From BOTTA@SIVAX.CINECA.IT Mon Feb 7 06:51:00 1994 Received: from phem3 for BOTTA@SIVAX.CINECA.IT by www.ccl.net (8.6.4/930601.1506) id GAA19072; Mon, 7 Feb 1994 06:44:56 -0500 From: Received: from SIVAX.CINECA.IT (MAILER@ICINECA2) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #3557) id <01H8LFB0PCWW8WXHY7@phem3.acs.ohio-state.edu>; Mon, 7 Feb 1994 06:44:49 EST Date: Mon, 07 Feb 1994 12:46 +0000 (N) Subject: PROF GOODFORD ADDRESS To: CHEMISTRY@ccl.net Reply-to: BOTTA@SIVAX.CINECA.IT Message-id: <2538@SIVAX.CINECA.IT> Content-transfer-encoding: 7BIT X-Original-To: CHEMISTRY@ccl.net Comments: INFN.IT domain is equivalent to BITNET domain: INFNET; INFNET has been disestablished Dec 31, 1988 Dear Netters: I would like to know the contact point of Professor Goodford, Oxford. Does anyone know his address(preferably e-mail address)? Please reply me to botta@sivax.cineca.it. Thanks in advance Maurizio Botta, Ph.D. From WILLIAMS%XRAY2@ULKYVX.LOUISVILLE.EDU Mon Feb 7 10:50:29 1994 Received: from ulkyvx.louisville.edu for WILLIAMS%XRAY2@ULKYVX.LOUISVILLE.EDU by www.ccl.net (8.6.4/930601.1506) id KAA23255; Mon, 7 Feb 1994 10:22:01 -0500 From: Received: from DECNET-MAIL (WILLIAMS@XRAY2) by ULKYVX.LOUISVILLE.EDU (PMDF V4.2-11 #3949) id <01H8LMTE9FW08WX225@ULKYVX.LOUISVILLE.EDU>; Mon, 7 Feb 1994 10:20:16 EST Date: Mon, 07 Feb 1994 10:20:16 -0500 (EST) Subject: SGI deprioritization To: chemistry@ccl.net Message-id: <01H8LMTE9Z6A8WX225@ULKYVX.LOUISVILLE.EDU> X-VMS-To: ULKYVX::IN%"chemistry@ccl.net" X-VMS-Cc: WILLIAMS MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT I recently sent out the following message over the net. Several persons who replied requested that I post a summary of the responses. An unedited listing of the reponses follows. The message was > I recall that there was a message over the net about something > better than "nice" (which hardly works at all). Can anyone tell me > how to keep background jobs from slowing foreground jobs to a > crawl? Thanks. > -Don Williams ------------- Return-path: Received: from mailhub.cc.columbia.edu by ULKYVX.LOUISVILLE.EDU (PMDF V4.2-11 #3949) id <01H8GHNG56QO8WY4OB@ULKYVX.LOUISVILLE.EDU>; Thu, 3 Feb 1994 17:58:10 EST Received: from still3.chem.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA12656 (5.65c+CU/IDA-1.4.4/HLK for WILLIAMS%XRAY2@ULKYVX.LOUISVILLE.EDU); Thu, 3 Feb 1994 17:59:30 -0500 Received: by still3.chem.columbia.edu (930416.SGI/930416.SGI.AUTO) for @cunixf.cc.columbia.edu:chemistry@ccl.net id AA22244; Thu, 3 Feb 94 17:59:28 -0500 Date: Thu, 03 Feb 1994 17:59:28 -0500 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Subject: RE: CCL:Deprioritizing SGI unix runs To: WILLIAMS%XRAY2@ULKYVX.LOUISVILLE.EDU, chemistry@ccl.net Message-id: <9402032259.AA22244@still3.chem.columbia.edu> Content-transfer-encoding: 7BIT > From: > Date: Thu, 03 Feb 1994 14:21:38 -0500 (EST) > Precedence: bulk > > I recall that there was a message over the net about something > better than "nice" (which hardly works at all). Can anyone tell me > how to keep background jobs from slowing foreground jobs to a > crawl? Thanks. "man npri"; example: (as superuser, unless it's your job): npri -h 150 -p will give the existing job a non-degrading priority of 150. High priorities (like high "nice" values) slow the process down. 150 is a good value for background jobs which should never preempt interactive work to a significant extent. In other words, a job with this priority, if it's the only user process on the system, will use 99+% of the CPU (e.g., at night), but it will use essentially 0% if someone is at the console interacting with, say, a molecular graphics program. The difference between npri and nice is that npri gives a *non- degrading* priority. "nice" affects the aging of priorities. You can also say, "npri -h 150 " to start up a job with a non-degrading priority of 150. Hope this helps.... -P. ***************************************************************************** ********************** "So much for global warming...." ********************* Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 -------------- Return-path: Received: from mserv.rug.ac.be by ULKYVX.LOUISVILLE.EDU (PMDF V4.2-11 #3949) id <01H8GZEGIWI88WYNBA@ULKYVX.LOUISVILLE.EDU>; Fri, 4 Feb 1994 02:26:18 EST Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA29773 (5.65c/IDA-1.4.4 for ); Fri, 4 Feb 1994 08:27:22 +0100 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA01137; Fri, 4 Feb 94 08:24:51 +0100 Date: Fri, 04 Feb 1994 08:24:50 +0100 (MET) From: Kris Boulez Subject: RE: CCL:Deprioritizing SGI unix runs In-reply-to: <01H8GA1EJWOY8WXIBT@ULKYVX.LOUISVILLE.EDU> To: WILLIAMS%XRAY2@ULKYVX.LOUISVILLE.EDU Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Content-Length: 270 Hello Look for the manual page on 'npri'. Giving the command 'npri -n 39 -p pid' gives the proces with proces id pid the lowest priority and it isn't hardly noticed any more that it runs. Best regards, Kris Boulez Biomolecular NMR unit University of Gent Belgium ----------------- Return-path: Received: from mail.netcom.com (netcom2.netcom.com) by ULKYVX.LOUISVILLE.EDU (PMDF V4.2-11 #3949) id <01H8GFH1ZDM88WWIP4@ULKYVX.LOUISVILLE.EDU>; Thu, 3 Feb 1994 16:55:44 EST Received: from localhost by mail.netcom.com (8.6.4/SMI-4.1/Netcom) id NAA21114; Thu, 3 Feb 1994 13:57:51 -0800 Date: Thu, 03 Feb 1994 13:55:56 -0800 (PST) From: Didier Vanderveken Subject: RE: CCL:Deprioritizing SGI unix runs In-reply-to: <01H8GA1EJWOY8WXIBT@ULKYVX.LOUISVILLE.EDU> To: WILLIAMS%XRAY2@ULKYVX.LOUISVILLE.EDU Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Take a look at "npri"... It's really better than "nice". I'm using a priority around 150 for background jobs. Didier --------------- Return-path: Received: from hau410.uk.sb.com by ULKYVX.LOUISVILLE.EDU (PMDF V4.2-11 #3949) id <01H8H0PUK6S08WZ6PC@ULKYVX.LOUISVILLE.EDU>; Fri, 4 Feb 1994 03:03:48 EST Received: by hau410.uk.sb.com (920330.SGI/921111.SGI.ANONFTP) for WILLIAMS%XRAY2@ULKYVX.LOUISVILLE.EDU id AA03507; Fri, 4 Feb 94 08:04:54 GMT Date: Fri, 04 Feb 1994 08:01:42 +0000 (GMT) From: Mike Tennant Subject: RE: CCL:Deprioritizing SGI unix runs In-reply-to: <01H8GA1EJWOY8WXIBT@ULKYVX.LOUISVILLE.EDU> To: WILLIAMS%XRAY2@ULKYVX.LOUISVILLE.EDU Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT On Thu, 3 Feb 1994 WILLIAMS%XRAY2@ULKYVX.LOUISVILLE.EDU wrote: > I recall that there was a message over the net about something > better than "nice" (which hardly works at all). Can anyone tell me > how to keep background jobs from slowing foreground jobs to a > crawl? Thanks. Hi Don, there's only really a couple of ways to affect a running job. Using the npri command you can decrease the amount of CPU time and the nice value (which, as you said, isn't very good) a process has. You can also do a kill -20 pid to suspend a job (kill -28 pid restarts it). Unfortunately, neither of these will free the memory a process is using, so if it's using a lot of memory, SGI has no solution! cheers, Mike. _____________________________________________________________________________ | _____ ____ || SmithKline Beecham Pharmaceuticals Ltd | | / ___\\\\ _ \ || Coldharbour Rd | | | |___ \\|_| | || Harlow | | \____ \ | _ < || Essex | | ___| | | |_| | || CM19 5AD | | \_____/ |____/ || England | | || Harlow (0279) 622000x3328 | |_________________________________||__________________________________________| | | | Mike Tennant | | Email: tennant%hau410.uk.sb.com@phinet.sb.com | |*****************************************************************************| | 'Do you have 2 fives for a ten?' M. Jackson to W. Allen. | ------------------------------------------------------------------------------- ----------------- Return-path: Received: from cumbnd.bioc.columbia.edu by ULKYVX.LOUISVILLE.EDU (PMDF V4.2-11 #3949) id <01H8HI8UKLOW8WYIZF@ULKYVX.LOUISVILLE.EDU>; Fri, 4 Feb 1994 11:25:30 EST Received: from sirius by cumbnd.bioc.columbia.edu (NX5.67d/NX3.0M) id AA05318; Fri, 4 Feb 94 11:26:46 -0500 Received: by sirius.bioc.columbia.edu (NX5.67d/NX3.0X) id AA00710; Fri, 4 Feb 94 11:26:46 -0500 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) Date: Fri, 04 Feb 1994 11:26:46 -0500 From: Andreas Windemuth Subject: RE: CCL:Deprioritizing SGI unix runs To: WILLIAMS%XRAY2@ULKYVX.LOUISVILLE.EDU Cc: windemut@cumbnd.bioc.columbia.edu Message-id: <9402041626.AA05318@cumbnd.bioc.columbia.edu> Content-transfer-encoding: 7BIT Don, There are only three ways to do what you want: 1) Suspend background jobs completely while you are at the console ("kill -STOP" or "kill -17", resume jobs with "kill -CONT" or "kill -19") 2) run jobs that use less memory 3) get more memory for your machine background/foreground interference is almost always due to memory contention, not cpu contention. "nice" only works for cpu-time. I don't think there is a way to restrict a jobs access to virtual memory, other than suspending it. Andreas Windemuth +-------------------------------------------------------------------- |Columbia University, Department of Biochemistry and Biophysics |630 West 168th St. BB-221 | tel: (212)-305-6884, fax: 6926, NeXTmail |New York, NY 10032 | email: windemut@cumbnd.bioc.columbia.edu +-------------------------------------------------------------------- ---------------- Return-path: Received: from sgi1 (sgi1.wag.caltech.edu) by ULKYVX.LOUISVILLE.EDU (PMDF V4.2-11 #3949) id <01H8GCPFBNIO8WY71I@ULKYVX.LOUISVILLE.EDU>; Thu, 3 Feb 1994 15:36:16 EST Received: by sgi1 id AA11455 (931110.SGI/IDA-1.4.4); Thu, 3 Feb 94 12:37:35 -0800 Date: Thu, 03 Feb 1994 12:37:35 -0800 From: "Terry R. Coley" Subject: RE: CCL:Deprioritizing SGI unix runs To: WILLIAMS%XRAY2@ULKYVX.LOUISVILLE.EDU Cc: terry@wag.caltech.edu, dewill01@ULKYVX.LOUISVILLE.EDU Message-id: <9402032037.AA11455@sgi1> Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Don, I suggest you try "Nanny" which can be obtained from ftp.wag.caltech.edu:/pub/nanny. I am biased because I am one of the creators of the program, but it works very well in our computational chemistry test site at Caltech. Nanny uses SGI non-degrading priorities to guarantee good interactive response while letting batch jobs only fill background cycles. Send me mail if you need assistance trying it out. Regards, - Terry Terry R. Coley terry@Pgrams.COM Parallelograms PO Box AA Pasadena, CA 91102 818-577-5515 Voice/Fax From loup@sasg019.fuelan.sandia.gov Mon Feb 7 13:20:41 1994 Received: from sasg019.fuelan.sandia.gov for loup@sasg019.fuelan.sandia.gov by www.ccl.net (8.6.4/930601.1506) id MAA00344; Mon, 7 Feb 1994 12:32:12 -0500 Received: by sasg019.fuelan.sandia.gov (920330.SGI/920502.SGI) for CHEMISTRY@ccl.net id AA06269; Mon, 7 Feb 94 10:22:46 -0700 Date: Mon, 7 Feb 1994 10:19:20 -0700 (MST) From: Jean-loup Faulon Subject: ACS Computational Geochemistry Symposium To: CHEMISTRY@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-2068873470-1826959599-760641765:#6194" ---2068873470-1826959599-760641765:#6194 Content-Type: TEXT/PLAIN; charset=US-ASCII ---2068873470-1826959599-760641765:#6194 Content-Type: APPLICATION/octet-stream; name=ACS Content-ID: Content-Description: ***************************************************************************** CALL FOR PAPER Symposium on Molecular Modeling in Geochemical Sciences (First Annoucement) ACS Geochemistry Div. Washington, DC Aug. 21-25, 1994. Organizers Patrick G. Hatcher Jean-Loup Faulon Penn State University Sandia National Laboratories 209 Acadenic Project Bldg., P.O. Box 5800, University Park, PA 16802 Albuquerque, NM 87185-0710 Ph : (814) 865-7838 Ph : (505) 844-3186 Fax: (814) 865-3075 Fax: (505) 845-9500 e-mail: loup@fuelan.sandia.gov loup@geosc.psu.edu ***************************************************************************** Scope of the meeting A symposium sponsored by the Geochemistry division of the American Chemical Society will be hold at the ACS Washington meeting in August 94. Applications of computational chemistry to geochemical sciences will be considered. MO calculations, molecular simulations, sorption simulations, and computer-aided structure elucidation are possible topics if they are related to organic or inorganic geochemistry. Four copies of 150-words abstract (original on ACS Abstract Form) have to be sent to the organizers by April 1, 1994. Jean-Loup Faulon ---2068873470-1826959599-760641765:#6194-- From wsn-adm@mmlds1.pha.unc.edu Mon Feb 7 14:24:31 1994 Received: from mmlds1.pha.unc.edu for wsn-adm@mmlds1.pha.unc.edu by www.ccl.net (8.6.4/930601.1506) id OAA01762; Mon, 7 Feb 1994 14:00:58 -0500 Received: by mmlds1.pha.unc.edu (5.57/TAS/11-16-88) id AA05098; Mon, 7 Feb 94 14:04:42 -0500 Date: Mon, 7 Feb 1994 14:01:42 -0500 (EST) From: Water Science Network Administrator Subject: Water Science Network - new discussion list To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Water Science Network (WSN) : Physics, Chemistry and Biology of Water and Aqueous Systems WSN is an interdisciplinary forum for scientists interested in physical and chemical properties of water and aqueous solutions, and in the role water plays in biological systems. WSN is created to facilitate communication between experimental and theoretical scienists with different bacgrounds, whose research interests are related to: * water structure and hydrogen bond network * thermodynamic and kinetic properties of water * phase transitions in water * hydrophobic effects * hydration forces * water around solutes and water at interfaces * hydration of biomolecules * water in membranes * water in cell * experimental techniques for studying water properties * computer simulations of water Postings to the WSN would contain: * discussions of new ideas and developments in related fields * questions and answers about particular problems * bibliographic information on current and forthcoming books and articles * information on funding sources * meeting announcements * position announcements * product and service announcements To subscribe to the WSN, send to listserv@gibbs.oit.unc.edu a one-line message: subscribe water Your Name Your e-mail address will be recorded from the header of your message, so all WSN postings would be send to the account where the subscription request came from. Contributions sent to the WSN are automatically archived. Archives would be available for search using various network information search tools. Please feel free to forward this announcement to all interested parties. WSN coordinator: Iosif Vaisman (wsn-adm@mmlds1.pha.unc.edu or vaisman@gibbs.oit.unc.edu) Laboratory for Molecular Modeling School of Pharmacy University of North Carolina at Chapel Hill From marty@ionchannel.med.harvard.edu Mon Feb 7 15:20:56 1994 Received: from ionchannel.med.harvard.edu for marty@ionchannel.med.harvard.edu by www.ccl.net (8.6.4/930601.1506) id OAA02590; Mon, 7 Feb 1994 14:37:53 -0500 Received: by ionchannel.med.harvard.edu (931110.SGI/931108.SGI.AUTO.ANONFTP) for CHEMISTRY@ccl.net id AA16450; Mon, 7 Feb 94 11:40:51 -0800 Date: Mon, 7 Feb 94 11:40:51 -0800 From: marty@ionchannel.med.harvard.edu (Marty Gallagher) Message-Id: <9402071940.AA16450@ionchannel.med.harvard.edu> To: CHEMISTRY@ccl.net Subject: rational drug design On Friday I asked about the successful rational design of an HIV protease inhibitor. I have two corrections to that post 1.) It is in Science vol 263, not vol 23 (typo) 2.) The group is from Dupont-Merck which is not the same thing as Merck (my ignorance) -- Didn't we have a post a while back on corporate names? Hope these corrections help. -- Marty ======================================================================== Martin J. Gallagher phone: (617) 432-1729 Dept. of Neurobiology fax: (617) 734-7557 Harvard Medical School E-mail: marty@ionchannel.med.harvard.edu 220 Longwood Ave Boston, MA 02115 Neither Schrodinger nor Einstein "suberted the dominant paradigm." Rather, they complemented it in order to descibe areas of the Ultimate Reality that Newton did not see. Those who categorically reject tradition in order to avoid conformity are still bound by it. Those who seek truth for truth's sake are truly free. -- Me From ZPZCM@jazz.ucc.uno.edu Mon Feb 7 15:22:09 1994 Received: from jazz.ucc.uno.edu for ZPZCM@jazz.ucc.uno.edu by www.ccl.net (8.6.4/930601.1506) id OAA02602; Mon, 7 Feb 1994 14:38:38 -0500 Received: from jazz.ucc.uno.edu by jazz.ucc.uno.edu (PMDF #2820 ) id <01H8LTMORK5W8X16ZO@jazz.ucc.uno.edu>; Mon, 7 Feb 1994 13:38:14 CST Date: 07 Feb 1994 13:38:14 -0600 (CST) From: "Zoran P. Zdravkovski" Subject: IGLO summary To: chemistry@ccl.net Message-id: <01H8LTMORK5Y8X16ZO@jazz.ucc.uno.edu> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hello, Thanks to all who answered (and had questions) on my posting about the IGLO program. I tried to contact Ulrich Fleischer by e-mail but have not been successful yet. Zoran Zdravkovski Department of Chemistry University of New Orleans Original posting: Saw recently a reference to the IGLO (Individual Gauge for Localized Orbitals) method for calculating chemical shifts. Any information as on what platforms it runs, resources it requires, references, and how to obtain it would be appreciated. Replies: ********* Contact Ulrich.Fleischer@RUBA.RZ.ruhr-uni-bochum.de for info pertaining IGLO Cheers, Margot ********* Hi, I know that IGLO runs on an IBM RS/6000 (and other systems). For more details contact Ulrich Fleischer in Bochum (ulrich.fleischer@ruba.rz.ruhr-uni-bochum.de). He is one of the authors and can tell you also how to get the program. Joerg-R. Hill ********* Dear Dr. Zdravkovski, IGLO is an ab initio approach for calculation of susceptibilities and NMR chemical shieldings. I would suggest that you contact Dr. Michael Schindler at the following address for more information: Bayer AG, ZF-DID D-5090 Leverkusen Germany The only literature I have on IGLO is in the form of preprints or Seminarvortrag notes (in German). Sorry I cannot point you to more helpful references. I am told IGLO methods are really the best to date for shift calculations. Paul Weber NMR Product Manager Tripos Associates ********* Hello the best reference I know is: W. Kutzelnigg, U. Fleischer, M. Schindler NMR Basic Principles and Progress: 23 (1990) 165 Springer Verlag: "The IGLO - Method: Ab-initio Calculation and Interpretarion of NMR Chemical Shifts and Magneric Susceptibilities." the program was developed by the group of Kutzelnigg in Bochum Germany and is available as unix quellcode which should not be difficult to adapt at new platforms, but the input is quite user-unfriendly in fact I believe that the program is distributed only after a learning visit in bochum but I am not shure. there is a new direct version which runs with turbomole they have developed together with bayer. alberto %%% ***** % % # %%% | | Y ========================================================= Alberto Gobbi gobbi@sg1501.chemie.uni-marburg.de Bantzerstr. 9 137.248.151.1 D-35039 Marburg Tel. 8.00-18.00: 0049 6421 285549 Fax: 0049 6421 285547 ********** Contact Ulrich.Fleischer@ruba.rz.ruhr-uni-bochum.de regards, Wolfgang. -- +======================================+=====================================+ | Wolfgang Sauer | | Institut fuer Organische Chemie I | Computational Chemistry Centre | | Henkestr. 42 | Naegelsbachstr. 25 | | D-91054 Erlangen, FRG | D-91052 Erlangen, FRG | | sauer@organik.uni-erlangen.de | | Tel.: +49/0 - 9131 - 85 - 2952 | Tel.: +49/0 - 9131 - 85 - 6582 | | Fax: - 9132 | Fax: - 6566 | +======================================+=====================================+ | "You have to be three standard deviations away from a normal personality | | to like UNIX." Morris Jones (C&T) | +======================================+===================================== ********** From CHEM8@VAX.YORK.AC.UK Mon Feb 7 16:20:30 1994 Received: from sun2.nsfnet-relay.ac.uk for CHEM8@VAX.YORK.AC.UK by www.ccl.net (8.6.4/930601.1506) id PAA03129; Mon, 7 Feb 1994 15:20:25 -0500 Message-Id: <199402072020.PAA03129@www.ccl.net> Via: uk.ac.york.vax; Mon, 7 Feb 1994 19:37:20 +0000 Date: Mon, 7 Feb 94 19:36 GMT From: "John Waite, Tel 1-7238958, N.H.R.F., Vas. Konstantinou 48, Athens 116-35" To: CHEMISTRY Subject: Di-Ruthenium complexes, multiplicities? Hi Netters, Does anyone know the more generally prefered multiplicity of di-Ruthenium complexes? Any references concerning calculations on such systems would probably be useful. Hopefully, John Waite (chem8@vax.york.ac.uk) From SAUNDERS@chem.chem.rochester.edu Mon Feb 7 16:21:37 1994 Received: from chem.chem.rochester.edu for SAUNDERS@chem.chem.rochester.edu by www.ccl.net (8.6.4/930601.1506) id PAA03517; Mon, 7 Feb 1994 15:43:46 -0500 From: Received: from UORCHEM by UORCHEM (PMDF #12506) id <01H8LY32ONHS0002P4@UORCHEM>; Mon, 7 Feb 1994 15:42 EDT Date: Mon, 7 Feb 1994 15:42 EDT Subject: basis sets for bromine To: chemistry@ccl.net Message-id: <01H8LY32ONHS0002P4@UORCHEM> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Hello We have been engaged in Gaussian 92 calculations on methyl halides and their conjugate bases at the 6-31+G* level. Gaussian 92 contains built-in basis sets at this level only for fluorine and chlorine. Can anyone suggest a good basis set for bromine at this level or at an approximately equivalent level? We have done a literature search but would appreciate some help on how to choose the best set for our purposes. Does anyone have experience on alkyl halides with basis sets that use effective core potentials? Bill Saunders From msennet@watertown-emh1.army.mil Mon Feb 7 16:22:19 1994 Received: from mitvma.mit.edu for msennet@watertown-emh1.army.mil by www.ccl.net (8.6.4/930601.1506) id PAA03302; Mon, 7 Feb 1994 15:22:16 -0500 Message-Id: <199402072022.PAA03302@www.ccl.net> Received: from watertown-emh1.army.mil by mitvma.mit.edu (IBM VM SMTP V2R2) with TCP; Mon, 07 Feb 94 15:21:37 EST Date: Mon, 7 Feb 94 15:16:34 EST From: Michael Sennett To: chemistry%ccl.net@MITVMA.MIT.EDU Subject: High Cost of Comp. Chem. Dear netters, In the past there has been some discussion here about quantifying the value of computational chemistry activities to various organizations, principally industrial firms which want a certain rate of return on any investment made in R&D. These discussions have generally revolved around the notion that we (modelers, simulators, theorists, or whatever..) need a collection of case studies or success stories which we can publicize to enhance the image of the field in the eyes of the R&D managers who are asked to fund our efforts. The response to calls for such success stories never seems to be forthcoming to any great extent, probably because (as has been previously pointed out) any such stories would involve proprietary information which cannot be disclosed. Also, it is difficult to assess the value of "negative success." By this I mean the scenario where the modeling group advises the synthesis group NOT to proceed with the preparation of their proposed compound based on the results of simulations. Is the modeling group credited with saving the organization the hundreds or thousands of man-hours the synthetic project would have consumed? Not likely. At any rate, there are two sides to the cost/benefit ratio being considered here. Since we can't get a firm grip on the benefits (for whatever reasons), what about the costs? I bring this up since I find myself in a bind which I expect is extremely common, though I don't think I've seen it discussed explicitly. The situation is this: After making a substantial (don't ask for specifics.... this will be the proprietary part of THIS end of the equation) investment in hardware and software to inaugurate a molecular modeling effort a VERY few years ago, and paying maintenance fees (large enough to be noticed by the budget analysts) in the meantime, we find ourselves with FUNCTIONALLY OBSOLETE hardware, the capabilities of which have been largely outstripped by upgrades of: a) the application software b) the OPERATING SYSTEM (for crying out loud) This revolting development comes about as a result of a series of events that goes something like this.... 1) You need software support both for the applications and the OS. You have a staff of people whose principal training is in chemistry using the application. You don't have dedicated programmers or software developers or system operators. You have to have on-line support to keep the system going when bugs, etc. are encountered. You also find the support of the software vendor valuable in developing your applications for the software. So..... 2) You procure software maintenance, which includes phone support AND periodic software upgrades. These agreements typically require you to be running the current release of software. You may get away with being one version behind but no more than that. But.... 3) Each new release has more capabilities. Which is great, right? Except that these additional capabilities demand additional hardware resources. But.... 4) Your hardware isn't being upgraded at the same rate as your software. Hardware doesn't upgrade the same way that software does. It is rarely economical to upgrade a CPU with hardware "patches"... discard and replace is the only cost effective thing to do. But.... 5) Your budget division says you JUST BOUGHT a lot of expensive hardware. Even very up-to-date R&D managers have a hard time swallowing the idea of total system obsolescence in a 3-year period. Word processing hardware lasts longer than that.... so do the computer controllers on typical lab instruments. There are plenty of PC-AT's still happily running IR's, HPLC's and a whole bunch of other analytical equipment. 6) So the answer is just to stand still, right? That is, don't upgrade hardware or software for as long as possible. If it ain't broke, don't fix it....? This will work only as long as something doesn't break, which probably won't be long. If your hardware holds out, you are bound to try something new with the software which will cause a problem. When you call for support, you find that the problem was fixed in an upgrade (which you didn't get) or that no one will talk to you about your situation since you aren't running the current software release. So... 7) You try to get funding to upgrade your system.... So the R&D manager wants to see what the money so far invested has purchased, and you end up back on the BENEFIT side of the equation, which we have seen is hard to quantify. (Especially for a non-profit organization). Faced with this situation, only individuals with extremely high levels of vision, intestinal fortitude and conviction will opt to continue to spend the kind of resources necessary to operate a molecular modeling activity based on the big commercial software packages. It is easy to see how this kind of scenario can and probably will force (or keep) small industrial labs and even many government labs out of computational chemistry or keep them on the fringes in terms of the level of theory or size of calculations being performed. This in turn delays the realization of the enormous potential of computational chemistry (I'm biased) and makes it hard on the ever-increasing number of computational chemistry graduates being turned out by academia. There is also the potential for backlash by the R&D management community against computational chemistry (modeling, simulation etc...) (this idea has been mentioned in previous cost/benefit discussions) which could lead to retrograde steps for the field as a whole. The academics can continue to play, aided by enormously discounted licensing fees and what I perceive as generally easier access to high performance computing than the average industrial R&D facility. Sure, you don't have to buy the big commercial software packages. You can go to QCPE and get a whole suite of programs for relatively small change that will enable you to do lots of valuable things. But this collection of software still has to be mastered and maintained. Also, there is no real universal molecular data format which guarantees the interoperability of all these applications, so your comp. chem. staff has to divert its time from working on chemical development to working on the software applications themselves. What is gained through reduced software costs is lost to increased labor costs, reduced productivity, etc. Well, what is to be done? At the risk of opening the floodgates, I'd be interested in seeing some discussion of this issue. Is this experience as common as I think? Is everyone else's comp. chem. program thriving? How can small R&D organizations maintain high-level molecular modeling capabilities long enough for the value of the methods to be "proven?" The experience of the pharmaceutical industry should be relevant here. Computational chemistry is a pretty secure fixture in that industry (or so it seems to me), but it wasn't always this way. How did computational chemistry come to be accepted as a valuable and necessary part of an R&D operation in the drug industry? Are the issues addressed by the modeling efforts in pharmaceutical firms so much more tractable than those of interest to materials scientists (by virtue of being focused on small molecules and on bi-molecular, i.e. probe-receptor, interactions) ? I look forward to seeing people's comments. Michael Sennett ***************** disclaimer ******************* The ideas and opinions expressed above are entirely my own and do not represent the position or policy of any other person or agency whatsoever. ************************************************** From dufner@ws01.pc.chemie.th-darmstadt.de Mon Feb 7 18:20:34 1994 Received: from rs2.hrz.th-darmstadt.de for dufner@ws01.pc.chemie.th-darmstadt.de by www.ccl.net (8.6.4/930601.1506) id SAA04973; Mon, 7 Feb 1994 18:01:07 -0500 Received: from ws01.pc.chemie.th-darmstadt. (ws01.pc.chemie.th-darmstadt.de) by rs2.hrz.th-darmstadt.de with SMTP id AA35769 (5.65c/IDA-1.4.4 for <@rs2.hrz.th-darmstadt.de:chemistry@ccl.net>); Tue, 8 Feb 1994 00:01:03 +0100 Received: by ws01.pc.chemie.th-darmstadt.de (5.52/9106280.SGI) (for @rs2.hrz.th-darmstadt.de:chemistry@ccl.net) id AA12953; Tue, 8 Feb 94 00:00:58 CET Date: Tue, 8 Feb 94 00:00:58 CET From: dufner@ws01.pc.chemie.th-darmstadt.de (Hagen Dufner) Message-Id: <9402072300.AA12953@ws01.pc.chemie.th-darmstadt.de> To: chemistry@ccl.net Subject: G92 and key word CHARGE Hi netters, I have a question concerning the external point charges incorporated in the Hamiltonian of an HF-calculation. What I want to know, how does GAUSSIAN handle the point charges when the key word CHARGE is chosen? How does the potential term look like? Is it V=V(ab initio model) + 0.5*(SUM[I=1,M]SUM[J=1,M](qI*qJ/rI-rJ)) + SUM[i=1,m]SUM[J=1,M](Zi*qJ/ri-rJ) with upper-case indices for point charges and lower-case indices for ab initio atoms q: point charge Z: nuclear charge of ab initio atom Thanks a lot for help # #+----------------------------------------------+ #| Hagen Dufner | #| Technische Hochschule Darmstadt | #| Physikalische Chemie I | #| Petersenstr. 20 | #| 64287 Darmstadt, Germany | #| Phone: (+int) 6151 165397 | #| Fax: (+int) 6151 164298 | #| Network : | #+----------------------------------------------+ From pbays@saintmarys.edu Mon Feb 7 19:21:14 1994 Received: from jade.saintmarys.edu for pbays@saintmarys.edu by www.ccl.net (8.6.4/930601.1506) id TAA05384; Mon, 7 Feb 1994 19:02:05 -0500 Received: by jade.saintmarys.edu (1.37.109.8/16.2) id AA16786; Mon, 7 Feb 1994 19:06:03 -0500 Date: Mon, 7 Feb 1994 19:06:02 -0500 (EST) From: Phil Bays Subject: MM3/SYBYL To: Chemistry Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone have a quick and dirty unix program (SGI) for quickly interconverting SYBYL Mol or MOL2 files to MM3 format, and back? Phil Bays pbays@saintmarys.edu From garlima@uspif.if.usp.br Mon Feb 7 19:24:42 1994 Received: from USPIF.IF.USP.BR for garlima@uspif.if.usp.br by www.ccl.net (8.6.4/930601.1506) id SAA05312; Mon, 7 Feb 1994 18:51:21 -0500 From: Received: by uspif.if.usp.br (MX V3.3 VAX) id 23479; Mon, 07 Feb 1994 21:51:31 GMT-03:00 Date: Mon, 07 Feb 1994 21:49:23 GMT-03:00 To: chemistry@ccl.net Message-ID: <00979B8B.A9E314E0.23479@uspif.if.usp.br> Subject: CCL:CAOS Computer Aided Organic Syntesis Dear Netters Does anyone know where I can find CAOS (Computer Aided Organic Syntesis ) software, commercial or any public domain site. Please send replay to the e-mail below.The summary will be placed in the CCL. garlima@uspif.if.usp.br thank you in advance. Dr. G.A.R.Lima From raman@bioc01.uthscsa.edu Mon Feb 7 20:21:15 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.4/930601.1506) id UAA06475; Mon, 7 Feb 1994 20:12:44 -0500 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Mon, 7 Feb 1994 19:13:30 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA24447; Mon, 7 Feb 94 19:13:06 CST From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9402080113.AA24447@bioc01.uthscsa.edu> Subject: Fractal space To: chemistry@ccl.net Date: Mon, 7 Feb 1994 19:13:05 -0600 (CST) X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1195 Dear netters: Does anyone use Levy statistics in random processes that are scale-invariant? By this I mean, a trajectory which will contain many different scales, but no ONE scale will necessarily dominate the process. So, in fractal space, is "A SUM OF GAUSSIANS = A GAUSSIAN"? I would appreciate receiving proofs and explanations if anyone has access to the same. Any references that discuss this problem are also welcome! Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ******************************************************************************