From EILMES@Trurl.ch.uj.edu.pl Tue Mar 31 03:21:24 1998 Received: from if.uj.edu.pl for EILMES@Trurl.ch.uj.edu.pl by www.ccl.net (8.8.3/950822.1) id CAA03914; Tue, 31 Mar 1998 02:55:02 -0500 (EST) Received: from Trurl.ch.uj.edu.pl (trurl.ch.uj.edu.pl [149.156.71.254]) by if.uj.edu.pl (8.8.7/8.7.1) with ESMTP id KAA08953 for ; Tue, 31 Mar 1998 10:04:06 +0200 (MET DST) Received: from TRURL/MAILQUEUE by Trurl.ch.uj.edu.pl (Mercury 1.40); 31 Mar 98 09:54:39 GMT+2 Received: from MAILQUEUE by TRURL (Mercury 1.40); 31 Mar 98 09:54:30 GMT+2 From: "Andrzej Eilmes" Organization: Faculty of Chemistry, UJ To: chemistry@www.ccl.net Date: Tue, 31 Mar 1998 09:54:25 MET+2 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Alpha 566 vs. 600 MHz Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: Dear CCLers, By the time my question (whether it is reasonable to pay 17% more to buy Alpha 600 MHz instead of 566) got to the list I got the answer from the dealer. The only difference between the two machines is the processor, so the gain in the speed in only about 6%. The 600 MHz machine is for people who want to pay 17% more only to get fastest processor available (but they will be lucky only for a couple of weeks, as Alpha 633 has appeared in the catalogue) To answer the question I got: >Hi, > I am surprised with such a low price. are you sure the DEC alpha 600 >will just cost $8200? This is not a DEC workstation but based on DEC Alpha (i.e. only motherboard and CPU is from DEC). Check http://www.microway.com/ for more info. Andrzej Eilmes ---------------------------------------------------------------- Dr Andrzej Eilmes eilmes@trurl.ch.uj.edu.pl Faculty of Chemistry, Jagiellonian University, Cracow, Poland Phone: (48-12) 6336377 ext. 213 Fax: (48-12) 6340515 ---------------------------------------------------------------- From laaksone@csc.fi Tue Mar 31 07:21:25 1998 Received: from pobox.csc.fi for laaksone@csc.fi by www.ccl.net (8.8.3/950822.1) id GAA05325; Tue, 31 Mar 1998 06:35:16 -0500 (EST) Received: from laaksonen.csc.fi (laaksonen.csc.fi [193.166.1.75]) by pobox.csc.fi (8.8.8/8.8.8/CSC/Rtrs-1.13) with SMTP id OAA15932 for ; Tue, 31 Mar 1998 14:35:17 +0300 (EET DST) Date: Tue, 31 Mar 1998 14:32:14 +0300 (GFT Daylight Time) From: Leif Laaksonen To: chemistry@www.ccl.net Subject: Scarecrow Computing Presents gOpenMol 1.11 Message-ID: X-X-Sender: laaksone@laaksonen.csc.fi MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members, The new version 1.11 of gOpenMol is now available at: http://laaksonen.csc.fi/gopenmol/ The binary release is available for the platforms: * Windows Intel 95/NT * Windows NT Alpha * SGI Irix using MESA * SGI Irix using OpenGL * DEC OSF using MESA * Linux Intel using MESA The version contains very few new features compared to 1.0 apart from fixed bugs. The only new feature is the possibility to project for example the electrostatic potential on a Connolly surface. For examples please look at: http://laaksonen.csc.fi/gopenmol/gallery/ If you like the program and you have used it to produce graphics or animations please let me know and I include your graphics into the gOpenMol Gallery page either as a link or as graphic files. I'm also running out of time so if you are interested to make the binary release for the next version of gOpenMol , whenever it will be available, for a Unix platform please let me know. Have Fun with gOpenMol! Regards, -leif laaksonen ------------------------------------------------------------------- Center for Scientific Computing | Phone: 358 9 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 9 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi -------- URL: http://laaksonen.csc.fi/leif.laaksonen.html --------- From otavio@NPD.UFPE.BR Tue Mar 31 12:21:28 1998 Received: from NPD1.NPD.UFPE.BR for otavio@NPD.UFPE.BR by www.ccl.net (8.8.3/950822.1) id LAA15767; Tue, 31 Mar 1998 11:49:25 -0500 (EST) Received: from Arnobio2.dqf.ufpe.br ([150.161.5.23]) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with ESMTP id <01IVBGZZ66LS0004WP@NPD.UFPE.BR> for chemistry@www.ccl.net; Tue, 31 Mar 1998 13:47:47 GMT-3 Date: Tue, 31 Mar 1998 13:50:41 -0300 From: Otavio Luis de Santana Subject: Summary: Fock Matrix - gaussian output. To: chemistry@www.ccl.net Message-id: <35211EE1.A125B03E@npd.ufpe.br> MIME-version: 1.0 X-Mailer: Mozilla 4.01 [en] (Win95; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Priority: 3 (Normal) Dear CCLers, Last week I placed the following subject in the list: "as to obtain the Fock matrix from gaussian output?". Many gratefulness for the received answers. Summary: iop=(5/33=4) or iop=(5/33=5), that print Fock matrix in the end of each cycle scf. ---------------------- Otavio Luis de Santana otavio@npd.ufpe.br ---------------------- From jkl@ccl.net Tue Mar 31 12:27:46 1998 Received: from ccl.net for jkl@ccl.net by www.ccl.net (8.8.3/950822.1) id MAA15880; Tue, 31 Mar 1998 12:12:28 -0500 (EST) Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id MAA20788; Tue, 31 Mar 1998 12:12:21 -0500 (EST) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.8.3/920428.1525) id MAA29077; Tue, 31 Mar 1998 12:12:14 -0500 (EST) Date: Tue, 31 Mar 1998 12:12:14 -0500 (EST) Message-Id: <199803311712.MAA29077@krakow.ccl.net> To: chemistry@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU Subject: Workshop: Comp. Methods in Toxicology, Apr 20-22, Dayton, OH Cc: chemind-l@derwent.tecc.co.uk, toxicology@ccl.net This is a sort reminder that we can still accept a few more participants for the workshop entitled: COMPUTATIONAL METHODS IN TOXICOLOGY April 20-22, 1998 Holiday Inn/I-675, Dayton, Ohio, USA though we will have to close registrations shortly. For registration information, program, abstracts, etc., consult Web pages for this workshop: http://www.ccl.net/CCM/toxicology/ Thank you, The Organizers: toxicology@ccl.net From hein@dg7.chemie.uni-konstanz.de Tue Mar 31 12:29:41 1998 Received: from dg7.chemie.uni-konstanz.de for hein@dg7.chemie.uni-konstanz.de by www.ccl.net (8.8.3/950822.1) id LAA15747; Tue, 31 Mar 1998 11:45:47 -0500 (EST) Received: from localhost (hein@localhost) by dg7.chemie.uni-konstanz.de (8.8.8/8.8.8) with SMTP id SAA01485 for ; Tue, 31 Mar 1998 18:51:12 +0200 (MET DST) Date: Tue, 31 Mar 1998 18:51:10 +0200 (MET DST) From: Frank Schaper To: chemistry@www.ccl.net Subject: Re: Problems running Spartan on Dec Alpha In-Reply-To: <3520c514131f018@sunsrv5.lrz-muenchen.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, some time ago, I posted due to problems with Spartan after updating out Alpha to Digital Unix V40.B. > Dear netters, > > after updating our Alpha to Digital UNIX V4.0B (including the Open-GL > Interface) we receive the following error messages, when trying to run > Spartan 4.1.1. : > > > spartan/builder error: unable to find visual to support double buffer, > RGB, Z-buffered rendering. > > Many thanks to everyone who responded. The solution was embarassing simple. Spartan seems to have problems in detecting the graphic and trys to run the OpenGL-version instead of the X-Windows-version. Simple editing of the batch-file and removal of the automatic detection solves the problem. Hein From lmoskal@emory.edu Tue Mar 31 15:21:30 1998 Received: from graf.cc.emory.edu for lmoskal@emory.edu by www.ccl.net (8.8.3/950822.1) id OAA17280; Tue, 31 Mar 1998 14:24:23 -0500 (EST) Received: from curly.cc.emory.edu (lmoskal@curly.cc.emory.edu [170.140.1.66]) by graf.cc.emory.edu (8.8.8/8.8.8) with SMTP id OAA03746 for ; Tue, 31 Mar 1998 14:24:24 -0500 (EST) Date: Tue, 31 Mar 1998 14:24:22 -0500 (EST) From: Lyudmila V Moskaleva X-Sender: lmoskal@curly.cc.emory.edu Reply-To: Lyudmila V Moskaleva To: chemistry@www.ccl.net Subject: B3LYP Raman activities are possible Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello: This is a little addition to the question of B3LYP raman activities. As Stefan Faux noticed, the cubic option to the freq-keyword produces numerical 3rd derivatives if analytic 2nd derivatives are available. # ... freq=cubic ... will give you Raman activities and depolarization ratios This works for B3LYP. Lyudmila From charwel@chrs1.chem.lsu.edu Tue Mar 31 17:21:30 1998 Received: from chrs1.chem.lsu.edu for charwel@chrs1.chem.lsu.edu by www.ccl.net (8.8.3/950822.1) id QAA18401; Tue, 31 Mar 1998 16:44:31 -0500 (EST) Received: from localhost by chrs1.chem.lsu.edu (AIX 4.1/UCB 5.64/4.03) id AA16746; Tue, 31 Mar 1998 15:49:47 -0600 Date: Tue, 31 Mar 1998 15:49:47 -0600 (CST) From: Chris Harwell To: ccl Subject: convergence of electric field gradients Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ccl'ers: Is anyone aware of detailed basis set convergence studies (like Dunning's on energy etc) for electric field gradients? I would be greatly appreciative of any pointers, charwel@chrs1.chem.lsu.edu "Everything positive originates in a positive attitude from someone" :> From mn1@helix.nih.gov Tue Mar 31 17:28:35 1998 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id RAA18604; Tue, 31 Mar 1998 17:08:49 -0500 (EST) Received: (from mn1@localhost) by helix.nih.gov (8.8.5/8.8.5) id RAA27321; Tue, 31 Mar 1998 17:08:33 -0500 (EST) Date: Tue, 31 Mar 1998 17:08:33 -0500 (EST) From: "M. Nicklaus" Message-Id: <199803312208.RAA27321@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: MB (or MW) in Gaussian 94 Cc: mn1@helix.nih.gov Hi, I hope this is not a FAQ. How does G94 count one MB (or MW) in the %Mem command? Is it 1 x (or 8 x) 1,000,000; or 1 x (or 8 x) 2^20 = 1 x (or 8 x) 1,048,576 ? Hence, do the commands %Mem=8000000 %Mem=8MW %Mem=64MB all mean exactly 64,000,000 or 67,108,864 bytes? I tend toward the first interpretation, but since the manual does not seem to spell this problem out explicitly, I thought I'd ask... Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 37 Convent Dr, MSC 4255 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute, & Center for Molecular Modeling, Div. of Computer Research and Technology ------------------------------------------------------------------------ From eyoung@biosci.cbs.umn.edu Tue Mar 31 19:21:29 1998 Received: from biosci.cbs.umn.edu for eyoung@biosci.cbs.umn.edu by www.ccl.net (8.8.3/950822.1) id SAA19300; Tue, 31 Mar 1998 18:45:15 -0500 (EST) Received: from localhost (eyoung@localhost) by biosci.cbs.umn.edu (8.8.8/8.6.9) with SMTP id RAA16935 for ; Tue, 31 Mar 1998 17:41:04 -0600 (CST) Date: Tue, 31 Mar 1998 17:41:03 -0600 (CST) From: Eva Young To: ccl Subject: pdb to VRML conversion tool Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi folks: Is there an authoring tool available that will convert pdb files to VRML? I'll summarize any replies to the list. Eva Eva Young University of Minnesota eyoung@biosci.umn.edu From jon@gate.sinica.edu.tw Tue Mar 31 21:21:31 1998 Received: from gate.sinica.edu.tw for jon@gate.sinica.edu.tw by www.ccl.net (8.8.3/950822.1) id UAA20111; Tue, 31 Mar 1998 20:53:24 -0500 (EST) Received: (from jon@localhost) by gate.sinica.edu.tw (8.8.7/8.8.7) id JAA01265; Wed, 1 Apr 1998 09:54:13 +0800 (CST) Date: Wed, 1 Apr 1998 09:54:13 +0800 (CST) From: Jon Wright To: chemistry@www.ccl.net Subject: Other Processors benchmark Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I lot of people have asked me about my figures about running some common comp chem programs under Linux. As they requested I have used the options they suggested for g77 (-ffast-math -O2 -malign-double) and redone the calculations. The programs tested where a charmm mini and a charmm dyn run + a Modeller homology modelling run. I would like to take in a few other programs such as g94 and Amber but really I don't have the time and available time on the machines. The new results are posted for Ppro 200 and PII 266 procs vs common IBM and SGI machines. For the PII I have also compared g77 (0.5.21) vs Portland Group compiler under Linux. The page can be found at: http://www.ibms.sinica.edu.tw/~jon/machines.html (if the new server keeps up) Initially I am very impressed with the PII and Ppro esp with the Portland compiler, g77 is roughly 2/3 the speed of the portland one. (In my previous posting I compared Portland to g77 0.5.19.1 which was alot slower). The PII performed significantly better than the other workstations I tested (O2, Indigo2 R8000 and IBM 3CT). I shall be off to Mainland China for a week from Fri so if anyone emails me and doesn't get a reply it doesn't mean I am ignoring you! Regards Jon jon@sinica.edu.tw Disclaimer, if anybody from IBM/SGI gets in touch with me to complain about any aspect of these results I will listen to you but pls remember I am a computer user not a computer benchmarker. From gammadas@telis.org Tue Mar 31 23:21:31 1998 Received: from mail-01.telis.org for gammadas@telis.org by www.ccl.net (8.8.3/950822.1) id WAA20572; Tue, 31 Mar 1998 22:43:59 -0500 (EST) Received: from [207.49.123.153] (s04-pm45.snaustel.campus.mci.net [207.49.123.153]) by mail-01.telis.org (8.8.8/8.8.8) with SMTP id TAA03493 for ; Tue, 31 Mar 1998 19:33:41 -0800 (PST) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 31 Mar 1998 21:36:49 +0100 To: chemistry@www.ccl.net From: gammadas@telis.org (Goutam Das) Subject: CCL: symm enforced solutions Dear CCLer's: I wonder if there is a way to enforce symmetry on the optimized structure of a molecule (using a key word) in Gaussian94 without having to define a Z-matrix using the identical variables for bond lengths, angles and dihedrals (or in other words making the initial str symmetrical). I understand GAMESS has an option which allows one to specify the symmetry point group of the optimized structure--I would like to know if anyone has used this feature and whether there are any advantages/disadvantages of enforcing symmetry during optimizations. The small section on symmetry in the G94 user's guide didn't help--would anyone be so kind to provide example input files for example say acetone/nbutane in various conformations. Also, would a tighter optimization req (lower gradient at which opt stops) necessarily make the final str symmetrical? Thanx in anticipation Goutam Das GOUTAM DAS, Ph.D RESEARCH SCIENTIST BETZDEARBORN, HPG INC PO BOX 4300 9669 GROGANS MILL ROAD THE WOODLANDS, TX 77387-4300 (H) 281 259 2887 (W) 281 367 6201 ext425 email:gammadas@telis.org goutam.das@betzdearborn.com