From cmral@cluster6.urz.uni-halle.de Wed May 28 03:45:15 1997 Received: from mlucom3.urz.uni-halle.de for cmral@cluster6.urz.uni-halle.de by www.ccl.net (8.8.3/950822.1) id DAA16331; Wed, 28 May 1997 03:11:23 -0400 (EDT) From: Received: from cluster6.urz.uni-halle.de by mlucom3.urz.uni-halle.de with Local SMTP (PP); Wed, 28 May 1997 09:11:09 +0200 Received: by cluster6.urz.uni-halle.de (AIX 4.1/UCB 5.64/4.03) id AA21698; Wed, 28 May 1997 09:11:06 +0200 Message-Id: <9705280711.AA21698@cluster6.urz.uni-halle.de> Subject: CCL:Looking for efficient post-HF calculation To: CHEMISTRY@www.ccl.net Date: Wed, 28 May 1997 09:11:05 +0200 (MESZ) Cc: cmral@cluster6.urz.uni-halle.de (seifert) X-Mailer: ELM [version 2.4 PL25] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit Dear colleagues, in order to examine the reliability of the DFT-treatment, I've been looking for the most efficient way of performing some single point energy calculations on our catalyst models with highly sophisticated single reference post-HF methods, such as CCSD[T], CPF or MCPF. A system under investigation is f.i. cationic NiC9H15 (C1-symmetry), consisting of 86 electrons within 246 basis functions, . Which commercial program system should best be suitable of doing this large job regarding efficient consumption of cpu-time and storage space and possible restart facilities ? Any suggestions are highly appreciated. -- Elvira From Eugene.Leitl@lrz.uni-muenchen.de Wed May 28 06:45:18 1997 Received: from sunsrv5.lrz-muenchen.de for Eugene.Leitl@lrz.uni-muenchen.de by www.ccl.net (8.8.3/950822.1) id FAA17370; Wed, 28 May 1997 05:52:04 -0400 (EDT) Received: from sun6.lrz-muenchen.de by sunsrv5.lrz-muenchen.de; Wed, 28 May 97 11:52:05 +0200 Received: by sun6.lrz-muenchen.de (5.x/SMI-SVR4) id AA29668; Wed, 28 May 1997 11:52:05 +0200 Date: Wed, 28 May 1997 11:52:05 +0200 (MET DST) From: Eugene Leitl X-Sender: ui22204@sun6 To: chemistry Subject: FYI:who's afraid of the Beowulf? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I think below information might be interesting for those CCLers currently pondering which hardware to purchase... I still think a cluster of SuperDSPs (Analog Devices SHARC, TI's new C6x family) offers significantly more bang for the money (about 60 parallel GFLOPS for a 64-node 15 k$ cluster, or 70 Tera OPS/15 k$ (sic) in case of TI's chip). Regards, Eugene Leitl > On Sat, 24 May 1997, r q watt wrote: > homebrew Linux maspar supercomputers... or something that might > evolve into that... > > http://loki-www.lanl.gov/ > http://cesdis.gsfc.nasa.gov/linux-web/beowulf/beowulf.html > > and some fun software packages to run on them > > http://www.ai.uga.edu/students/jae/ai.html > http://sal.kachinatech.com/ # try searching for molecular nanotech > http://world.std.com/~wware/ncad.html > > [ Will Ware's statement ] From dew01@xray5.chem.louisville.edu Wed May 28 11:45:18 1997 Received: from xray5.chem.louisville.edu for dew01@xray5.chem.louisville.edu by www.ccl.net (8.8.3/950822.1) id LAA19643; Wed, 28 May 1997 11:19:28 -0400 (EDT) Received: (from dew01@localhost) by xray5.chem.louisville.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id LAA15697 for CHEMISTRY@www.ccl.net; Wed, 28 May 1997 11:23:00 -0400 Date: Wed, 28 May 1997 11:23:00 -0400 From: dew01@xray5.chem.louisville.edu (Donald E. Williams) Message-Id: <199705281523.LAA15697@xray5.chem.louisville.edu> Apparently-To: CHEMISTRY@www.ccl.net NEW INTERMOLECULAR FORCE FIELD DEVELOPMENT SOFTWARE AVAILABLE Program nbp (for nonbonded potentials) is a software tool which derives an optimized intermolecular force field from molecular crystal and/or molecular cluster data. Customized force fields can be developed and optimized from any training set of data. Nonbonded potential functions can be of either the (exp-6-1) or (n-6-1) type, including the possibility of non-atomic sites. A given element may be subdivided into several potential types. Input to the program is a set of any number of structures encoded in the mpa/mpg (molecular packing analysis/molecular packing graphics) format. The force field can also be scaled to one or more energies such as heats of sublimation or heats of association. For further information contact: Dr. Donald E. Williams Department of Chemistry University of Louisville Louisville, KY 40292 USA email: dew01@xray5.chem.louisville.edu From andy@neptune.chem.uga.edu Wed May 28 12:48:21 1997 Received: from neptune.chem.uga.edu for andy@neptune.chem.uga.edu by www.ccl.net (8.8.3/950822.1) id MAA20085; Wed, 28 May 1997 12:11:20 -0400 (EDT) Received: (from andy@localhost) by neptune.chem.uga.edu (8.7.4/8.7.3) id MAA22656 for chemistry@www.ccl.net; Wed, 28 May 1997 12:11:29 -0400 Date: Wed, 28 May 1997 12:11:06 -0400 (EDT) From: Andy Dustman Sender: andy@neptune.chem.uga.edu Reply-To: Andy Dustman To: Computational Chemistry List Subject: G: The unoffical GAUSSIAN mailling list Message-ID: -----BEGIN PGP SIGNED MESSAGE----- There seemed to be a lot of sentiment towards having a mailing list for GAUSSIAN questions and problems, so I made one, and it's called G. To subscribe, send the subject "subscribe" to g-request@CCMSD.chem.uga.edu. If you want the digested version, send the subject "subscribe" to g-d-request@CCMSD.chem.uga.edu. To post messages to the list, send them to g@CCMSD.chem.uga.edu. I have no official connection to GAUSSIAN, Inc., and I am more likely to ask questions than to answer them. Remember, this list is for GAUSSIAN-related topics ONLY. Other more general computational chemistry questions should go to CCL. NO CROSSPOSTING, PLEASE. Report any errors to me. Everything should be working properly, but you never know. Andy Dustman / Computational Center for Molecular Structure and Design / UGA To get my PGP public key, send me mail with subject "send file key". For the ultimate anti-spam procmail recipe, send me mail with subject "spam" "Encryption is too important to leave to the government." -- Bruce Schneier http://www.ilinks.net/~dustman mailto:andy@CCMSD.chem.uga.edu <}+++< -----BEGIN PGP SIGNATURE----- Version: 2.6.3ia Charset: noconv iQEPAwUBM4xZLBOPBZTHLz8dAQFMegfPXuBxdM/A6cZXfdDzubJmjKBTcHVtan7G 4JEbecjOI1M+m3AnYMn3HLDoYUPGXzeUs+wdYp5z2GwYozUW4Db/ZSessYr71IW2 d+WIgSMsbxx2doe8EGfCV5q6gQ41SsA9PDlnd6OYpiz9hXvasGmdh72qUYUIiLCL frTCJxS/DIdZuwCpMxY3V2N8JHeCY3hArJzNvuT8gDPi1Am8dJVT1scOQvQg3S2M p7WAiSyxsy9K1mfwh4YpLGyq0qmxfchmVZT9ce6xRC69qJJC05efKDfVrrhoHI0U nWFPTGXI4gW/ZSD2LKiZE3X3ME14NlKMrlYBf6L0eK89CQ== =Kup+ -----END PGP SIGNATURE----- From gford@post.smu.edu Wed May 28 13:50:35 1997 Received: from post.cis.smu.edu for gford@post.smu.edu by www.ccl.net (8.8.3/950822.1) id NAA20424; Wed, 28 May 1997 13:08:29 -0400 (EDT) Received: by post.cis.smu.edu (/\==/\ Smail3.1.28.1 #28.3) id ; Wed, 28 May 97 12:08 CDT Message-Id: Date: Wed, 28 May 97 12:08 CDT From: "George P. Ford" Reply-To: "George P. Ford" To: CHEMISTRY@www.ccl.net Subject: CCL:2 unrelated questions Dr. S. Shapiro writes: > > > Dear Colleagues; > > I have two quite unrelated questions for which perhaps some CCLers > might be able to provide useful replies: > > Question 1: In order to obtain Mulliken partial atomic charges for some > work in which we are engaged, I prepared a Z-matrix for the molecule > p-tolylacetylene ("tolac.mop"), as follows: > > > am1 nointer > p-tolylacetylene > > C 0.000000 0 0.000000 0 0.000000 0 0 0 0 > C 1.401729 0 0.000000 0 0.000000 0 1 0 0 > C 1.399999 0 120.081459 0 0.000000 0 2 1 0 > C 1.399809 0 120.056900 0 0.000000 0 3 2 1 > C 1.399806 0 119.942001 0 0.000000 0 4 3 2 > C 1.400006 0 120.056679 0 0.000000 0 5 4 3 > C 1.312333 0 120.109207 0 180.000000 0 1 2 3 > C 1.200200 0 179.891647 0 180.000000 0 7 1 2 > H 1.103619 0 119.699532 0 180.000000 0 2 3 1 > H 1.103127 0 119.972672 0 180.000000 0 3 2 1 > H 1.103111 0 120.028992 0 180.000000 0 4 3 2 > H 1.103127 0 119.970596 0 180.000000 0 5 4 3 > H 1.103619 0 119.699341 0 180.000000 0 6 5 4 > H 1.059943 0 180.000000 0 180.000000 0 8 7 1 > > The problem is that the dihedral angle for the acetylenic hydrogen is ill-defined because the defining atoms (8, 7, 1) are linear. The standard solutionis to add a dummy atom. For example, you could replace the last line of your Z-matrix by: XX 1.0 0 90.0 0 0.0 0 8 7 6 H 1.059943 0 90.000000 0 180.000000 0 8 9 7 This adds a dummy (XX) which redefines H14 in terms of three non-linear atoms: X9 C6-C5 | / \ H14-C8-C7-C1 C4 \ / C2-C3 An alternative approach would be to use a Cartesian definition (include the keyword XYZ). This of course depends on your either having a compelete set of xyz coords available or being willing to figure out the missing set (for H14) and add them manually. > > > Question 2: I would like to know if there is some established quantitative > measure of the "degree" of chirality. For example, consider the chiral > molecules CR1R2R3R4, where in one case R1 = H, R2 = D, R3 = T, and R4 = F, > whereas in another case R1 = H, R2 = naphthyl, R3 = n-octyl, and R4 = NO2. > Whilst both molecules are chiral, it is clear that the structural variation > when R1 = H, R2 = naphthyl, R3 = n-octyl, and R4 = NO2 makes this a "more" > chiral molecule than when R1 = H, R2 = D, R3 = T, and R4 = F. But how to > express in a quantitative fashion that the second chiral molecule is "more" > chiral than the first? I thought that perhaps the RMS deviation between the > two enantiomorphs of each of these chiral molecules might provide > quantification of chirality. Does anyone have any further, possibly better, > suggestions? > By definition a molecule is either chiral or it isn't. Admittedly, the physical manifestation of chirality when the chirality is due only to isotopic substitution (the rotation of plane polarized light), is tiny. But this is a special situation. Such generalizations are rare for chemical substitutions. I think that to define "degree of chirality" in the way you suggest is just to define a degree of molecular similarity. In that sense it's not fundamentally different from comparing the similarity of any two molecules. Without knowing more about your ultimate goals its hard to be specific. However, I would incline towards some definition that was itself inherently chiral. Indices obtained in this way would then have a diasteriomeric character which might have a better chance of paralleling the chemical consequences of what you are refering to as "degree of chirality". Perhaps you could design some kind of real or artificial chiral "probe group" for investigating the surface of one of the enantiomers, or perhaps some kind of chiral envelope or cavity onto which to fit it. A different approach, for molecules with chiral centers, might be to try to quantify the R/S definition. Instead of using the sequence rules perhaps you could use some kind of electronic and/or size criterion. Again, this rather depends on your ultimate purpose. Hope some of this is useful. George P. Ford ============================================================================ George P. Ford | email: gford@smu.edu Department of Chemistry | telephone: (214)768-2479 Southern Methodist University | fax: (214)768-4089 Dallas, Texas 75275 | http://www.smu.edu/~gford/ ============================================================================ From cccc@qc.chem.ualberta.ca Wed May 28 19:45:21 1997 Received: from quartz.ucs.ualberta.ca for cccc@qc.chem.ualberta.ca by www.ccl.net (8.8.3/950822.1) id SAA22469; Wed, 28 May 1997 18:54:20 -0400 (EDT) Received: from qc.chem.ualberta.ca (qc.chem.ualberta.ca [129.128.2.12]) by quartz.ucs.ualberta.ca (8.8.5/8.8.5) with ESMTP id QAA32160 for ; Wed, 28 May 1997 16:54:21 -0600 Received: (from cccc@localhost) by qc.chem.ualberta.ca (8.6.12/8.6.10) id QAA14253; Wed, 28 May 1997 16:50:37 -0600 Date: Wed, 28 May 1997 16:50:37 -0600 From: 3rd Canadian Computational Chemistry Conference Message-Id: <199705282250.QAA14253@qc.chem.ualberta.ca> To: CHEMISTRY@www.ccl.net Subject: 3rd Canadian Computational Chemistry Conference (3rd Announcement) Cc: mariusz@qc.chem.ualberta.ca X-Sun-Charset: US-ASCII 3rd Canadian Computational Chemistry Conference 1997 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Third Announcement Updated information about the 3rd Canadian Computational Chemistry Conference (July 19 - 23 in Edmonton, Alberta) is available from the web site of the conference: http://www.chem.ualberta.ca/~cccc Invited Lecturers ================= Christopher Bayly, Merck Frosst, Canada Axel D. Becke, Queen's University, Canada Russell J. Boyd, Dalhousie University, Canada David A. Case, Scripps Research Institute, U.S.A. Anne M. Chaka, The Lubrizol Corporation, U.S.A. Delano P. Chong, University of British Columbia, Canada Thomas R. Cundari, The University of Memphis, U.S.A. Ernest R. Davidson, Indiana University, U.S.A. Michel Dupuis, Pacific Northwest National Laboratory, U.S.A. David F. Feller, Pacific Northwest National Laboratory, U.S.A. Martin Head-Gordon, University of California (Berkeley), U.S.A. Kimihiko Hirao, University of Tokyo, Japan Ray Kapral, University of Toronto, Canada Jacek Karwowski, N. Copernicus University, Poland Peter Margl, University of Calgary, Canada Gren N. Patey, University of British Columbia, Canada Andrzej J. Sadlej, University of Lund, Sweden Dennis Salahub, Universite de Montreal, Canada H.F. Schaefer III, University of Georgia, U.S.A. Peter Taylor, San Diego Supercomputer Center, U.S.A. Thanh N. Truong, University of Utah, U.S.A. John S. Tse, Steacie Institute for Molecular Science, Canada Donald F. Weaver, Queen's University, Canada Michael Anthony Whitehead, McGill University, Canada Michael C. Zerner, University of Florida, U.S.A. Deadlines ========= 1. Conference Registration (regular conference fee) June 30, 1997 2. Submission of Abstracts June 30, 1997 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! ! ! The final title and abstract must be received by the organizers in Edmonton ! ! before June 30 in order to be included in the Conference Program. ! ! ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Conference Fees =============== Regular Participants $220 Graduate Students $170 Conference fee covers the costs of the Opening Social, seven refreshment breaks, munchies and beverage tickets during Poster Sessions, as well as the costs of running the Conference (rental of the Timms Centre, printing of Conference materials, etc). Please note that the Conference fee includes 7% GST. All costs are in Canadian dollars. Please make your cheques or money orders payable to: 3rd CCCC and mail them to 3rd Canadian Computational Chemistry Conference c/o Dr. M. Klobukowski Department of Chemistry University of Alberta Edmonton, AB, Canada T6G 2G2 Accommodations ============== All hotel reservations must be done by participants. There are several hotels with easy access to the Conference site: (A) Lister Hall Cost is $26.88 per day for single room, $35.84 for twin room (all taxes included). Contact: The University of Alberta Guest Services 44 Lister Hall Edmonton, AB T6G 2H6 Phone: 403-492-4281 Fax: 403-492-7032 (B) Campus Tower Suite Hotel Cost is $65 per day (plus tax). The number of suites is limited. Contact: Campus Tower Suite Hotel 11145 - 87 Avenue Edmonton, AB T6G 0Y1 Phone: 403-439-6060 Fax: 403-433-4410 Registration ============ You may register by WWW at the web site http://www.chem.ualberta.ca/~cccc. Alternatively, you may send us (or fax) the text version of the Registration Form, available from the Web site of the Conference (http://www.chem.ualberta.ca/~cccc). Correspondence regarding the Conference should be sent to: 3rd Canadian Computational Chemistry Conference c/o Dr. M. Klobukowski Department of Chemistry University of Alberta Edmonton, AB, Canada T6G 2G2 FAX: 403-492-8231 You may also reach us at cccc@qc.chem.ualberta.ca or EDGECOMK@QUCDN.QUEENSU.CA We are looking forward to seeing you at the 3rd CCCC. For the Organizing Committee of the 3rd CCCC, Mariusz Klobukowski and Ken Edgecombe