From h.rzepa@ic.ac.uk Thu Jul 14 10:53:24 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.9/930601.1506) id KAA24235; Thu, 14 Jul 1994 10:30:15 -0400 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <07561-0@punch.ic.ac.uk>; Thu, 14 Jul 1994 15:29:41 +0100 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA24761; Thu, 14 Jul 94 15:32:20 +0100 Message-Id: <9407141432.AA24761@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@sg1.cc.ic.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 14 Jul 1994 15:30:14 +0100 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Rzepa,Henry) (Rzepa,Henry) Subject: Chemical MIME type Examples Announcing two Web pages illustrating the application of Chemical MIME ___________________________________________________________ As part of a program to illustrate how "live" chemistry can be exported on the Internet, we have considerably extended our "mime" action page. Connect to; http://www.ch.ic.ac.uk/chemical_mime.html or http://chem.leeds.ac.uk/Project/MIME.html Here we have put hyperlinks into a number of files in various formats such as pdb, MOPAC and Gaussian and suggested helper programs that can read these files and visualise them. We illustrate the use of RasMol, XMol and Explorer EyeChem. The latter suite was written by Omer Casher, and provides a set of modular tools to visualise molecular properties. We show how a MOPAC FORCE calculation can be read and animated, how a Gaussian G92 optimisation can be animated, how a pdb file can be ribbon rendered and how a collaborative visualisation involving two separate sites can be achieved. Many other permutations of the EyeChem modules are possible, and a few more will appear over the next few days. All three programs are freely distributable, and can be downloaded from ftp archives. Hyperlinks to do this are built into the pages. The EyeChem modules were first released on the IRIX 5.2 CD-ROM installation set, but updated versions are available from our ftp server, along with scripts and installation instructions. You will need to use an SGI machine running Irix 5.2 and Explorer 2.2 to use EyeChem. If anyone wishes to put up similar examples of chemical MIME in action, perhaps illustrating a different set of files (see http://www.ch.ic.ac.uk/internet/ for the chemical MIME Internet draft) please let us know so that we can link to them. If other helper programs have been used, we would also be interested (initially, we would prefer "free" programs that can be downloaded by users from ftp archives). Contact hoc@ic.ac.uk, rzepa@ic.ac.uk or benw@chemistry.leeds.ac.uk for further details. From jstewart@fujitsuI.fujitsu.com Thu Jul 14 11:22:41 1994 Received: from mail.barrnet.net for jstewart@fujitsuI.fujitsu.com by www.ccl.net (8.6.9/930601.1506) id KAA24306; Thu, 14 Jul 1994 10:41:26 -0400 Received: from fujitsu1.fai.com by mail.barrnet.net (5.67/1.37) id AA25853; Thu, 14 Jul 94 07:42:25 -0700 Received: by fujitsu1.fujitsu.com (4.1/SMI-4.1) id AA15026; Thu, 14 Jul 94 07:42:07 PDT Date: Thu, 14 Jul 94 07:42:07 PDT From: jstewart@fujitsu.com (Dr. James Stewart) Message-Id: <9407141442.AA15026@fujitsu1.fujitsu.com> To: chemistry@ccl.net Subject: PF6(-) PM3, AM1, SAM1 results Semiempirical users might be interested in comparing PM3, AM1 and SAM1 applied to PF6(-). The starting geometry used was the SAM1 results reported by Prof Holder. To summarize: PM3 results: H.o.F.= -508.54 KCAL, I.P.=9.106 EV P-F = 1.592 Q(F)=-0.4889 AM1 results: H.o.F.= -504.47 KCAL, I.P.=8.766 EV P-F = 1.571 Q(F)=-0.6505 SAM1 results: H.o.F.= -547.84 KCAL, I.P.=9.533 EV P-F = 1.595 Q(f)=-0.5250 Jimmy Stewart SUMMARY OF PM3 CALCULATION MOPAC 93.00 F6 P Thu Jul 14 08:25:10 1994 SYMMETRY PM3 PRECISE CHARGE=-1 GRAD BONDS T=200 PF6- (Oh) by Jie HEAT OF FORMATION MINIMIZED IN ONE LINE SEARCH SCF FIELD WAS ACHIEVED HEAT OF FORMATION = -508.544085 KCAL = -2127.74845 KJ ELECTRONIC ENERGY = -7964.833810 EV CORE-CORE REPULSION = 5191.527143 EV GRADIENT NORM = 0.000655 DIPOLE = 0.00000 DEBYE SYMMETRY: Oh NO. OF FILLED LEVELS = 24 CHARGE ON SYSTEM = -1 IONIZATION POTENTIAL = 9.106107 EV HOMO LUMO ENERGIES (EV) = -9.106 5.391 MOLECULAR WEIGHT = 144.964 SCF CALCULATIONS = 8 COMPUTATION TIME = 1.517 SECONDS FINAL GEOMETRY OBTAINED CHARGE SYMMETRY PM3 PRECISE CHARGE=-1 GRAD BONDS T=200 PF6- (Oh) by Jie P 0.00000000 0 0.0000000 0 0.0000000 0 0 0 0 1.9335 F 1.59208412 1 0.0000000 0 0.0000000 0 1 0 0 -0.4889 F 1.59208412 0 90.0000000 0 0.0000000 0 1 2 0 -0.4889 F 1.59208412 0 90.0000000 0 90.0000000 0 1 2 3 -0.4889 F 1.59208412 0 90.0000000 0 90.0000000 0 1 2 4 -0.4889 F 1.59208412 0 90.0000000 0 90.0000000 0 1 2 5 -0.4889 F 1.59208412 0 90.0000000 0 180.0000000 0 1 3 2 -0.4889 2 1 3 4 5 6 7 From tgm@SSD.intel.com Thu Jul 14 13:53:18 1994 Received: from SSD.intel.com for tgm@SSD.intel.com by www.ccl.net (8.6.9/930601.1506) id NAA27696; Thu, 14 Jul 1994 13:21:04 -0400 Received: from idaho.SSD.intel.com by SSD.intel.com (4.1/SMI-4.1) id AA04577; Thu, 14 Jul 94 10:21:31 PDT Date: Thu, 14 Jul 94 10:21:31 PDT From: "Timothy G. Mattson" Message-Id: <9407141721.AA04577@SSD.intel.com> To: CHEMISTRY@ccl.net Subject: Call for Referees I am editing a book on Parallel computing in computational chemistry. This book is based on the sympossium of this title at last springs ACS meeting. I need volenteers to help me referee the contributions to the book. If you have experience with parallel computing and computational chemistry, I would appreciate the help. Thank You --Tim -------------------------------------------------------------------- Timothy G. Mattson, Ph.D. - Science Support (Chemistry, Biology, etc) Intel Supercomputer Systems Division | Phone: (503) 531-5627 Mail Stop CO6-09 | FAX: (503) 531-5501 14924 N.W. Greenbrier Pkwy | email: tgm@ssd.intel.com Beaverton, OR 97009 --------------------------------------------------------------------