From owner-chemistry@ccl.net Thu Jun 29 02:37:53 1995 Received: from schroeder.newcastle.edu.au for tony@schroeder.newcastle.edu.au by www.ccl.net (8.6.10/930601.1506) id CAA26319; Thu, 29 Jun 1995 02:37:29 -0400 Received: by schroeder.newcastle.edu.au (AIX 3.2/UCB 5.64/4.03) id AA16364; Thu, 29 Jun 1995 16:35:29 GMT Date: Thu, 29 Jun 1995 16:35:28 +0000 (CUT) From: Tony Dyson To: Computational Chemistry List Subject: CCL: Browse Quantum Chemistry Database System Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII This database system is referred to in the Gaussian manual, but I have not been able to find just what it is, or where it can be obtained from. Does anybody care to comment on the usefulness of this software? I will write to help@gaussian.com and ask where to get hold of it if nobody on the list knows. Tony ================================================================ Mr. Anthony J. Dyson tony@schroeder.newcastle.edu.au Dept. of Physics phone: +49 21 5425 University of Newcastle fax: +49 21 6907 Callaghan, Australia, 2308 ================================================================ From owner-chemistry@ccl.net Thu Jun 29 03:22:48 1995 Received: from owl.und.ac.za for TSHEHLA@che.und.ac.za by www.ccl.net (8.6.10/930601.1506) id DAA26744; Thu, 29 Jun 1995 03:12:42 -0400 Received: from Charon1.CC.und.ac.za by owl.und.ac.za with SMTP (PP) id <27944-1@owl.und.ac.za>; Thu, 29 Jun 1995 09:12:10 +0200 Received: From STUD-AFF/WORKQUEUE by charon1.cc.und.ac.za via Charon-4.0A-VROOM with IPX id 100.950629091012.992; 29 Jun 95 09:12:07 -0200 Message-ID: From: Tankiso Tshehla - PG Organization: University of Natal - Durban To: chemistry@ccl.net Date: Thu, 29 Jun 1995 09:09:56 +0200 (SAST) Subject: generating force constants from wavenumbers ...code Priority: normal X-mailer: Pegasus Mail v3.22 Hi; I have some g92 frequency output with no force fields. I would like to know if anybody out there has or knows of a code (prefferably fortran) which can generate the force constants/fields from such an output. I will summarise the reponses to the list if there is interest. T M Tshehla University of Natal Durban. From owner-chemistry@ccl.net Thu Jun 29 03:39:44 1995 Received: from owl.und.ac.za for TSHEHLA@che.und.ac.za by www.ccl.net (8.6.10/930601.1506) id DAA26934; Thu, 29 Jun 1995 03:30:45 -0400 Received: from Charon1.CC.und.ac.za by owl.und.ac.za with SMTP (PP) id <28298-0@owl.und.ac.za>; Thu, 29 Jun 1995 09:30:21 +0200 Received: From STUD-AFF/WORKQUEUE by charon1.cc.und.ac.za via Charon-4.0A-VROOM with IPX id 100.950629091913.2080; 29 Jun 95 09:30:17 -0200 Message-ID: From: Tankiso Tshehla - PG Organization: University of Natal - Durban To: chemistry@ccl.net Date: Thu, 29 Jun 1995 09:18:55 +0200 (SAST) Subject: wrong sign of the BSSE component... Priority: normal X-mailer: Pegasus Mail v3.22 Hi netters; I have some interesting findings here. I was trying to apply Basis set superposition error corrections to the interaction energies of some of the systems I have been studying using mp2/6- 31g**. What is interesting is that the BSSE value has a negative sign which blows the value of delta E corrected way beyond the simple van der Waal complex (indeed it is beyond the strongest chemical bonding systems). The complex is a fairly weak one from the geometry distortions. I would not have expected the interaction energy to be anything over 200 kJ/mol. I thus assummed that the results I got are inconlusive. The question I would to pose is this? What are the implications of a negative BSSE? Comments to be summarised T M Tshehla From owner-chemistry@ccl.net Thu Jun 29 04:52:49 1995 Received: from VMS.HUJI.AC.IL for SIEW@vms.huji.ac.il by www.ccl.net (8.6.10/930601.1506) id EAA27402; Thu, 29 Jun 1995 04:40:17 -0400 Received: by HUJIVMS (HUyMail-V7b); Thu, 29 Jun 95 11:40:04 +0200 Received: by HUJIVMS (HUyMail-V7b); Thu, 29 Jun 95 11:37:26 +0200 Date: Thu, 29 Jun 95 11:37 +0200 Message-id: <29060095113722@HUJIVMS> From: To: chemistry@ccl.net MIME-version: 1.0 Content-type: Text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Bacteriorhodopsin Dear CCLers, I looked at the bacteriorhodopsin files (for example, pdb1bad.ent). It is not clear to me to what extent is the structure theoretical, and to what extent it is based on the experimental data. If the coordinates are based on experiment, why is the model reffered to as theoretical? Another question concerns the bacteriorhodopsin sequence. I couldn't find the pdb sequence in swiss-prot: the sequences there are different than the ones in pdb. Am I mistaken, or is there an explanation to this? I would be very grateful to any information you can provide me. Naomi Siew siew@vms.huji.ac.il From owner-chemistry@ccl.net Thu Jun 29 07:22:53 1995 Received: from fpsp.fapesp.br for BOSCO%VAXDQF@itep.itep.br by www.ccl.net (8.6.10/930601.1506) id HAA28409; Thu, 29 Jun 1995 07:14:00 -0400 From: Received: from itep.itep.br by fpsp.fapesp.br with PMDF#10108; Thu, 29 Jun 1995 08:05 BSC (-0300 C) Received: from DECNET-MAIL (BOSCO@VAXDQF) by itep.itep.br (PMDF V4.2-11 #3257) id <01HS9RVGEZK0000795@itep.itep.br>; Thu, 29 Jun 1995 08:10:05 -0300 Date: Thu, 29 Jun 1995 08:10:05 -0300 Subject: how to become a new member? To: chemistry@ccl.net Message-id: <01HS9RVGVV6Q000795@itep.itep.br> X-Envelope-to: chemistry@ccl.net X-VMS-To: ITEP::IN%"chemistry@ccl.net" X-VMS-Cc: BOSCO MIME-version: 1.0 Content-transfer-encoding: 7BIT Hi I would like to become a new member of the COMPCHEM list. How can I get it? Please send the mansages with the necessary e-mail to: BOSCO@VAXDQF.UFPE.BR Thanks in advance. Bosco From owner-chemistry@ccl.net Thu Jun 29 08:00:42 1995 Received: from serieu.cpd.ufjf.br for dantas@ibitipoca.fisica.ufjf.br by www.ccl.net (8.6.10/930601.1506) id HAA28765; Thu, 29 Jun 1995 07:50:32 -0400 Received: from ibitipoca (ibitipoca.fisica.ufjf.br) by serieu.cpd.ufjf.br (4.1/SMI-4.1) id AA06284; Thu, 29 Jun 95 13:56:21 GMT Received: by ibitipoca (Linux Smail3.1.28.1 #1) id m0sRJ7t-0003k2C; Thu, 29 Jun 95 09:55 EST Message-Id: Date: Thu, 29 Jun 95 09:55 EST From: dantas@ibitipoca.fisica.ufjf.br (Socrates de Oliveira Dantas) To: chemistry@ccl.net Subject: manual of DENSITY... Cc: -v@ibitipoca.fisica.ufjf.br Dear Colleagues, We are interested in a manual of DENSITY program, from J.J. Stewart. Can anyone help us? Please send mail to dantas@fisica.ufjf.br . Thank you in advance. (Dr.) Socrates de Oliveira Dantas Departamento de Fisica Instituto de Ciencias Exatas Universidade Federal de Juiz de Fora CEP: 36036-330 - Juiz de Fora - Minas Gerais - Brasil Phone: (055032) 229-3307/229-3313 Fax: (055032) 229-3312 E-mail: dantas@fisica.ufjf.br From owner-chemistry@ccl.net Thu Jun 29 09:22:52 1995 Received: from kvant2.klb.dtu.dk for hasch@kvant2.klb.dtu.dk by www.ccl.net (8.6.10/930601.1506) id JAA00103; Thu, 29 Jun 1995 09:09:06 -0400 Received: (from hasch@localhost) by kvant2.klb.dtu.dk (8.6.11/8.6.9) id PAA01017; Thu, 29 Jun 1995 15:35:07 +0200 Date: Thu, 29 Jun 1995 15:35:07 +0200 From: Hartmut Schmider Message-Id: <199506291335.PAA01017@kvant2.klb.dtu.dk> To: BOSCO%VAXDQF@itep.itep.br CC: chemistry@ccl.net Subject: Re: CCL:how to become a new member? Hi, to get on the computational-chemistry list, just send a request with your name, email address and affiliation to chemistry-request@ccl.net A short time later theh messages will start trickling in. Welcome to the list, Hartmut Schmider From owner-chemistry@ccl.net Thu Jun 29 10:22:58 1995 Received: from earn.cvut.cz for strajbl@silicon.karlov.mff.cuni.cz by www.ccl.net (8.6.10/930601.1506) id KAA01796; Thu, 29 Jun 1995 10:17:13 -0400 Received: from ns.karlov.mff.cuni.cz by earn.cvut.cz (IBM VM SMTP V2R1) with TCP; Thu, 29 Jun 95 16:17:15 MET Received: from silicon.karlov.mff.cuni.cz by ns.karlov.mff.cuni.cz id aa12062; 29 Jun 95 16:13 MESZ Received: by silicon.karlov.mff.cuni.cz (931110.SGI/930416.SGI) for @NS.KARLOV.MFF.CUNI.CZ:CHEMISTRY@ccl.net id AA23689; Thu, 29 Jun 95 16:15:46 -0700 From: Marek Strajbl Message-Id: <9506291615.ZM23687@silicon.karlov.mff.cuni.cz> Date: Thu, 29 Jun 1995 16:15:45 -0700 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@ccl.net Subject: g92 performance Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Dear netters, I have g92 on Indigo2 (32MB RAM). I use external HD scratch (1.6 GB). When I run any computations (typically optimalization HF/6-31g*, 180 basis functions) CPU usage for my job is only about 20-30%. CPU idles due to waiting for I/O operations. Monitoring the input/output activity to block devices reveals reading large bulks of data. Has anybody hint how to increase the performance of computations. Thanks to all who respond. Regards, Marek ------------------------------------------ Marek Strajbl Institute of Physics of Charles University, Prague, Czech Republic e-mail: From owner-chemistry@ccl.net Thu Jun 29 11:22:55 1995 Received: from vangogh.chem.uab.edu for gavin@vangogh.chem.uab.edu by www.ccl.net (8.6.10/930601.1506) id LAA03226; Thu, 29 Jun 1995 11:14:48 -0400 From: Received: by vangogh.chem.uab.edu (AIX 3.2/UCB 5.64/4.03) id AA16077; Thu, 29 Jun 1995 10:10:24 -0500 Date: Thu, 29 Jun 1995 10:10:24 -0500 Message-Id: <9506291510.AA16077@vangogh.chem.uab.edu> To: CHEMISTRY@ccl.net Subject: G94-IPCM model Dear sirs, I try to run the IPCM solvent model in G94. Below is my input line: "#MP2/6-311++g** SCRF=IPCM sp" " Z-matrix" "80.0 0.001" But it is always crash at the "One-electron integrals computed using PRISM." The SCI-PCM model also have the similar results, but I can calculate the opt and freq at the SCI-PCM model! Can anyone help me ? Thanks! Gavin Tsai From owner-chemistry@ccl.net Thu Jun 29 11:37:55 1995 Received: from WAPagcc.chemie.th-merseburg.de for qc@WAPagcc.chemie.th-merseburg.de by www.ccl.net (8.6.10/930601.1506) id LAA03595; Thu, 29 Jun 1995 11:30:50 -0400 Received: by WAPagcc.chemie.th-merseburg.de (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@ccl.net id RAA15487; Thu, 29 Jun 1995 17:26:09 +0200 From: "Guest FTP Account" Message-Id: <9506291726.ZM15485@WAPagcc.chemie.th-merseburg.de> Date: Thu, 29 Jun 1995 17:26:04 -0600 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: CCL:serious G94-problems in loadleveler environment Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear colleagues, there is a question to the whole community of G94-users. We have much trouble with the G94-relaese (Revision B1) running on an rs6000 cluster supervised by the ibm loadleveler. Within the loadleveler configuration one can specify the maximum size of the data segment that is used by the submitted job; in our configuration this value is set to 1280 MB (this should be enough for conventional programs and there is no way to increase this ). Nevertheless all trails to submit an G94 job via the loadleveler breaks down, because the size of data segments used by G94 seems to be large than the configurated value of 1280 MB ( the so-called hardlimit). Therefore the job is not able to start, it is immediately killed by the system. By starting a small gaussain job from a 'pure' unix shell (without any loadleveler environment) all is O.K., but for larger production jobs we have to use the loadleveler environment. After inspection the sources i can not found any call of system-functions like vlimit, setrlimit, brk or sbrk (in order to explicit choose the size), so i was not able to modify the source to reduce the amount of data segments needed. The same or maybe similar problems might be arise also in within other queueing systems like NQS ... . I have no idea about solving this problem, so any suggestions or hints are highly appreciated. Desperatly hoping any responds regards Sven -- From owner-chemistry@ccl.net Thu Jun 29 13:09:11 1995 Received: from theory.tc.cornell.edu for jeanne@tc.cornell.edu by www.ccl.net (8.6.10/930601.1506) id MAA06008; Thu, 29 Jun 1995 12:50:46 -0400 Received: from [128.84.181.75] (JEANNE.TC.CORNELL.EDU [128.84.181.75]) by theory.tc.cornell.edu (8.6.9/8.6.6) with SMTP id MAA76368; Thu, 29 Jun 1995 12:35:29 -0400 Date: Thu, 29 Jun 1995 12:35:29 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Priority: 2 (High) To: cnsfusers@eagle, cluster@emerald.tc.cornell.edu, jhc@TC.Cornell.EDU, jzarb@rhqum21.ibm.com, Jhose@cs.ucsd.edu, FC03@Lehigh.edu, Servin@venus.gsd.harvard.edu, Jisham@DALVM41B.vnet.ibm.com, super@siam.org, Lalor@kgnvma.vnet.ibm.com, RRH@DFWVM04.vnet.ibm.com, Farazdel@nycvmic1.vnet.ibm.com, GUDURU%TSU.BITNET@bitnet-mail-gw.cornell.edu, titseng@galluj.gallaudet.edu, ciampa@ipifidpt.difi.unipi.it, trevorp@gandalf.umcs.maine.edu, 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dvakil@as.arizona.edu, welchan@yzli.chm.clarkson.edu, mwhitman@ic.sunysb.edu, tye@ic.sunysb.edu, qfu@hamilton.edu, sfkaplan@cs.amherst.edu, ltracy@slate.mines.colorado.edu, ben@ganymede.seas.upenn.edu, aalcaraz@campus.ccm.itesm.mx, al@SCHERAGA2.CHEM.CORNELL.EDU, b4i%mace.cc.purdue.educarlosmz@vnet.ibm.com, charmm-bbs-sysop@emperor.harvard.edu, d@exnet.co.uk, Douglas.Ritchie@nrc.ca, dwoodall@ted.cs.uidaho.edu, dxm17@psu.edu, gardnerk@craft.camp.clarkson.edu, garven@indigo.eps.jhu.edu, it4j@eagle.tc.cornell.edu, jcchen@mit.edu, karin@cam.nist.gov, kedziera@RAM.suny.geneseo.edu, kenneth@erin1.ucd.ie, lo@ams.sunysb.edu, lobaugh@a.chem.upenn.edu, mhumi@TC.Cornell.EDU, mitch@umiacs.UMD.EDU, MLEWIS@muskingum.edu, raul@ciencias.mty.itesm.mx, rvramire@academ01.mty.itesm.mx, rvramire@campus.mty.itesm.mx, sds3@cornell.edu, sethna@HELIOS.LASSP.CORNELL.EDU, SMITHVH@QUCDN.QueensU.CA, tomc@eng.uiowa.edu, U0291@WVNVM.WVNET.EDU, wa6j@eagle.TC.CORNELL.EDU, kwindom@iastate.edu, wandaj@eng.clemson.edu, deb@msc.cornell.edu, negron@ukarman.upr.clu.edu, ellis@cs.hamptonu.edu, lho@ncat.edu, martin@etta.auc.edu, j_lewis@vger.nsu.edu, johnh@ecsvax.uncecs.edu, eggwzq@vaxc.hofstra.edu, lalor@TC.Cornell.EDU, pmarun@intevep.pdv.com, jovan@cpa.mae.cornell.edu, lromero@dino.conicit.ve, USDWJS@VTVM1.CC.VT.EDU, bsmith@math.ucla.edu, parallel-request@cs.felk.cvut.cz, selinger@enh.nist.gov, STOCK@YUKON.PSC.EDU, STOCK@PSC.EDU, fisher@aries.scs.uiuc.edu, philippe@pablo.physics.lsa.umich.edu, na.digest@na-net.ornl.gov, russell.chang@corp.sun.com, plessel@vislab.epa.gov, eseidel@ncsa.uiuc.edu, S-COMPUT%UGA.BITNET@interbit.cren.net, AJCUCOMP%GUVM.BITNET@interbit.cren.net, SUPER-L%MCGILL1.BITNET@interbit.cren.net, COMP-CEN%UCCVMA.BITNET@interbit.cren.net, PFUG-L%JHUVM.BITNET@interbit.cren.net, VFORT-L%JHUVM.BITNET@interbit.cren.net, SUPERIBM%UKCC.BITNET@interbit.cren.net, CNSF-L%UBVM.BITNET@interbit.cren.net, sp1@uga.cc.uga.edu, dqs-l@vm.its.rpi.edu, ll-l@uga.cc.uga.edu, sp-discussion@MCS.ANL.GOV, leslie@ccl.net, kschulte@lisboa.ks.uiuc.edu, wolynes@aries.scs.uiuc.edu, crofts@nemo.life.uiuc.edu, katzenell@c.scs.uiuc.edu, lwalsh@aries.scs.uiuc.edu, rock@uxa.cso.uiuc.edu, jake@c.scs.uiuc.edu, sligar@aries.scs.uiuc.edu, zimmerma@aries.scs.uiuc.edu, joel@mcnc.org, lewisd@mail.UTexas.edu, suh@alw.nih.gov, Raimondas.Ciegis@mii.lt, raimondas.ciegis@rasa.vtu.lt, abrito@campus.ccm.itesm.mx, alexb@architect.ccm.itesm.mx, gary.boggs@sandiegoCA.ATTGIS.COM, vgupta@cs.binghamton.edu, sun@monsoon.atms.purdue.edu, carls@vnet.ibm.com, ksams@vnet.ibm.com, ewfisher@facstaff.wisc.edu From: jeanne@TC.Cornell.EDU (Jeanne C. Butler) Subject: Cornell Theory Center Symposium CORNELL THEORY CENTER SYMPOSIUM "PROTEIN STRUCTURE AND FOLDING" OCTOBER 10 -11, 1995 700 CLARK HALL CORNELL UNIVERSITY CAMPUS SPEAKERS Ken Dill, University of California, San Francisco Jane Dyson, Scripps Research Institute Steven Ealick, Cornell University Richard Friesner, Columbia University Barry Honig, Columbia University Michael Levitt, Stanford University Montgomery Pettit, University of Houston Matthew Pincus, Veterans Administration Medical Center Eugene Shakhnovich, Harvard University David Shalloway, Cornell University John Straub, Boston University WHO WE ARE The Parallel Processing Resource for Biomedical Scientists at the Cornell Theory Center (CTC) supports research in macromolecular structure and dynamics through the advancement of scalable parallel processing technology and the improvement of computational methodologies. Core research focuses on the development of scalable, portable programs to run optimally on highly parallel computing systems; the assessment of innovative software tools; and the adaptation of these tools to parallel systems for application to problems involving large molecules. This resource, funded by the National Center for Research Resources (NCRR) at the National Institutes of Health (NIH), provides high-performance computing resources, computer science expertise, and technical and visualization support for a variety of projects. Researchers interested in requesting an allocations form can contact: Pat Colasurdo, Allocations Coordinator 607-254-8694 pat@tc.cornell.edu http://www.tc.cornell.edu/UserDoc/GenInfo/alloc.html. CTC activities are supported by major funding from the National Science Foundation and New York State, with additional funding from the Advanced Research Projects Agency, the National Center for Research Resources at the National Institutes of Health, IBM, and other members of CTC's Corporate Research Institute. General information on CTC is available at http://www.tc.cornell.edu/Highlights.html. POSTER SESSION / VIDEO THEATRE To apply for a poster session and/or video theatre presentation, please send a reasearch abstract to donna@tc.cornell.edu no later than September 15, 1995. -------------------------- REGISTRATION FORM Name: ___ Company: ___ Address: ___ Telephone: ___ Fax: ___ Email: ___ How did you hear about this sympsoium: ___ ___ I will be presenting a poster ___ I will be presenting a video -------------------------- Send to: Donna Smith Conference Coordinator Cornell Theory Center 422 Frank H. T. Rhodes Hall Ithaca, NY 14853-3801 Access via URL: http://www.tc.cornell.edu/ From owner-chemistry@ccl.net Thu Jun 29 14:53:03 1995 Received: from SSD.intel.com for tgm@SSD.intel.com by www.ccl.net (8.6.10/930601.1506) id OAA08579; Thu, 29 Jun 1995 14:39:41 -0400 Received: from idaho.SSD.intel.com by SSD.intel.com (4.1/SMI-4.1) id AA09383; Thu, 29 Jun 95 11:39:09 PDT Received: by idaho.SSD.intel.com (4.1/SMI-4.1) id AA00951; Thu, 29 Jun 95 11:39:06 PDT Date: Thu, 29 Jun 95 11:39:06 PDT From: "Timothy G. Mattson" Message-Id: <9506291839.AA00951@idaho.SSD.intel.com> To: CHEMISTRY@ccl.net Subject: Parallel Comp Chem. Book >>>> <<<< Here is a new book I thought this group would be interested <<<< in. All profits from the book go to a good cause -- the >>>> Computers in Chemistry Division of the ACS -- so we should >>>> all buy several copies. >>>> Parallel Computing in Computational Chemistry ============================================= ACS Symposium Series # 592 Edited by Timothy G. Mattson (tgm@ssd.intel.com) Order from ACS by calling: 800-ACS-5558 Cloth bound, 232 pages, Cost $69.95 This book explores the state of the art in parallel computing as applied to computational chemistry. The papers in the book range >from tutorials to discussions of the latest advanced algorithms. While the seasoned parallel programmer will gain a great deal >from this book, an introduction to parallel computing is included so novices will be able to read the book as well. Contents ======== 1. Parallel Computing, T. G. Mattson 2. Parallel Implementation of the Electronic Structure Code: GAMESS. T. Windus M.W. Schmidt, and M.S. Gordon 3. Applications of Parallel GAMESS. K.K. Baldridge, M.S. Gordon, J. H. Jensen, N. Matsunaga, M. Schmidt, T. Windus, J. A. Boatz and T. R. Cundari. 4. Object Oriented Implementation of Parallel ab initio Programs. C. L. Janssen, E.T. Seidl, and M. Colvin 5. Ab initial quantum chemistry on a workstation cluster. D. Turner, G. Trucks, and M. Frisch 6. Parallelization of a Multireference Configurations Interaction Program - the Parallel COLUMBUS Program, H. Lischka, H. Dachsel, R. Shepard, and R. J. Harrison. 7. Efficient Parallel Computation of Electron Transfer Resonance Matrix Elements between GVB wavefunctions: Algorithm Design and Chemical Results. E. P. Bierwagon, T. R. Coley, and W. A. Goddard 8. Promises and Perils of Parallel Semiempirical Quantum Methods, Kim Baldridge 9. Parallel Molecular dynamics Algorithms for Simulation of molecular Systems S. Plimpton and B. Hencrickson 10. Portable Molecular Dynamics Software for Parallel Computing, T. Mattson and G. Ravishanker 11. Advanced Algorithms for Molecular Dynamics Simulation: The program PMD. A. Windemuth 12. Parallelization of Poisson-Boltzmann and Brownian Dynamics Calculations. A. Ilin, B. Bagheri, L. R. Scott, J. M. Briggs, and J. A. McCammon. 13. Classical and Quantum Molecular Dynamics Simulation on Distributed memory Massively Parallel Computers. Z. Li, R. B. Gerber, and C.C. Martens 14. Biomolecular Structure Prediction Using the Double-Iterated Kalman Filter and Neural Networks. J. A. Lupo, S. B. Fairchild, R. Pachter, and W. Adams From owner-chemistry@ccl.net Thu Jun 29 16:53:00 1995 Received: from aardvark.ucs.uoknor.edu for SBOESCH@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.10/930601.1506) id QAA12826; Thu, 29 Jun 1995 16:46:30 -0400 From: Received: from aardvark.ucs.uoknor.edu by aardvark.ucs.uoknor.edu (PMDF V4.3-13 #7521) id <01HSA7M7AO9S00A5PB@aardvark.ucs.uoknor.edu>; Thu, 29 Jun 1995 15:47:42 -0500 (CDT) Date: Thu, 29 Jun 1995 15:47:42 -0500 (CDT) Subject: xvibs for g94 To: chemistry@ccl.net Message-id: <01HSA7M7BQUQ00A5PB@aardvark.ucs.uoknor.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT I was curious if anyone who uses gaussian 94 and xmol has a copy of an xvibs program that will extract the vibrational modes from gaussian 94 output. I will summarize any responses. Thanks. Scott E. Boesch Department of Chemistry University of Oklahoma Norman, OK 73019 From owner-chemistry@ccl.net Thu Jun 29 17:38:02 1995 Received: from Woad.CCIT.Arizona.EDU for POLLARD@CCIT.ARIZONA.EDU by www.ccl.net (8.6.10/930601.1506) id RAA13910; Thu, 29 Jun 1995 17:36:48 -0400 From: Received: from CCIT.ARIZONA.EDU by CCIT.ARIZONA.EDU (PMDF V4.3-13 #2381) id <01HSA5FKB61G8Y5IUK@CCIT.ARIZONA.EDU>; Thu, 29 Jun 1995 14:35:55 -0700 (MST) Date: Thu, 29 Jun 1995 14:35:55 -0700 (MST) Subject: Semi -empirical To: chemistry@ccl.net Message-id: <01HSA5FKB61I8Y5IUK@CCIT.ARIZONA.EDU> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT I was wondering if anyone knew of a book or review article that gave full run downs on semi-empirical methods such as AM1,PM3, MNDO-d, and all the others. I have a lot of books that give brief descriptions of the methods, but none that go into detail to what parameters are used and etc.. Thanks John Pollard From owner-chemistry@ccl.net Thu Jun 29 17:39:14 1995 Received: from coh.Coh.ORG for sherm@ccl.net by www.ccl.net (8.6.10/930601.1506) id RAA13815; Thu, 29 Jun 1995 17:31:07 -0400 Received: from iris.coh.org by coh.Coh.ORG (5.0/SMI-SVR4) id AA09323; Thu, 29 Jun 1995 14:31:01 +0800 Received: by iris.coh.org (920330.SGI/911001.SGI) for @coh.coh.org:chemistry@ccl.net id AA27886; Thu, 29 Jun 95 13:41:20 -0700 Date: Thu, 29 Jun 95 13:41:20 -0700 From: sherm@iris.Coh.ORG (Mark A. Sherman) Message-Id: <9506292041.AA27886@iris.coh.org> To: chemistry@ccl.net Subject: Molecular Modeling Facilities Reply-To: sherm@coh.Coh.ORG content-length: 1842 Dear Netters: On June 7, I posted a request asking how many universities/institutes maintain molecular modeling core facilities and how much they charge users. Here is a summary of the responses I received: Of the nine responses I received from universities, six claimed they do not charge users. The seventh respondent stated they charge $600/yr, flat rate. The eighth respondent stated they originally charged $15/hr, but later charged a flat rate (to be requested by users in their grant proposals). The ninth respondent stated that they charge $1.10 CPU-hr, $4.00/hr login time, and $0.80 Mbyte/month storage fee. Two drug companies responded. The first respondent stated that they do not charge other departments unless use becomes excessive. The second respondent stated that molecular modeling was distributed throughout many departments, with each department assuming financial responsibility for their users. One government sponsered institute responded (a Supercomputing Center). They stated that there was no charge for non-proprietary work, but that all proposals needed to first pass an internal review. No help is provided to users (you're on your own). One respondent made the following statement, which pretty well sums it up: "I can tell you from long experience that no matter how much people like having a molecular modeling facility available, the price they are willing to pay for it is effectively ZERO. By that I mean that there is little chance of recovering a reasonable fraction of expenses without raising the price high enough that people will start thinking about buying their own workstation and hoping they can wing it..." Thanks to all who responded. Mark A. Sherman, Ph.D. Director, Molecular Modeling Facility Beckman Research Institute of the City of Hope, Duarte, California 91010 sherm@coh.org From owner-chemistry@ccl.net Thu Jun 29 20:08:01 1995 Received: from anugpo.anu.edu.au for aps501@anugpo.anu.edu.au by www.ccl.net (8.6.10/930601.1506) id TAA15623; Thu, 29 Jun 1995 19:56:35 -0400 Received: from huxley.anu.edu.au (aps501@huxley.anu.edu.au [150.203.2.12]) by anugpo.anu.edu.au (8.6.12/8.6.12) with ESMTP id JAA24264; Fri, 30 Jun 1995 09:54:37 +1000 From: Anthony P Scott Received: (aps501@localhost) by huxley.anu.edu.au (8.6.12/8.6.12) id JAA20762; Fri, 30 Jun 1995 09:56:28 +1000 Date: Fri, 30 Jun 1995 09:56:28 +1000 Message-Id: <199506292356.JAA20762@huxley.anu.edu.au> To: chemistry@ccl.net, tony@schroeder.newcastle.edu.au Subject: Re: CCL:Browse Quantum Chemistry Database System Dear CCL readers, The CMU archive is a list of the results of the QM calculations performed by various researchers over a considerable period of time. We actually have an account to it based on our purchase of the browse program. This has entitled us to 4hrs of free connnect time. The browse program itself interfaces with gaussian through link9999 ( a new version of this link is supplied). You simply don't put "test" in the job line to allow the automatic archiving of the calculation. One problem with this method is that good as well as junk calculations tend to be archived with equal facility and the database gets filled with useless information or even more devious, information that is misleading. Removal of the junk info is possible, but our copy of browse does not allow this and although we have asked gaussian about it no version of browse has been made available to us that does allow the removal of useless info. One can of course be very careful with the use of the "test" directive, but in a research group that has many people many mistakes are bound to happen, with no possibility of recovery. Browse will allow the interogation of the database to obtain geometrical info, perform the l716 stuff to get vibrational frequencies etc etc. From this point of of view it is useful. In our research group however we have found that the automatic archiving of the calculation results is not particually useful, mainly for the reasons I have given above. Also we use other programs for which the results are at least as important as those derived from gaussian runs. To this end we have developed an archiving enviroment that is done initially on a personal level and at suitable times the personal archive can be made available to the research group as a whole. This enviroment allows the archiving of (at the moment) gaussian and aces2 results. The results from molpro94 and turbomole is under development. I hope this is some use to the wider CCL community, Anthony P. Scott Research Officer Computational Chemistry Group Research School of Chemistry Australian National University Canberra, ACT, Australia