From jacs@citrus.ucr.edu Wed May 29 02:50:21 1996 Received: from orange.ucr.edu for jacs@citrus.ucr.edu by www.ccl.net (8.7.5/950822.1) id BAA27378; Wed, 29 May 1996 01:58:36 -0400 (EDT) Received: from [206.29.0.111] by 206.29.0.111 with SMTP; Tue, 28 May 1996 22:57:50 -0700 (PDT) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 28 May 1996 23:01:35 +0100 To: chemistry@www.ccl.net From: jacs@citrus.ucr.edu (Jacqueline) Subject: InsightII electrostatic potential maps? Could someone give me information about how to create electrostatic potential maps in InsightII from Brookhaven pdb files? Thanks Jacqueline From joubert@ext.jussieu.fr Wed May 29 04:50:21 1996 Received: from shiva.jussieu.fr for joubert@ext.jussieu.fr by www.ccl.net (8.7.5/950822.1) id EAA28816; Wed, 29 May 1996 04:23:25 -0400 (EDT) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.7.5/jtpda-5.2) with ESMTP id KAA04913 for ; Wed, 29 May 1996 10:23:24 +0200 (METDST) Received: from [134.157.11.17] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Wed, 29 May 1996 10:23:22 +0200 X-Sender: joubert@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 29 May 1996 10:26:03 +0200 To: chemistry@www.ccl.net From: joubert@ext.jussieu.fr (Laurent Joubert) Subject: Initial Guess with G94 Dear Netters, I actually have some problems with a single point calculation with g94, using Stuttgart's pseudopotentials. Scf convergence seems to take a very long time with the default pseudo-extended huckel guess (I'm also using SCF=QC) I can obtain a convergence, but I wonder if I could use another initial guess to gain time. What is the best option for the keyword "Guess" in this kind of problem (I can't use "Core" with pseudopotentials) Thanks in advance. Laurent Joubert ------------------------------------------------------------------ Laurent JOUBERT (PhD student) Ecole Nationale Superieure de Chimie de Paris Laboratoire d'Electrochimie et de Chimie Analytique 11, rue Pierre et Marie Curie 75231 PARIS CEDEX 05- FRANCE Tel : 44-27-66-94 Fax : 44-27-67-50 E-Mail : joubert@ext.jussieu.fr WWW site : http://www.enscp.jussieu.fr ------------------------------------------------------------------ From andreas@majestix.msp.univie.ac.at Wed May 29 05:50:28 1996 Received: from majestix.msp.univie.ac.at for andreas@majestix.msp.univie.ac.at by www.ccl.net (8.7.5/950822.1) id FAA29596; Wed, 29 May 1996 05:46:51 -0400 (EDT) Received: by majestix.msp.univie.ac.at (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id JAA16511; Wed, 29 May 1996 09:46:13 GMT From: "Andreas Parusel" Message-Id: <9605290946.ZM16509@majestix.msp.univie.ac.at> Date: Wed, 29 May 1996 09:46:02 +0000 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: G: Excited State Optimization Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello CCL'lers! Since several months I am trying to work with the calculation and optimization of excited states with the GAUSSIAN94 package. As I have thought, there are several problems raising, which I have to solve. It would be great, if there is anybody outside, who works on the same subject and is willing to help me in this matter. Thanks for every single mail in advance, Andreas Parusel, Vienna -- ======================================================================= _/_/ _/_/ andreas@majestix.msp.univie.ac.at = _/ _/_/ _/ andreas@phys-chemie.uni-wuerzburg.de = _/ _/_/ _/ parusel@aries.scs.uiuc.edu = _/_/ _/_/ http://majestix.msp.univie.ac.at/~andreas = = Andreas Parusel = Institute of Theoretical Chemistry and Radiation Chemistry = Althanstr. 14 A-1090 Vienna = Tel +43 1 31336 1572 Fax +43 1 31336 790 = ======================================================================= From Jeffrey.Gosper@brunel.ac.uk Wed May 29 07:50:27 1996 Received: from etamin.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.7.5/950822.1) id HAA00681; Wed, 29 May 1996 07:35:43 -0400 (EDT) Received: from chem-pc-18 (actually chem-pc-18.brunel.ac.uk) by etamin.brunel.ac.uk with SMTP (PP); Wed, 29 May 1996 12:34:58 +0100 Date: Wed, 29 May 1996 12:34:53 BST From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: IRC with CI in MOPAC. To: chemistry@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear computational chemists (and other interested parties) I have been trying to perform a MOPAC93 IRC calculation using CI. Although I have located a TS which has a single negative frequency (-1362.6/cm) using the keywords: AM1 PRECISE T=10H C.I.=(3,2) SINGLET ROOT=1 ISOTOPE FORCE I have found that the IRC=1 run only proceeds for 27 cycles and terminates. At this point the GNORM is 6.79 and the negative frequency is still present (-1359/cm), it is therefore not another stationary point. I am getting an IEEE underflow error whilst running this calculation under SUN System V release 4 on a SparcStation. Could someone with access to MOPAC93 on another platform be king enough to run the two calculations given below and Email me their findings. (The FORCE is required before the can IRC cam be run). Also if anyone has experience or suggestions on getting over this problem could they please contact me. Z-matrix 1: AM1 PRECISE T=10H C.I.=(3,2) SINGLET ROOT=1 ISOTOPE FORCE TS optimized from reaction path step #32 C C 2.51767 1 1 C 1.45316 1 65.98506 1 2 1 C 1.34195 1 114.14147 1 -0.15694 1 3 2 1 H 1.09021 1 120.14083 1 -97.55633 1 2 3 4 H 1.08962 1 120.52845 1 87.97527 1 2 3 4 H 1.09360 1 119.89368 1 179.62546 1 3 2 1 H 1.09401 1 125.70927 1 -179.21734 1 4 3 2 H 1.09044 1 120.22678 1 -103.89030 1 1 4 3 H 1.09114 1 119.81015 1 87.55462 1 1 4 3 Z-matrix #2 AM1 PRECISE T=10H C.I.=(3,2) SINGLET ROOT=1 ISOTOPE IRC=-1 RESTART LARGE TS optimized from reaction path step #32 C C 2.51767 1 1 C 1.45316 1 65.98506 1 2 1 C 1.34195 1 114.14147 1 -0.15694 1 3 2 1 H 1.09021 1 120.14083 1 -97.55633 1 2 3 4 H 1.08962 1 120.52845 1 87.97527 1 2 3 4 H 1.09360 1 119.89368 1 179.62546 1 3 2 1 H 1.09401 1 125.70927 1 -179.21734 1 4 3 2 H 1.09044 1 120.22678 1 -103.89030 1 1 4 3 H 1.09114 1 119.81015 1 87.55462 1 1 4 3 /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http1.brunel.ac.uk:8080/~castjjg Re_View's Home page (A molecular display/animation/analysis program): http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From wall@phys.chem.ethz.ch Wed May 29 08:50:24 1996 Received: from bernina.ethz.ch for wall@phys.chem.ethz.ch by www.ccl.net (8.7.5/950822.1) id IAA00865; Wed, 29 May 1996 08:07:00 -0400 (EDT) Received: from helios (actually helios-chem.ethz.ch) by bernina.ethz.ch with SMTP inbound; Wed, 29 May 1996 14:06:26 +0200 Received: from jetson.ppc-sun by helios.ethz.ch id AA19740; Wed, 29 May 1996 14:06:25 +0200 Received: by jetson.ppc-sun (5.x/SMI-SVR4) id AA21206; Wed, 29 May 1996 14:06:22 +0200 Date: Wed, 29 May 1996 14:06:22 +0200 From: wall@phys.chem.ethz.ch (Ernst U. Wallenborn) Message-Id: <9605291206.AA21206@jetson.ppc-sun> To: chemistry@www.ccl.net Subject: [S] G94 Excited States X-Sun-Charset: US-ASCII Hi there, first of all thanks to all who responded. Below as usual a summary of the responses. The recommendations included a range of methods >from ZINDO to CASPT2. Several people asked me for a specification of the system i'm interested in. It is all-trans-(1,8)-Diphenyl-octatetraene, C20H16, C2h symmetry. (Some people in our group got into Science with a two-photon paper recently, that is why my boss wants me to do it). This is a (20,20) system in g94 nomenclature. Inspection of the CSF relevant for a simple CIS shows that at least the (10,10) part is relevant for the first excited singlet and triplet states. Several people told me to use ZINDO. I don't know how ZINDO would perform on our system, but would like to try. Unfortunately ZINDO is commercial. It is available as part of Biosym's insight ii, but only as an extension, which no insight installation i have access to features. HyperChem reportedly has ZINDO, too. But then again, this school here is Spartan territory. Han Zuilhof pointed out that g94 can do a CISMP2 (CISPT2?) calculation via Iop(9/23=1) (not 9/21=1 as the manual says). I tried this and quickly found out that this doesn't work as a direct method. I'll try again and if it works, i'll let you know. Then there were the CASPT2 advices. I don't know wether i can do this for the system of interest. But i'll try. Besides, is CASSCF MP2 identical to CASSPT2 as i.e. implemented in molcas? Nobody recommended a caculation of the excitation energy via E[CISDT(e)] - E[CISD(g)]. (This isn't possible with g94, but would be in GAMESS (but as i mentioned i don't think my scratch space will be enough). MOLCAS can do this, too.) Is there a reason for this? Or is this just a bit out of fashion? wondering... -- Ernst-Udo Wallenborn Laboratorium fuer Physikalische Chemie ETH Zentrum CH-8092 Zuerich Here's the list of messages The original message was: -----cut here----- Hi there, i need to calculate an electronic spectrum of an aromatic compound (yes it was my boss' idea, yes i did tell him that this is much easier to measure and no fun to calculate, no he didn't find my opinion useful and constructive). Now the problem is: the thing is far too big for US-GAMESS (USG has no direct CI, hence it's not expensive to calculate, it's plain impossible with our HD configuration), it is too big for a reasonable CAS in g94 (i have a Pi space of 20 orbitals, of which at least ten have to be included) CIS on the other hand takes (STO-3g, this was a test) about 30 minutes on my SPARC 2, but it's results are, well, not overwhelming. So the question is: Is there any possibility of doing anything better than CIS but cheaper than CAS in g94? In GAMESS i'd do a CISD versus CISD(T) calculation in the style of Shavitt's 70's calculation of the acetone spectrum, but as i mentioned, i think US-GAMESS is likely to fail. I tried #3-21g* casscf(10,10,nroot=1) iop(4/17=10,4/18=10,4/19=1) where the 4/19 option should have set up a FOCI MCSCF (in GAMESS language), but ended up with a eof error on stdin. After checking the programmer's manual i added 64 1 1 1 2 3 4 5 1 2 3 4 5 to the .com, where 64 is the number of occupied orbitals, and 1 2 3 4 5 1 2 3 4 5 the reference configuration. That gave me lots of TAPE READ ERRORs. Besides a test run on water showed a difference between 4/19=2 and GAMESS MCSCF SOCI=.T., so they are not identical anyway. Any help? -----cut here----- >From teomgs@garm.teokem.lu.se Mon May 20 12:01 MET 1996 An alternative would be to use MOLCAS and to do a CASSCF calculation with subsequent CASPT2. Up to 14 active electrons in 14 orbitals is possible with MOLCAS. The accuracy is within 0.2 eV, given that a reasonable choice of the active orbitals for the states of interest is made, and a reasonable basis set is used. Remember, the s-tetrazine calculations were done with MOLCAS on the C4 cluster. (Schuetz, Hutter, Luethi, JCP 103, 7048 (1995). One problem you may have is, that the codes are not integral direct. So you have to store the ERIs on disk, which may kill you, if your molecule is too large. In LUND we have a multifile I/O system in experimental status, which allows to go beyond the 2 GByte limit, imposed by AIX on the RS6K. Furthermore, distributed parallel, integral-direct implementations of CASSCF/CASPT2 are under development, but these won't be available until next year. Martin -- Martin Schuetz, Ph.D. Phone: +46 46 222 45 01 Dep. of Theoretical Chemistry FAX: +46 46 222 45 43 University of Lund SWEDEN E-mail: teomgs@teokem.lu.se, teomgs@garm.teokem.lu.se -----cut here----- >From ferenc@rchsg8.chemie.uni-regensburg.de Mon May 20 14:41 MET 1996 Dear Dr. Wallenborn, you did not specify your system of interest, which would have been helpfull ... Anyway, if your system gets to large you should consider using a semiempirical method like PPP (pi-electrons only) or the INDO/S hamiltonian! The INDO/S (and ZINDO also) hamiltonians where parametrized for spectroscopy and often give results comparable or even superior to ab initio calculations - especially on larger molecules! Hope this helps! Cheers, Ferenc -----cut here----- >From cmartin@trex.uchicago.edu Mon May 20 20:13 MET 1996 You could do a 10 orbital CASSCF and then add on the second order perturbation corrections. DOing a 20 orbital CASSCF will probably not be that great anyway because you do not include the dynamical correlation. I would bet that the smaller CAS + PT2 will work better. I doubt you can do better than 1/2 eV in accuracy with such a calculation and your small basis sets. What is the system you are trying to compute? Best Regards Chuck Martin W.M. Keck Center for Molecular Electronics Syracuse University cmartin@rainbow.uchicago.edu -----cut here----- >From zuilhof@chem.chem.rochester.edu Tue May 21 04:10 MET 1996 Dear Ernst, You might want to try the CIS-MP2 method as implemented in G94. This is available via overlay 9/23=1 (for closed-shell systems). I haven't gotten around to extensively testing this myself, but received very positive information on this from David Danovich (Hebrew University, Jerusalem), who suggested it for me to use on excited states of molecules with 11+ heavy atoms and C1 symmetry. (He also stated the manual was wrong by stating it is 9/21=1.) If you find this method works, please let me (and CCL) know. Of course I am also very interested in a summary of other people's responses, since clearly excellent methods as Roos' CASPT2 are still impractical for many, many low-symmetry systems.. Best regards, Han Zuilhof ****************************************************************************** ** Dr. Han Zuilhof ** e-mail: ZUILHOF@chem.chem.rochester.edu ** ** Department of Chemistry ** ** ** University of Rochester ** ** ** Rochester, NY, 14627 ** Fax: (716) 473-6889 ** ** USA ** Voice: (716) 275-2219 ** ****************************************************************************** ** ** ** "Excite a photochemist!" ** ** ** ****************************************************************************** -----cut here----- >From amasunov@email.gc.cuny.edu Sun May 26 01:24 MET 1996 Dear Ernst Wallenborn, If you can not afford descent basis set in ab initio, you'd better use MNDO/C. Even CAS will not give you anything useful with STO-3G. Artem __ _________ / \ / _ _ \ Artem Masunov - amasunov@shiva.hunter.cuny.edu / \\ \\ \\ \ Chemistry Department, Hunter College / /\ \\ \\ \\ \ City University of New York / ____ \\ \\ \\ \ 695 Park Avenue, New York, NY 10021 /__/\__/\__\\__\\__\\__\ Tel: (212) 725-0317, Fax: (212) 772-5332 \__\/ \/__//__//__//__/ -----cut here----- From rosas@irisdav.chem.vt.edu Wed May 29 10:50:24 1996 Received: from irisdav.chem.vt.edu for rosas@irisdav.chem.vt.edu by www.ccl.net (8.7.5/950822.1) id KAA03165; Wed, 29 May 1996 10:28:01 -0400 (EDT) Received: by irisdav.chem.vt.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id KAA08026; Wed, 29 May 1996 10:26:51 -0400 From: "Victor M. Rosas Garcia" Message-Id: <9605291026.ZM8024@irisdav.chem.vt.edu> Date: Wed, 29 May 1996 10:26:48 -0400 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: rigid vs relaxed scan in Gaussian Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi there, I'm trying to calculate a bond stretching constant for molecular mechanics work. I'm doing a Scan of the potential energy surface (well, curve in this case) for the stretching of the bond with the 6-31+G* basis set in Gaussian94. The problem is that the keyword "Scan" in gaussian has two options: rigid and relaxed. What is the recommendation for this kind of parametrization work? Should the scan keep the molecule rigid or let it relax at each point of the stretch? My boss says that it should be relaxed while I'm going for the rigid. I think that letting the molecule relax at each point would make the constant too specific for the model compound and, thus, not of general applicability; not to mention cross-contamination by other stretches and torsions present in the molecule. Any comments are appreciated. Thanx Victor. -- ----------------------------------------------------------------------- Victor M. Rosas Garcia * "How can we contrive to be rosas@irisdav.chem.vt.edu * at once astonished at the Virginia Tech doesn't necessarily share * world and yet at home in it?" the opinions you just read. * G. K. Chesterton ----------------------------------------------------------------------- From gmercier@helix.nih.gov Wed May 29 11:06:33 1996 Received: from helix.nih.gov for gmercier@helix.nih.gov by www.ccl.net (8.7.5/950822.1) id KAA03223; Wed, 29 May 1996 10:36:29 -0400 (EDT) Received: from [128.231.66.71] (ppc71.od.nih.gov [128.231.66.71]) by helix.nih.gov (8.6.13/8.6.12) with SMTP id KAA22228 for ; Wed, 29 May 1996 10:36:28 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 29 May 1996 10:37:16 -0500 To: chemistry@www.ccl.net From: gmercier@helix.nih.gov (Gustavo A. Mercier, Jr.) Subject: HONDO 8.4 in SGI R8K IRIX 6.1 Hi! Has anybody managed to port Hondo 8.4 to an SGI R8K running IRIX 6.1? I did a port to an R4000, but moving this version to the R8000 machine has not been simple. Half of the sample runs stop with error messages. Specifically, those with user defined basis sets (8,9,10,13,15,16,17) where an "illegal basis set" is detected by subroutine ATOMS, and those running the PALDUS subroutine (2,5) where a "too many rows. maximum is -2" error message is generated. I am aware of many of the 32/64 bits idiosyncracies, but using a variety of switches in the compilation does not help, eg. mips4 vs mips2 vs -n32 mips4 etc. Indeed, eliminating optimization by only using -O0 -static -G3 makes no difference. In looking at the code of ATOMS it seems that Hondo makes a rather unorthodox use of character data. For example, character data is loaded into R*8 variables, and many equivalences are made between R*8 and CHARACTER*8 data. Before I begin to mess with the code, has anybody done this port or knows of somebody who could help in this area? GAMESS is a similar program, so may be some of the GAMESS people have had a similar experience, and care to comment. :-) Thanks in advance ... Bye Gustavo A. Mercier, Jr. M.D.,Ph.D. NIH - LDRR OD OIR LDRR Building 10 Room B1N256 10 Center Dr MSC 1074 Bethesda, Maryland 20892-1074 phone: 301-402-3586, 301-402-1981 fax: 301-402-3216 e-mail: gmercier@helix.nih.gov **************************************** **************************************** Every attempt to employ mathematical methods in the study of chemical questions must be considered profoundly irrational and contrary to the spirit of chemistry ... If mathematical analysis should ever hold a prominent place in chemistry -- an aberration which is happily almost impossible -- it would occasion a rapid and widespread degeneration of that science. Auguste Comte Philosophie Positive, Paris, 1838 ------------------------------------------------------------- The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble. Dirac, Proc. Roy. Soc (London) 123:714 (1929) ------------------------------------------------------------- From young@argus.cem.msu.edu Wed May 29 11:11:09 1996 Received: from argus.cem.msu.edu for young@argus.cem.msu.edu by www.ccl.net (8.7.5/950822.1) id KAA03243; Wed, 29 May 1996 10:42:28 -0400 (EDT) From: Received: from slater.cem.msu.edu by argus.cem.msu.edu via ESMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI) for id KAA28545; Wed, 29 May 1996 10:42:26 -0400 Received: by slater.cem.msu.edu (951211.SGI.8.6.12.PATCH1042/) for CHEMISTRY@www.ccl.net id KAA08829; Wed, 29 May 1996 10:43:30 -0400 Date: Wed, 29 May 1996 10:43:30 -0400 Message-Id: <199605291443.KAA08829@slater.cem.msu.edu> To: CHEMISTRY@www.ccl.net Subject: Summer workshops Reply-To: Dr. James F. Harrison ------------------------------------------------------------------ This is a second posting to correct an error in the URL listed with the first posting. ------------------------------------------------------------------ The Chemistry Department, Michigan State University offers two workshops Concepts, Techniques & Applications of Electronic Structure Methods in Chemistry & Scientific Visualization Summer 1996 Schedule Concepts, Techniques & Applications of Electronic Structure Methods in Chemistry July 8, 9 & 10 July 15, 16 & 17 July 22, 23 & 24 Scientific Visualization July 11 &12 July 18 & 19 July 25 & 26 *** The two workshops are independent and may be taken individually *** Workshop Sponsors College of Natural Science Department of Chemistry Center for Fundamental Materials Research Crop and Food Bioprocessing Center MSU is an Affirmative Action/Equal Opportunity Institution ---------------------------------------------------------------------------- Concepts, Techniques & Applications of Electronic Structure Methods in Chemistry An intensive three day workshop on the application of modern electronic structure methods to chemistry. The workshop consists of lectures which provide an overview of theoretical techniques and laboratory sessions in which participants receive hands-on experience on a wide variety of chemical problems using the techniques discussed in lecture. An important goal of this workshop is to develop a sense of which computational techniques are appropriate for a particular problem and when computation may not be the best approach. The capabilities, limitations and characteristics of several electronic structure codes including Gaussian 92, GAMESS, SPARTAN, and DMol will be discussed and demonstrated. This workshop will be of interest to professionals in Chemistry, Biochemistry, or Materials Science who use or make use of the results of computational chemistry in their work. Each participant will have exclusive use of a Silicon Graphics workstation during the workshop and enrollment will be limited to six participants/course, ensuring individual attention. Course Fee $600 Fee includes tuition, lecture and laboratory materials. A limited number of partial tuition scholarships are available to faculty from four-year colleges. Workshop Instructor Dr. James F. Harrison, Professor, Department of Chemistry, Michigan State University received his Ph.D. from Princeton University in 1966, and was an NSF postdoctoral fellow at Indiana University from 1966 to 1968 when he joined the faculty in Chemistry at MSU. He has twenty five years experience in teaching theoretical chemistry at all levels of the chemistry curriculum. He has published 90 papers on various aspects of computational chemistry. Workshop Structure There will be lectures each day from 8:30 a.m. until noon and a laboratory session from 1:30 until 5:30 p.m. Included will be an optional laboratory in the evening from 7:30 until 10:00 p.m. during which participants can work on problems of their own with the guidance of the workshop instructor. Topics to be discussed include: Restricted and unrestricted Hartree-Fock theory and applicability Basis sets and the reliability of a calculation Geometry optimization and vibrational frequencies Density Functional theory and its applications Electron density and electrostatic potentials Semi-empirical methods: when to use one and why Moller-Plesset perturbation theory and configuration interaction: when to use them Multiconfiguration self-consistent field (MCSCF) Comparison of functionality of various codes including Gaussian 92, GAMESS, SPARTAN and DMol ---------------------------------------------------------------------------- Scientific Visualization An intensive 2 day workshop on the methods and techniques of scientific visualization. The workshop consists of lectures on visualization topics followed by a laboratory in which participants will gain practical experience in applying the concepts discussed in lecture. The workshop will be especially valuable to scientists and engineers who are interested in using visualization techniques in their data analysis and who want an overview of the procedures, scope, and limitations of scientific visualization. We will focus on the use of the visualization program Iris Explorer, which provides a powerful environment for visualizing 2- and 3-dimensional data sets using procedures that are independent of the means used to generate the data files being visualized. Each participant will have exclusive use of a Silicon Graphics workstation during the workshop and enrollment will be limited to six participants per course, ensuring individual attention. Course Fee $400 Fee includes tuition, lecture and laboratory materials. A limited number of partial tuition scholarships are available to faculty from four-year colleges. Workshop Instructors Mr. David Young, graduate assistant, Department of Chemistry, Michigan State University has degrees from MSU in Computational Mathematics and Chemistry and is working on his Ph.D. in Theoretical Chemistry. He has 4 years experience in using and teaching visualization techniques to undergraduate and graduate students in a variety of disciplines. Mr. Paul Reed, computer specialist, Department of Chemistry, Michigan State University has a B.S. in Computer Science from MSU and is working on his masters degree in Computer Science. He has five years experience in scientific visualization and has played a leading role in the development of the MSU Chemistry Visualization Facility. Dr. James F. Harrison (see previous page). Workshop Structure There will be a one-hour lecture and a three-hour laboratory each morning (8:00-12 noon) and afternoon (1:30-5:30) Topics to be discussed include: Explorer basics (modules, maps, libraries, linking modules, terminology) Building maps (data types, linking, strategy) Rendering (lights, colors, render modes, display modes) DataScribe (templates, glyphs, arrays, lattices, icons, procedure, limitations) Advanced Explorer topics (loops and scripting, building modules, customizing the setup parameter functions) Types of visualizations, (structure, 1D, 2D, 3D, vector quantities, animations) Colorizations (HSV vs. RGB, linear and nonlinear colormaps) ---------------------------------------------------------------------------- 1996 Summer Workshops Registration Form ---------------------------------------------------------------------------- Participants may register by returning the following form or electronically. (http://www.cem.msu.edu/sumws/sumws.html) However, payment must be submitted as described below. Name: --------------------------------------------------------------------- Affiliation: -------------------------------------------------------------- Address (First Line): ----------------------------------------------------- Address (Second Line): ---------------------------------------------------- State: -------------------------------------------------------------------- Zip: ---------------------------------------------------------------------- Telephone: ---------------------------------------------------------------- Email: -------------------------------------------------------------------- Fax: ---------------------------------------------------------------------- Please indicate first, second or third choice: Electronic Structure Fee: $600 Visualization Fee: $400 July 8-10 July 11-12 -------------- --------------- July 15-17 July 18-19 -------------- --------------- July 22-24 July 25-26 -------------- --------------- Make checks payable to: "Michigan State University", in U.S. funds. Workshop fees include tuition, lecture, and laboratory materials. A limited number of partial tuition scholarships provided by the Materials Research Science and Engineering Center (MRSEC) and the office of the Vice Provost for University Outreach are available to faculty from four-year colleges. All workshop sessions are limited to six participants, and spaces are reserved based on receipt of this completed form and prepaid workshop fee(s). All registrations must be received by June 21. Complete housing reservation information and workshop details will follow upon workshop confirmation. For further information or to arrange special handicapper accommodations Mail registration form and please contact: fees to: Professor James F. Harrison MSU College of Natural Science Chemistry Department Outreach Programs Michigan State University 215 North Kedzie Lab East Lansing, MI 48824-1322 East Lansing, MI 48824 Phone: 1-517-355-9715 ext. 295 Fax: 1-517-353-1793 email: harrison@cemvax.cem.msu.edu Deadline: June 21 MSU is an Affirmative Action/Equal Opportunity Institution Dave Young young@slater.cem.msu.edu -------------------------------------------------------------------------- Computational chemistry, teaching, visualization and programming. -------------------------------------------------------------------------- From jkromero@presto.ig.com Wed May 29 12:50:26 1996 Received: from presto.ig.com for jkromero@presto.ig.com by www.ccl.net (8.7.5/950822.1) id MAA03942; Wed, 29 May 1996 12:27:44 -0400 (EDT) Received: from [134.172.2.211] ([134.172.2.211]) by presto.ig.com (8.6.12/8.6.6) with SMTP id JAA04869; Wed, 29 May 1996 09:27:25 -0700 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 29 May 1996 09:31:32 -0700 To: chemistry@www.ccl.net From: jkromero@presto.ig.com (Jill Koering-Romero) Subject: Posting a press release Cc: jkromero@presto.ig.com Oxford Molecular Group Completes UniChem Software and Technology Acquisition from Cray Research, Inc. Agreement Strengthens Oxford Molecular's Competitiveness in Quantum Chemistry and Supports Cray's New Application Strategy CAMPBELL, Calif., May 24, 1996 - Oxford Molecular Group PLC (OMG: London Stock Exchange) and Cray Research, Inc. (NYSE: CYR) today announced that they have reached a definitive agreement for Oxford Molecular Group to acquire Cray's UniChem software package for computational chemistry applications. Under the agreement, Oxford Molecular Group purchased UniChem and a CRAY J90 supercomputer through a mixture of cash and the issue of shares to Cray. Also, Cray will become a distributor of UniChem software for Cray supercomputers. All future versions of the software will be developed by Oxford Molecular, and a comprehensive licensing and support transition plan has been developed to support current customers. The agreement includes transfer of technology and software licenses. According to Tony F. Marchington, D. Phil., chief executive officer of Oxford Molecular, the Unichem acquisition enables the company to strengthen its competitiveness in the quantum chemistry sector and adds supercomputing capabilities to the its range of software solutions for integrated molecular design. "This acquisition will complement Oxford Molecular Group's portfolio of integrated molecular design products, from gene sequencing to preclinical drug development, and continues our aggressive strategy to provide our customers with a comprehensive line of software and services to meet the needs of the multimillion-dollar drug design market," said Dr. Marchington. "We are committed to support and optimize the software for a wide range of computers, including the Cray supercomputers. Cray said the deal confirms its strategy of working primarily through independent software vendors for applications on its supercomputers. Cray officials supported the acquisition of the Unichem technology, recognizing the strong fit for the software within Oxford Molecular's future business and product development strategy. "We are happy to see our innovative UniChem technology go into the hands of a premier-quality firm like Oxford Molecular," said Mike Booth, vice president of Cray's Applications and Software Divisions. "We saw a great deal of interest from software vendors in this technology. Oxford Molecular will continue UniChem's success and broaden its use in the marketplace." UniChem is a well-established computational chemistry software package used by industry and research organizations, such as DuPont, Exxon Research & Engineering, and Phillips Petroleum, to speed the development of pharmaceuticals, materials and other chemicals. UniChem complements existing quantum mechanics solutions available from Oxford Molecular Group, giving customers greater choice in this sector. Following its realigned applications strategy last year, Cray will focus future development efforts on building unique capabilities and applications technology for its supercomputers, but discontinue its business of maintaining software like UniChem. "We have always worked closely with ISVs for mainstream applications optimized on our supercomputers," said Booth. "However, our high performance computing leadership and partnership approach with high-end industrial customers often places us in a position to develop unique applications technologies for problems that don't have solutions today. This was the case with UniChem." Cray Research, Inc., a subsidiary of Silicon Graphics, Inc., provides the leading supercomputing tools and services to help solve customers' most challenging problems. Oxford Molecular Group develops and markets solutions for integrated molecular design to companies and universities engaged in chemical, pharmaceutical and biotechnology research. In addition to a wide range of computer-aided molecular design software (CAMD), the company offers advanced bioinformatics tools as well as contract research for pharmaceutical drug discovery and design. Headquartered in Oxford, England, the company conducts U.S. operations in Campbell, Calif.; Beaverton, Ore.; Rochester, N.Y.; and Baltimore, M.D.; and European operations from Oxford; Erlangen (Germany); and Paris. Oxford Molecular Group is the largest supplier of CAMD software in Japan through its distributor Sony/Tektronix. CV.ff-5/23/96 *********************************************************************** Jill Koering-Romero Oxford Molecular Group Marketing Communications Coordinator 2105 S. Bascom Ave. jkromero@ig.com Suite 200 Tel: 408-879-6363 Campbell, CA 95008 Fax: 408-879-6302 http://www.oxmol.com/ *********************************************************************** From owner-chemistry@ccl.net Wed May 29 13:50:26 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id NAA04276; Wed, 29 May 1996 13:37:33 -0400 (EDT) Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by bedrock.ccl.net (8.7.5/950822.1) id NAA02560; Wed, 29 May 1996 13:37:32 -0400 (EDT) Received: by rani.chem.yale.edu; Wed, 29 May 96 13:37:32 -0400 From: Dongchul Lim Message-Id: <9605291737.AA19347@rani.chem.yale.edu> Subject: looking for implementations of ring finding algorithm To: chemistry@ccl.net (Computational Chemistry) Date: Wed, 29 May 96 13:37:31 EDT X-Mailer: ELM [version 2.3 PL11] It seems that there are at least two kinds of ring sets in the perception of rings in a chemical structure, i.e., the smallest set of smallest rings (SSSR) and the essential set of essential rings (ESER). References can be found in the following literature: Zamora, A., J. Chem. Inf. Comput. Sci. 1976, 16, 40. Fujita, S., J. Chem. Inf. Comput. Sci. 1988, 28, 78. Qian, C.; Fisanick, W.; Hartzler, D. E.; Chapman, S. W., J. Chem. Inf. Comput. Sci. 1990, 30, 105. I wonder if anyone has implementations of these algorithms. Thanks. D.Lim, lim@rani.chem.yale.edu From tgm@SSD.intel.com Wed May 29 16:50:29 1996 Received: from SSD.intel.com for tgm@SSD.intel.com by www.ccl.net (8.7.5/950822.1) id PAA05421; Wed, 29 May 1996 15:59:10 -0400 (EDT) Received: from idaho.SSD.intel.com by SSD.intel.com (4.1/SMI-4.1) id AA18391; Wed, 29 May 96 12:58:14 PDT Received: by idaho.SSD.intel.com (4.1/SMI-4.1) id AA01410; Wed, 29 May 96 12:58:09 PDT Date: Wed, 29 May 96 12:58:09 PDT From: "Timothy G. Mattson" Message-Id: <9605291958.AA01410@idaho.SSD.intel.com> To: CHEMISTRY@www.ccl.net Subject: Symposium CFP - Cluster and MPP computing Computational Chemistry on MPP's, workstation clusters, and other novel computer systems. Spring, 1997 ACS meeting San Fransisco, California Organized by: Timothy G. Mattson, Intel Corporation tgm@ssd.intel.com 503-677-5627 Theresa L. Windus, Northwestern University windus@chem.nwu.edu 847-491-3423 The goal of this symposium is to review the practice of computational chemistry on parallel, distributed and other novel computer systems. We are seeking two kinds of papers: 1. Papers about the algorithms and computer science required to take advantage of these computer systems. 2. Papers about the computational chemistry that is possible because of these novel computer systems. We are planning to publish a proceedings for this symposium - most likely as a volume in the ACS Symposium Series. Abstracts are due by October 25. To help with our planning, however, we need to know by early August if you are planning to submit an abstract. Contact either of the organizers if you are interested in submitting a paper. From cmartin@rainbow.uchicago.edu Wed May 29 18:50:30 1996 Received: from rainbow.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.7.5/950822.1) id SAA05847; Wed, 29 May 1996 18:00:08 -0400 (EDT) Received: (from cmartin@localhost) by rainbow.uchicago.edu (8.7.3/8.7.3) id QAA26075 for CHEMISTRY@www.ccl.net; Wed, 29 May 1996 16:59:15 -0500 (CDT) From: Charles Martin Message-Id: <199605292159.QAA26075@rainbow.uchicago.edu> Subject: Columbus in SGI R8K IRIX 6.01 or better To: CHEMISTRY@www.ccl.net Date: Wed, 29 May 1996 16:59:15 -0500 (CDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Since we are on the topic of porting ab initio programs to the SGI platform, does anyone have a version of the columbus package, including SIFS libraries, ported to the SGI R8K under IRIX 6.01 or better? It will compile with the -mips2 flag, but we would like to link the SIFS libraries to some of older in-house programs which do not compile with -mips2 but compile fine under standard f77 -O. Also, we have had some runtime problems with columbus on the SGI (it just sort-a hangs) [The other package we interface with is HONDO, so if someone has that IRIX 6 HONDO port, we would like to hear about that too] Best Regards Chuck Martin Syracuse University cmartin@rainbow.uchicago.edu From bernhold@npac.syr.edu Wed May 29 19:50:30 1996 Received: from postoffice.npac.syr.edu for bernhold@npac.syr.edu by www.ccl.net (8.7.5/950822.1) id TAA06241; Wed, 29 May 1996 19:14:20 -0400 (EDT) Received: from nova.npac.syr.edu (bernhold@nova.npac.syr.edu [128.230.7.2]) by postoffice.npac.syr.edu (8.7.5/8.7.1) with ESMTP id TAA06403; Wed, 29 May 1996 19:14:20 -0400 (EDT) Received: from localhost (bernhold@localhost) by nova.npac.syr.edu (8.7.5/8.7.1) with SMTP id TAA04162; Wed, 29 May 1996 19:14:19 -0400 (EDT) Message-Id: <199605292314.TAA04162@nova.npac.syr.edu> X-Authentication-Warning: nova.npac.syr.edu: bernhold owned process doing -bs X-Authentication-Warning: nova.npac.syr.edu: Host bernhold@localhost didn't use HELO protocol To: "Timothy G. Mattson" cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Symposium CFP - Cluster and MPP computing In-reply-to: Message from "Timothy G. Mattson" of "Wed, 29 May 1996 12:58:09 PDT." <9605291958.AA01410@idaho.SSD.intel.com> Date: Wed, 29 May 1996 19:14:13 -0400 From: "David E. Bernholdt" Hi Tim, I definitely plan to submit something, though I hate these long lead times. (I know they're not your fault.) Best, David -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu From balducci@phr.utexas.edu Wed May 29 20:50:32 1996 Received: from serine.phr.utexas.edu for balducci@phr.utexas.edu by www.ccl.net (8.7.5/950822.1) id QAA05460; Wed, 29 May 1996 16:14:51 -0400 (EDT) Received: by serine.phr.utexas.edu (950911.SGI.8.6.12.PATCH825/940406.SGI.AUTO) id PAA09794; Wed, 29 May 1996 15:01:20 -0500 From: "Renzo Balducci" Message-Id: <9605291501.ZM9792@serine.phr.utexas.edu> Date: Wed, 29 May 1996 15:01:13 -0500 In-Reply-To: Dongchul Lim "CCL:looking for implementations of ring finding algorithm" (May 29, 1:37pm) References: <9605291737.AA19347@rani.chem.yale.edu> X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: CHEMISTRY@www.ccl.net, Dongchul Lim Subject: Re: looking for implementations of ring finding algorithm Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On May 29, 1:37pm, Dongchul Lim wrote: > It seems that there are at least two kinds of ring sets > in the perception of rings in a chemical structure, > i.e., the smallest set of smallest rings (SSSR) and > the essential set of essential rings (ESER). > References can be found in the following literature: > > Zamora, A., J. Chem. Inf. Comput. Sci. 1976, 16, 40. > Fujita, S., J. Chem. Inf. Comput. Sci. 1988, 28, 78. > Qian, C.; Fisanick, W.; Hartzler, D. E.; Chapman, S. W., > J. Chem. Inf. Comput. Sci. 1990, 30, 105. > > I wonder if anyone has implementations of these algorithms. >-- End of excerpt from Dongchul Lim We have published in a recent paper our rigourous yet efficient algorithms for (i) the perception of a minimal basis set of the "ring space" (commonly referred to as SSSR) as well as (ii) the 'intelligent' perception of a canonically unique SSSR based upon a customizable set of chemically significant criteria. We are currently unable to provide any source code although the algorithms are described in an Object-Oriented fashion which should lead to rather straightforward implementations in C++. Here is the reference: R.Balducci and R.S.Pearlman "Efficient Exact Solution of the Ring Perception Problem" J.Chem.Inf.Comput.Sci. 1994, 34, 822-831 ---Renzo -- ------------------------------------------------------------------------ Renzo Balducci balducci@naphthyl.phr.utexas.edu Research Associate & System Manager balducci@vax.phr.utexas.edu College of Pharmacy Voice: (512) 471-8509 Univ. of Texas --- Austin, TX 78712 FAX: (512) 471-7474 ------------------------------------------------------------------------ "God made the integers; all else is the work of man" - Leopold Kronecker