From DSMITH@uoft02.utoledo.edu Wed Feb 24 19:25:05 1993 Date: Thu, 25 Feb 1993 00:25:05 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: symposium: Modeling the Hydrogen Bond To: chemistry@ccl.net, mmodinfo@uoft02.utoledo.edu, hyperchem@autodesk.com Message-Id: <01GV4AS4IK9U000C0A@UOFT02.UTOLEDO.EDU> Dear Fellow Computational Chemists: At the ACS National Meeting in Chicago, August 22-27, 1993 I will be chairing a symposium entitled "Modeling the Hydrogen Bond." I am starting in earnest the job of planning and preparing for that symposium, which is sponsored by the Computers in Chemistry division. Right now, it appears that we will have enough people for at least two days of talks and posters. There is still room for more, so... In order to assist in planning, I would ask that you, the readers of this mail exploder, help by letting me know if you are interested in speaking and/or presenting at this symposium. The more I know now, the more time and money I can ask for and the better the symposium will be. Please reply to me directly. If you have already spoken to me about presenting, you need not reply to this message Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From Kurt.Hillig@um.cc.umich.edu Thu Feb 25 04:44:28 1993 Date: Thu, 25 Feb 93 09:44:28 EST From: Kurt.Hillig@um.cc.umich.edu To: PODOSNNA@ACFCLUSTER.NYU.EDU, Chemistry@ccl.net Message-Id: <20321923@um.cc.umich.edu> Subject: X-Window terminal emulator for Mac There is a product (from Apple, I believe; since we're site licensed for it here I haven't paid much attention to where it comes from) called "MacX" which is an X-windows client for the Mac. It needs a lot of memory - 8 MB is recommended - and a large screen really helps, and if you've got a machine slower than an SE-30 it's not worth trying. There are a couple more gotchas, too: 1) It requires either SLIP/PPP or a true ethernet connection - and while I haven't tried it myself, I expect performance to be abysmal using SLIP or PPP through a phone line. Of course if you have an ISDN line this would work, probably with acceptable (though slow) performance - but ISDN isn't very common yet, and may not be available in your area. 2) Much of the graphics-oriented SGI software (which I assume is why you want to run X instead of a simple terminal emulator) is based on SGI's GL protocol and won't run under X. A good test is to try running it >from a DECstation or Sun (or any other non-GL platform) - if it works, it's X-based, and if it doesn't work then MacX will also fail. The bottom line is that you really need a high-end Mac and a fast communication link to make MacX functional, and you need to check the software you want to use to make sure it runs under X-windows and doesn't require a GL machine. Kurt Hillig Dept. of Chemistry I always tell the khillig@umich.edu University of Michigan absolute truth Telephone (313)747-2867 Ann Arbor, MI 48109-1055 as I see it. hillig@chem.lsa.umich.edu From markb@orl.mmc.com Thu Feb 25 05:58:52 1993 Message-Id: <9302251558.AA15893@enterprise.orl.mmc.com> To: CHEMISTRY@ccl.net Subject: Molecular Dynamics References From: mark-bower@orl.mmc.com Date: Thu, 25 Feb 93 10:58:52 -0500 I apologize for asking a "beginner's question", but I am looking for references on the determination and graphical display of simple protein structure and enzyme interaction for a molecular dynamics display program I am writing to run under X, MS-Windows, and SGI "gl". My code is object-oreinted allowing me to switch between the platforms easily. I am mainly interested in showing the protein construction process in 3-D through a very functional GUI. I also have some tools from some previous non-linear optimization work that I would like to try out on the protein structure problem. I would be more than happy to post a complete bibliography of the responses I recieve if there is interest. News of other peoples efforts would also be fantastic. Are there any electronic archives of papers? source code? Thanks in advance, and, again, sorry for the trouble. Mark. mark-bower@orl.mmc.com U. Central Florida Dept. of Mathematics From shepard@dirac.tcg.anl.gov Thu Feb 25 05:10:57 1993 Date: Thu, 25 Feb 93 11:10:57 CST From: shepard@dirac.tcg.anl.gov (Ron Shepard) Message-Id: <9302251710.AA03468@dirac.tcg.anl.gov> To: chemistry@ccl.net Subject: RE: X-Window terminal emulator for Mac > There is a question which is not directly related to computational >chemistry. Does anyone happen to know any X-window terminal emulator for Mac. >I would like to log on SGI from home using Mac as a terminal. Do you know >if anything is available as public domain. Thanks in advance. > > > Sincerely, > > Andrew Podosenin > >PODOSNNA@ACFCLUSTER.NYU.EDU I have been trying to use Telnet and MacX with MacTCP and the VersaTerm SLIP tool to do this, but I haven't gotten all of the pieces to work yet. There are a lot of variables, and not many ways to isolate problems. Any suggestions >from anyone who has a similar setup working correctly would be appreciated. -Ron Shepard shepard@tcg.anl.gov From SOPHIEC@FRMOP11.bitnet Thu Feb 25 16:45:13 1993 Message-Id: <199302251703.AA15673@oscsunb.ccl.net> Date: Thu, 25 Feb 93 16:45:13 GMT From: Sophie Creuzet C3NI/CNUSC Subject: Re: Parallel AMBER summary To: Jim Vincent , Dear CCLers, More information on AMBER parallel versions : an AMBER parallel version has been developped for the new SP1 IBM parallel machine (which was announce early februar and will be available in september). The work was done in the ECSEC/IBM (Roma). For any further information, please contact Stefano Patarnello (patarnel at vnet.ibm.com) who is responsible for this program. Among the list of programs which should be implemented in parallel on the SP1 machine : Quantum Chemistry : HONDO (IBM) DMOL (BIOSYM) SPARTAN (Wavefunction Inc.) NCSAdisco (South Dakota State Univ.) GAMESS (Iowa State Univ.) Molecular Modeling : DISCOVER (Biosym Techn. Inc.) CHARMm (MSI, Inc.) AMBER (Univ. California at San Franscico) MM-BATCHMIN (Columbia Univ.) X-PLOR (MSI, Inc.) PROLSQ (Columbia Univ.) DGEOM (QCPE) For any information contact M. Dupuis (michel at kgnvma.vnet.ibm.com). ************************************************************* * * * * Sophie Creuzet * Phone : 33-67-14-14-67 * * C3NI/CNUSC * Userid: sophiec * * 950 rue de saint Priest * E-node: frmop11 * * 34184 Montpellier Cedex 4 *Internet: frmop11.cnusc.fr * * * (131.196.7.3) * * * * ************************************************************* From h.rzepa@ic.ac.uk Thu Feb 25 18:04:33 1993 Message-Id: <9302251805.AA14232@cscmgb.cc.ic.ac.uk> Date: Thu, 25 Feb 1993 18:04:33 +0000 To: Chemistry@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Gopher+ Gopher+ is a distributed data base, archive and bulletin board system which supports graphics types, quicktime and other visuals. Anyone wishing to try can connect to argon.ch.ic.ac.uk. On a Mac you need Turbogopher 1.06b2, available from Minnesota. My request is the following. It only supports generic file types, ie TIFF, PICT, GIF, as well as Quicktime and not surprisingly Microsoft Word. We need, as a chemical community to lobby for generic chemistry types. For example, SMD molecule formats, or perhaps the public MDL MOLFILE format. This would enable structure diagrams to be "gophered" and translated remotely. To persuade the Gopher developers to adopt such non computing science file types need much support from us. If you believe that this is the way forward, perhaps messages sent to gopher@boombox.micro.umn.edu might do the trick! Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.3, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From d3e129@cagle.pnl.gov Thu Feb 25 02:29:29 1993 Date: Thu, 25 Feb 93 10:29:29 PST From: d3e129@cagle.pnl.gov Subject: X-Window terminal emulator for Mac To: Chemistry@ccl.net Message-Id: <9302251829.AA12674@cagle.pnl.gov> If you need to go to the high performance mac there is a better/cheaper solution. I have a NCD color xterminal at home. I can run nearly everything that is x-based, xdbx, gnuplot, emacs, xterm, etc. work great. The only problem I do have is with Liken which is a mac emulator for the sparcstation (and other Unix) box. The cost is around $3500 (probably a little cheaper for University?). Grayscale is even cheaper. The performance is slow for opening new windows but once everything is open then going through windows is very quick. There is a built in Server (in PROMS) that is required. NCD supplies all the slip software and extra fonts etc. I am very please with this and it is better (over 9600 modem) than the performance of my Mac IIfx on ethernet and orders of magnitude better than a single window from a Mac over the modem. Rick ============================================================================= === Ricky A. Kendall === === Mail Stop K1-90 === === Molecular Science Software Group === === Theory, Modeling, and Simulation Program === === Molecular Science Research Center === === Pacific Northwest Laboratory === === Richland, WA 99352 === ============================================================================= ============================================================================= === All opinions are my own and not those of any other life form, === === living, dead or unknown. === ============================================================================= ============================================================================= === Parallel computing is the way of the future === === Always was ........ always will be!!!!! === ============================================================================= From feng@sgi.chem.temple.edu Thu Feb 25 12:19:09 1993 Date: Thu, 25 Feb 93 17:19:09 -0500 From: feng@sgi.chem.temple.edu (Feng Chen) Message-Id: <9302252219.AA02319@sgi.chem.temple.edu> To: chemistry@ccl.net Subject: X-windows Server on MS-Windows Hi, I am looking for a Shareware version's X-windows server running on MS-windows. Any info is greatly appreciated. Thank you feng@sgi.chem.temple.edu From h.rzepa@ic.ac.uk Thu Feb 25 17:59:09 1993 Message-Id: <9302251800.AA13840@cscmgb.cc.ic.ac.uk> Date: Thu, 25 Feb 1993 17:59:09 +0000 To: chemistry@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Re: X-Window terminal emulator for Mac >There is a product (from Apple, I believe; since we're site licensed >for it here I haven't paid much attention to where it comes from) >called "MacX" which is an X-windows client for the Mac. It needs a >lot of memory - 8 MB is recommended - and a large screen really helps, >and if you've got a machine slower than an SE-30 it's not worth trying. > Well, we run a lab of 10 4 Mbyte LCs (not LC IIs!) and its ok for editing, and simple tasks. We also use localtalk, and its no problem. >2) Much of the graphics-oriented SGI software (which I assume is why you >want to run X instead of a simple terminal emulator) is based on SGI's >GL protocol and won't run under X. A good test is to try running it >from a DECstation or Sun (or any other non-GL platform) - if it works, >it's X-based, and if it doesn't work then MacX will also fail. Yes. For example the JOT SGI editor will not work! > >The bottom line is that you really need a high-end Mac and a fast >communication link to make MacX functional See above. Functional editing is possible on a 4 Mbyte LC. You may even be able to run MacroModel at a pinch! Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.3, Tel:+44 71 225 8339, Fax:+44 71 589 3869.