EST) Received: by backup.hoechst.com (SMI-8.6/SMI-SVR4) id PAA01896; Thu, 30 Jan 1997 15:59:18 +0100 Received: from unknown(134.81.79.248) by backup via smap (V1.3) id sma001549; Thu Jan 30 15:41:50 1997 Received: from 134.81.76.36 by fra29.hiserv.de with SMTP (Microsoft Exchange Internet Mail Connector Version 4.0.994.63) id C3C5GCNL; Thu, 30 Jan 1997 15:46:30 +0100 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id PAA02064; Thu, 30 Jan 1997 15:42:19 +0100 Message-ID: <32F0B34B.ABD@h1tw0036.hoechst.com> Date: Thu, 30 Jan 1997 15:42:19 +0100 From: "Dr. Heinz Schiffer" Organization: Hoechst Corporate Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Computational Chemistry List Subject: Mulliken Population Analysis Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, why does no one uses ( or is even aware of ) the population analysis method of Davidson, Roby, and Ahlrichs ? In my opinion, it is the cheapest one ( compared to Bader or NBO ) with the highest interpretation potential ( no one should use population charges to model the electrostatic potential of a molecule. These are quiet different things !!! ). Here are the references : (1) Ernest R. Davidson Electronic Population Analysis of Molecular Wavefunctions J. Chem. Phys. 46 (1967) 3320-3324 (2) Keith R. Roby Quantum theory of chemical valence concepts I. Definition of the charge on an atom in a molecule and of occupation numbers for electron density shared between atoms Mol. Phys. 27 (1974) 81-104 (3) Rolf Heinzmann and Reinhart Ahlrichs Population Analysis Based on Occupation Numbers of Modified Atomic Orbitals (MAOs) Theoret. Chim. Acta 42 (1976) 33-45 (4) D. W. J. Cruickshank, F.R.S., and Elizabeth J. Avramides The Interpretation of Molecular Wave Functions: The Development and Application of Roby's Method for Electron Population Analysis Phil. Trans. R. Soc. Lond. A 304 (1982) 533-565 (5) Claus Ehrhardt and Reinhart Ahlrichs Population analysis based on occupation numbers II. Relationship between shared electron numbers and bond energies and characterization of hypervalent contributions Theor. Chim. Acta 68 (1985) 231-245 Ciao, Heinz --- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main schiffer@msmwia.hoechst.com From marti108@gold.tc.umn.edu Thu Jan 30 12:19:53 1997 Received: from mhub1.tc.umn.edu for marti108@gold.tc.umn.edu by www.ccl.net (8.8.3/950822.1) id MAA27171; Thu, 30 Jan 1997 12:17:41 -0500 (EST) Received: from gold.tc.umn.edu by mhub1.tc.umn.edu; Thu, 30 Jan 97 11:17:37 -0600 Received: by gold.tc.umn.edu; Thu, 30 Jan 97 11:17:36 -0600 Date: Thu, 30 Jan 1997 11:17:35 -0600 (CST) From: Marcus G Martin To: chemistry@www.ccl.net Subject: Modeling Electrostatics Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 30 Jan 1997, Dr. Heinz Schiffer wrote: -SNIP- > Hi, > why does no one uses ( or is even aware of ) the population analysis > method of Davidson, Roby, and Ahlrichs ? In my opinion, it is the > cheapest one ( compared to Bader or NBO ) with the highest > interpretation potential ( no one should use population charges > to model the electrostatic potential of a molecule. These are quiet > different things !!! ). Here are the references : -SNIP- What should I do if I want to fit the electrostatic potential of a molecule? I have been fitting lennard-jones 12-6 force fields to alkanes and would like to move into the (frightening) world of slightly charged molecules. Nothing extremely painful, such as water, but more like alkanols or carboxillic acids. The running discussion on charges appears to me to say that the charges computed from quantum mechanics are of little use for fitting a force field. I would like to know if the computational community has a feel for what the 'best' and most efficient way of fitting point charges to these molecules would be. thanks, I will summarize the responses if there is interest. Marcus Martin Graduate Student Department of Chemistry, University of Minnesota marti108@gold.tc.umn.edu http://siepmann6.chem.umn.edu/~marcus From slawek@alchmist.scs.uiuc.edu Thu Jan 30 13:19:54 1997 Received: from labrador.scs.uiuc.edu for slawek@alchmist.scs.uiuc.edu by www.ccl.net (8.8.3/950822.1) id NAA27629; Thu, 30 Jan 1997 13:09:55 -0500 (EST) Received: from piglet.scs.uiuc.edu (piglet.scs.uiuc.edu [130.126.227.130]) by labrador.scs.uiuc.edu (AIX4.2/UCB 8.7/8.7) with SMTP id MAA17366 for ; Thu, 30 Jan 1997 12:11:40 -0600 (CST) Received: by piglet.scs.uiuc.edu with Microsoft Mail id <01BC0EA6.7FF0AA90@piglet.scs.uiuc.edu>; Thu, 30 Jan 1997 12:09:53 -0600 Message-ID: <01BC0EA6.7FF0AA90@piglet.scs.uiuc.edu> From: Slawomir Janicki To: "'CCL'" Subject: Re :FW: G:A (silly) problem with G94 Date: Thu, 30 Jan 1997 12:09:51 -0600 Encoding: 5 TEXT To all who sent me the correct keyword (AddRedun or AddR) - Thanks a lot! Slawek Janicki slawek@alchmist.scs.uiuc.edu From qibvigap@lg.ehu.es Thu Jan 30 14:19:53 1997 Received: from lgsx01.lg.ehu.es for qibvigap@lg.ehu.es by www.ccl.net (8.8.3/950822.1) id NAA27960; Thu, 30 Jan 1997 13:56:18 -0500 (EST) Received: from lgdx02.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA13697; Thu, 30 Jan 97 19:55:22 GMT Received: by lgdx02.lg.ehu.es (5.65/4.7) id AA12591; Thu, 30 Jan 1997 20:03:37 GMT Date: Thu, 30 Jan 1997 20:03:37 +0000 (WET) From: Pablo Vitoria Garcia X-Sender: qibvigap@lgdx02 To: ccl Subject: Fulfillment of virial theorem with pseudopotentials Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am doing some calculations on MoO4(2-) (molybdate) with G94 using the following basis sets: LANL2DZ (Hay-Wadt pseudopotentials) on Mo, and D95 on O. The estructure is correctly optimized, but the -V/T ratio is different from 2, around 2.15. I guess this means that the wavefunction is not really a good one. Is this effect due to the use of pseudopotentials? Does anybody have some experience with this kind of calculations and how to get around this problem? Thanks a lot for your time Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lgdx02.lg.ehu.es Phone: +34 4 4647700 Ext. 2450 -------------------------------------------------------------------------------- From qiang@euch4e.chem.emory.edu Thu Jan 30 16:19:55 1997 Received: from euch4e.chem.emory.edu for qiang@euch4e.chem.emory.edu by www.ccl.net (8.8.3/950822.1) id PAA28885; Thu, 30 Jan 1997 15:38:07 -0500 (EST) From: Received: from localhost by euch4e.chem.emory.edu (AIX 3.2/UCB 5.64/4.03) id AA20345; Thu, 30 Jan 1997 15:37:48 -0500 Date: Thu, 30 Jan 1997 15:37:48 -0500 (EST) To: Pablo Vitoria Garcia Cc: ccl Subject: Re: CCL:G:Fulfillment of virial theorem with pseudopotentials In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 30 Jan 1997, Pablo Vitoria Garcia wrote: > > Hi, > > I am doing some calculations on MoO4(2-) (molybdate) with G94 using the > following basis sets: LANL2DZ (Hay-Wadt pseudopotentials) on Mo, and D95 > on O. The estructure is correctly optimized, but the -V/T ratio is > different from 2, around 2.15. I guess this means that the wavefunction > is not really a good one. Actually I've asked this question before. And the conclusion we have reached is: Virial theorem only holds for Coulumb-type potentials, (look at any book with proof of Virial). In ECP, u have non-Coulumb type functionals, thus the virial theorem is violated. And because the core electrons have the dominant contributions, when u r doing calculation with both metal and main group elements, the value is quite close to 2. If u do calculations with ECP only, say metal clusters, u r gonna get huge quotient. Doesn't necc. mean ur wf. is bad. > > -------------------------------------------------------------------------------- > Pablo Vitoria Garcia > Departamento de Quimica Inorganica, Facultad de Ciencias > Universidad del Pais Vasco (UPV/EHU) > Apartado 644, E-48080 Bilbao > SPAIN > e-mail: qibvigap@lgdx02.lg.ehu.es > Phone: +34 4 4647700 Ext. 2450 > -------------------------------------------------------------------------------- > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: qibvigap@lg.ehu.es > -- Original Sender From: Address: qibvigap@lg.ehu.es > 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. Emory Univ. 508 Webster Dr. Apt.#2 Atlanta, GA 30322. Decatur, GA 30033. (404)-727-2381 (404)-636-6149 http://tswww.cc.emory.edu/~qcui ______________________________________________________________ From yuan@nka1.med.uc.edu Thu Jan 30 17:19:55 1997 Received: from nka1.med.uc.edu for yuan@nka1.med.uc.edu by www.ccl.net (8.8.3/950822.1) id RAA00154; Thu, 30 Jan 1997 17:17:14 -0500 (EST) Received: from localhost by nka1.med.uc.edu via SMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) for id RAA17318; Thu, 30 Jan 1997 17:17:14 -0500 Date: Thu, 30 Jan 1997 17:17:14 -0500 (EST) From: Jie Yuan To: Computational Chemistry List Subject: DIBUG - inactive? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII It seems that DIBUG (Discover InsightII Biosym User Group) mailing list is not active any more. Anyone know why? Is there a new list that replaces this one? I know my mails to DIBUG went nowhere. I have not received any email from DIBUG for more than 2 months. Anyone did? MSI's web site is not too helpful on this, IMHO. On DIBUG's web site, http://www.icm.edu.pl/local-lists-archive/dibug/ archives up to September 1996 can be read, but the December archive is inaccessible. Thanks! Jie -- Jie Yuan, PhD - U. of Cincinnati - Dept. of Pharmacology & C.B. -- == POBox 670575, Cin., OH 45267-0575 = 513-558-2352 = x-1169 (fax) == == www.uc.edu/~yuanj = Jie.Yuan@UC.edu = using Pine (Irix5.3) == == PGP key: finger -l yuanj@ucunix.san.uc.edu == From scip5031@leonis.nus.sg Thu Jan 30 22:19:56 1997 Received: from sable.nus.sg for scip5031@leonis.nus.sg by www.ccl.net (8.8.3/950822.1) id WAA01120; Thu, 30 Jan 1997 22:19:14 -0500 (EST) Received: from leonis.nus.sg (scip5031@leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.8.4/8.6.9) with ESMTP id LAA04295 for ; Fri, 31 Jan 1997 11:19:04 +0800 (SST) Received: from localhost (scip5031@localhost) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) with SMTP id LAA00281 for ; Fri, 31 Jan 1997 11:19:01 +0800 Date: Fri, 31 Jan 1997 11:19:01 +0800 (SST) From: "FANG L." To: chemistry@www.ccl.net Subject: ccl: electronic structure of glass Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CCL readers: I want to some references about calculation of electronic structure of oxide or halide glass systems. Also I want to know which program ( ab initio or semiempirical) can treat elements like Mo, Cu, W, Ag and V. Thanks for your help and if more answers received I will summarize. FANG Ling Dept. of Physics National Univ. of Singapore Lower Kent Ridge Rd. Singapore 119260 Tel.7722605