From eloranta@jyu.fi Thu Jul 21 02:55:10 1994 Received: from epr.chem.jyu.fi for eloranta@jyu.fi by www.ccl.net (8.6.9/930601.1506) id CAA24300; Thu, 21 Jul 1994 02:40:43 -0400 Received: by epr.chem.jyu.fi id AA15228 (5.65c8/IDA-1.4.4 for chemistry@ccl.net); Thu, 21 Jul 1994 09:45:32 +0300 Date: Thu, 21 Jul 1994 09:45:32 +0300 From: Jussi Eloranta Message-Id: <199407210645.AA15228@epr.chem.jyu.fi> To: chemistry@ccl.net Subject: g92 & sun fp problem X-Charset: ISO_8859-1 X-Char-Esc: 29 Hi, I'm trying to do spin density plots with g92 (using cube=(density,spin)) and the appropriate data at the end of the g92 input file (origin and other grid info). Normally things work fine but in some cases when there are very small values at the grid points the floating point numbers become like: 3.13920-108 instead of 3.13920E-108. This seems to be the case for all fp numbers with exponent smaller than -99. I just wonder if this is a g92 problem or Sun fortran problem? Is there anything I can do to avoid this (for example tell g92 not to print so small numbers)? Thanks, Jussi Eloranta From mholtha@helium.chem.TU-Berlin.DE Thu Jul 21 06:55:08 1994 Received: from helium.chem.TU-Berlin.DE for mholtha@helium.chem.TU-Berlin.DE by www.ccl.net (8.6.9/930601.1506) id GAA25604; Thu, 21 Jul 1994 06:41:57 -0400 Received: by helium.chem.TU-Berlin.DE (AIX 3.2/UCB 5.64/4.03) id AA30154; Thu, 21 Jul 1994 12:39:40 +0200 From: mholtha@helium.chem.TU-Berlin.DE (Max Holthausen) Message-Id: <9407211039.AA30154@helium.chem.TU-Berlin.DE> Subject: G92/DFT Hybrid Methods? To: chemistry@ccl.net Date: Thu, 21 Jul 1994 12:39:38 +0200 (DFT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 715 Hi Gaussian Professionals! Studying the addendum and the source code of the DFT Package of G92/DFT Rev F.2 we found several inconsistencies ... Who has a definite answer to the following? a) If "BHANDHLYP" is used : Is Beckes non-local correction to exchange included in the functional? The manual sais explicitely No, an output protokolls the values for ScaDFX .5000 .5000 1.000 1.000 which means (as far we came through the code) Yes. b) concerning "Becke3LYP" What are the exact weights for VWN and LYP in the correlation part of this functional. Desperately hoping for any hint Max Max C. Holthausen Instute for Organic Chemistry Technical University of Berlin Germany From mealli@cacao.issecc.fi.cnr.it Thu Jul 21 08:55:17 1994 Received: from cacao.issecc.fi.cnr.it for mealli@cacao.issecc.fi.cnr.it by www.ccl.net (8.6.9/930601.1506) id IAA26249; Thu, 21 Jul 1994 08:16:49 -0400 From: Received: by cacao.issecc.fi.cnr.it (5.57/Ultrix3.0-C) id AA18756; Thu, 21 Jul 94 14:15:05 GMT Message-Id: <9407211415.AA18756@cacao.issecc.fi.cnr.it> To: chemistry@ccl.net Subject: CACAO 4.0 now available Date: Tue Jul 19 14:15:15 1994 Dear Cacao Users, the new CACAO (ver. 4.0) is now ready for distribution. You can retrieve it by ftp-ing to our server at cacao.issecc.fi.cnr.it (149.139.10.2) as an anonymous user (password= your e-mail address). Get and read the ascii file README.1ST. Then, set the binary mode and get the self-extracting file CACAO40.EXE. Finally switch into the subdirectory PRINTGL and get all of the files in there. These contain the printing routines which are only redistributed by us as shareware. You may wish to contact the authors of the latter to fulfill their patent requirements. Please don't hesitate to contact us for problems and suggestions. Best regards, Carlo Mealli and Davide M. Proserpio. Dr. Carlo Mealli ISSECC, CNR Via J.NARDI 39, 50132 Firenze, ITALY e-mail: mealli@cacao.issecc.fi.cnr.it Tel. 0039-55-2346653 (243990) - Fax 2478366 - Home 4492709 From lin@gkcl.ists.ca Thu Jul 21 11:55:12 1994 Received: from gkcl.ists.ca for lin@gkcl.ists.ca by www.ccl.net (8.6.9/930601.1506) id LAA29983; Thu, 21 Jul 1994 11:45:04 -0400 Received: by gkcl.ists.ca (5.61/1.34) id AA29641; Thu, 21 Jul 94 11:46:13 -0400 From: lin@gkcl.ists.ca (Delin Shen) Message-Id: <9407211546.AA29641@gkcl.ists.ca> Subject: g92 installation To: chemistry@ccl.net Date: Thu, 21 Jul 94 11:46:12 ADT X-Mailer: ELM [version 2.2 PL0] Dear Netters, Does someone has experience in installing Gaussian 92 in MIPS computer? It is old Indigo r3000 machine with 4_52 operating system. Any suggestion will be appreciated. lin From cooksj@ttown.apci.com Thu Jul 21 12:31:39 1994 Received: from ttown.apci.com for cooksj@ttown.apci.com by www.ccl.net (8.6.9/930601.1506) id LAA29477; Thu, 21 Jul 1994 11:22:55 -0400 Received: by ttown.apci.com (5.57/Ultrix3.0-C) id AA00837; Thu, 21 Jul 94 11:26:16 -0400 Date: Thu, 21 Jul 94 11:26:16 -0400 From: cooksj@ttown.apci.com (Stephen J. Cook) Message-Id: <9407211526.AA00837@ttown.apci.com> To: chemistry@ccl.net Subject: PARALLEL: Chemistry codes for the SP-1 or 2 Reply-To: cooksj@ttown.apci.com I am looking for information about the availability of computational chemistry codes for the SP-x machines from IBM. We are primarily interested in molecular dynamics codes (e.g. Discover, CHARMm, etc) and quantum codes (both Hartree-Fock and DFT). I will summarize to the list if there is sufficient interest. Thanks..Steve Cook ********************************************************************* * Steve Cook cooksj@ttown.apci.com * * Air Products and Chemicals, Inc. Tel. (610) 481-2135 * * 7201 Hamilton Blvd. FAX (610) 481-2446 * * Allentown, PA 18195 * * USA * ********************************************************************* * Emacs - the choice of a GNU generation * ********************************************************************* From chp1aa@surrey.ac.uk Thu Jul 21 12:55:13 1994 Received: from mail-server.surrey.ac.uk for chp1aa@surrey.ac.uk by www.ccl.net (8.6.9/930601.1506) id MAA00533; Thu, 21 Jul 1994 12:19:16 -0400 Received: from central.surrey.ac.uk by mail-server.surrey.ac.uk with SMTP using (PP) id <29117-0@mail-server.surrey.ac.uk>; Thu, 21 Jul 1994 17:19:49 +0100 Received: by central.surrey.ac.uk (1.37.109.8/16.2) id AA01209; Thu, 21 Jul 1994 17:19:47 +0100 From: Mr Andrew D Allen Message-Id: <9407211619.AA01209@central.surrey.ac.uk> Subject: CCL: STATS: Wanted: Program to do cluster analysis To: chemistry@ccl.net Date: Thu, 21 Jul 94 17:19:47 BST Mailer: Elm [revision: 70.85] I have a set of data, basically x vs y, which forms a scatter graph. I would like to analyses the data to see if there is any significant clusters, ie if some of the points all fall within a cluster, and what the probability is that this is a random effect. I have been through just about every system locally to see if any of the stats packages here that can do this but have struck a big 0. After going through a MAILSERV@ccl.net search for "cluster", "analysis" and "program", I came up lots of potential programs, but they all seem to deal with cluster analysis of rms deviations of whole or parts of molecules, either in a dynamics trajectory or of another database. All I want to do is enter x,y values and get the clusters defined in some statistical way to show that families exists in the data. What is the best way to proceed? Andy. -- ############################################################################### Structural and Computation Chemistry Group_________chp1aa@uk.ac.surrey - JANET. Department of Chemistry____________________________phone_______+44(483)-259591. University of Surrey_______________________________fax_________+44(483)-300803. Guildford, Surrey, GU2 5XH, UK_____________________ftp____________131.227.110.2 ############################################################################### From a2wj@loki.cc.pdx.edu Thu Jul 21 13:55:13 1994 Received: from loki.cc.pdx.edu for a2wj@loki.cc.pdx.edu by www.ccl.net (8.6.9/930601.1506) id NAA02077; Thu, 21 Jul 1994 13:27:07 -0400 Received: (from a2wj@localhost) by loki.cc.pdx.edu (8.6.9/8.6.6) id KAA01598; Thu, 21 Jul 1994 10:28:06 -0700 Date: Thu, 21 Jul 1994 10:28:06 -0700 (PDT) From: "James M. Williams" Subject: pLEASE REMOVE ME FROM YOUR LIST To: CHEMISTRY@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Jan, I dont know how to sign off this list would you do it for me. thanks, Jim ***************************************************************************** * Jim Williams internet a2wj@loki.cc.pdx.edu * * Systems Analyst voice (503) 725-3112 * * Portland State University * * Portland, OR * ***************************************************************************** From CUNDARIT@MSUVX1.MEMPHIS.EDU Thu Jul 21 14:02:10 1994 Received: from msuvx1.memphis.edu for CUNDARIT@MSUVX1.MEMPHIS.EDU by www.ccl.net (8.6.9/930601.1506) id NAA01657; Thu, 21 Jul 1994 13:10:42 -0400 From: Received: from MSUVX1.MEMPHIS.EDU by MSUVX1.MEMPHIS.EDU (PMDF V4.3-8 #5958) id <01HEYUB2R178A3L2SM@MSUVX1.MEMPHIS.EDU>; Thu, 21 Jul 1994 12:11:35 -0500 (CDT) Date: Thu, 21 Jul 1994 12:11:35 -0500 (CDT) Subject: Re: CCL:PARALLEL: Chemistry codes for the SP-1 or 2 To: cooksj@ttown.apci.com Cc: chemistry@ccl.net Message-id: <01HEYUB2R17AA3L2SM@MSUVX1.MEMPHIS.EDU> X-VMS-To: IN%"cooksj@ttown.apci.com" X-VMS-Cc: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi, We've been using parallel-GAMESS on the SP1 at Cornell National Supercomputing Center for over a year. It is possible to run GAMESS using TCGMSG message passing software over the Ethernet connections or MPL message passing software and run over the high performance switch. If the similarities of the SP1 and SP2 are as I have heard, parallel GAMESS should run on it with minor, if any, modification. GAMESS, parallel or serial, can be obtained at no charge from its developers, the Iowa State Quantum Chemistry Group (mike@si.fi.ameslab.gov). We have only used parallel-GAMESS, but I believe there is a parallel HONDO for the SP1. Tom Cundari ------------------------------------------------------------------------------ Thomas R. Cundari Address until the end of August Asst. Professor of Chemistry Tom Cundari Computational Inorganic Chemistry Lab Visiting Scientist University of Memphis CST-3, C346 Memphis, TN 38152 Los Alamos National Lab phone: 901-678-2629 Los Alamos, NM 87545 fax: 901-678-3447 e-mail: cundarit@memstvx1.memst.edu http://www.memst.edu/chemistry/umchem.html ------------------------------------------------------------------------------- From vasz@bif.creighton.edu Thu Jul 21 14:55:14 1994 Received: from bif.creighton.edu for vasz@bif.creighton.edu by www.ccl.net (8.6.9/930601.1506) id OAA03015; Thu, 21 Jul 1994 14:04:31 -0400 Received: by bif.creighton.edu (920330.SGI/911001.SGI) for CHEMISTRY@ccl.net id AA14837; Thu, 21 Jul 94 12:36:22 -0500 Date: Thu, 21 Jul 94 12:36:22 -0500 From: vasz@bif.creighton.edu (Sandor Lovas) Message-Id: <9407211736.AA14837@bif.creighton.edu> To: CHEMISTRY@ccl.net Subject: distance dependent dielectric constant Dear Readers, What would be the best value to simulate trifluoro ethanol enviroment in MD/MM calculations using distance-dependent dielectric constant ? Sandor Lovas Dept. Biomed. Sci. Creighton Univ. Omaha, NE 68178 USA E-mail: vasz@bif.creifgton.edu From states@ibc.wustl.edu Thu Jul 21 17:55:16 1994 Received: from wugate.wustl.edu for states@ibc.wustl.edu by www.ccl.net (8.6.9/930601.1506) id RAA06405; Thu, 21 Jul 1994 17:25:13 -0400 Received: by wugate.wustl.edu (5.67b/WUSTL-0.3) with SMTP id AA12134; Thu, 21 Jul 1994 16:25:45 -0500 Received: by ibc.WUStL.EDU (8.6.9/SMI-SVR4) id QAA00862; Thu, 21 Jul 1994 16:25:44 -0500 Date: Thu, 21 Jul 1994 16:25:44 -0500 From: states@ibc.wustl.edu (David J. States) Message-Id: <199407212125.QAA00862@ibc.WUStL.EDU> To: chemistry@ccl.net, chp1aa@surrey.ac.uk Subject: Re: CCL:STATS: Wanted: Program to do cluster analysis X-Sun-Charset: US-ASCII |> I have a set of data, basically x vs y, which forms a scatter graph. I would |> like to analyses the data to see if there is any significant clusters, ie if |> some of the points all fall within a cluster, and what the probability is |> that this is a random effect. ... |> Andy. |> Structural and Computation Chemistry Group_________chp1aa@uk.ac.surrey - JANET. What you are asking for is actually a quite high level interpretation. Not only do you want to know if is there a significant clustering of the data, but also, how many classes there are. Is there a classification that describes the data better than lumping everything together as one class? This has been addressed in machine learning where the technique goes by the name "Bayesian Classification". Peter Cheeseman (cheeseman@pluto.arc.nasa.gov) at the NASA Aimes Research Center wrote a program, Autoclass, that implements the technique. You might also contact Lloyd Allison at Monash University and Larry Hunter at the National Library of Medicine who have done work in related areas. David States Institute for Biomedical Computing / Washington University in St. Louis