From rks2@crux2.cit.cornell.edu Tue Feb 8 09:21:29 1994 Received: from crux2.cit.cornell.edu for rks2@crux2.cit.cornell.edu by www.ccl.net (8.6.4/930601.1506) id IAA12967; Tue, 8 Feb 1994 08:31:08 -0500 Received: by crux2.cit.cornell.edu (5.65/2.0) id AA08090; Tue, 8 Feb 1994 08:30:04 -0500 Date: Tue, 8 Feb 1994 08:30:03 -0500 (EST) From: "Rebecca K. Schmidt" Subject: Automatic UNIX backups To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello: Does anyone have a shell script to perform an automatic backup of UNIX system (IBM RS6000) to a dat tape drive on a daily basis? I want the computer to signal the user to insert a tape every day, and then all the rest is done automatically with minimal interference once the original shell script is written. Please reply to rks2@cornell.edu. Thank you, Rebecca Schmidt Cornell University From thondorf@biochemtech.uni-halle.d400.de Tue Feb 8 11:20:44 1994 Received: from ixgate01.dfnrelay.d400.de for thondorf@biochemtech.uni-halle.d400.de by www.ccl.net (8.6.4/930601.1506) id KAA15032; Tue, 8 Feb 1994 10:42:20 -0500 From: Received: from ixgate02.dfnrelay.d400.de by ixgate01.dfnrelay.d400.de with SMTP (PP); Tue, 8 Feb 1994 16:42:54 +0100 X400-Received: by mta d400relay in /PRMD=dfnrelay/ADMD=d400/C=de/; Relayed; Tue, 8 Feb 1994 16:42:08 +0100 X400-Received: by /PRMD=UNI-HALLE/ADMD=D400/C=DE/; Relayed; Tue, 8 Feb 1994 16:40:29 +0100 Date: Tue, 8 Feb 1994 16:40:29 +0100 X400-Originator: thondorf@biochemtech.uni-halle.d400.de X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=UNI-HALLE/ADMD=D400/C=DE/;mlumta1279940208164029-B0X] X400-Content-Type: P2-1984 (2) Message-ID: <940208164029*/S=thondorf/OU=biochemtech/PRMD=UNI-HALLE/ADMD=D400/C=DE/@MHS> To: CHEMISTRY@ccl.net Subject: activation barrier Hi netters, I was wondering whether someone can help me with the following problem: I have done several molecular dynamics simulations of an organic ring system at different temperatures using SYBYL. At "low" temperatures only one conformation could be detected (< 2000 K), whereas at high temperatures (> 2000 K) an additional conformation occurs. Can I draw any conclusions on the height of the activation barrier between the two conformations from the dynamics runs? Many thanks in advance. Iris. ---- Iris Thondorf Department of Biochemistry and Biotechnology Martin-Luther-University D-06099 Halle, Germany e-mail: thondorf@biochemtech.uni-halle.d400.de From srheller@asrr.arsusda.gov Tue Feb 8 11:24:20 1994 Received: from asrr.arsusda.gov for srheller@asrr.arsusda.gov by www.ccl.net (8.6.4/930601.1506) id KAA15070; Tue, 8 Feb 1994 10:52:40 -0500 Message-Id: <199402081552.KAA15070@www.ccl.net> Date: 8 Feb 94 10:53:00 EDT From: "STEPHEN R. HELLER" Subject: ACS Book Series on Computers in Chemistry To: "chem-l" cc: "chminf-l" , "chemistry" , "orgchem" 8 February, 1994 ANNOUNCEMENT The ACS has initiated a new Computers in Chemistry - Reference Book Series. I have been appointed over-all editor of the series. The goal of the ACS is to produce a series of books which will be useful reference books in various areas of computer chemistry. This is NOT a book series for symposia or other highly timely, but narrow areas. The ACS will continue to publish the ACS Symposium Series of books. Each book in the series will be written and/or edited by various individuals who are experts in their respective areas of computer chemistry. The first book in this series in now going into production. It is by Hansch & Leo - "QSAR in Chemistry & Biology". This message is a "call for authors". I would like to hear from anyone who is interested in writing or editing a book for this series. A number of areas come to mind, such as: 1. Applications of Super Computers 2. Internet/Telecommunications/Computer Networks 3. Molecular Modeling/Drug Design 4. LIMS 5. Polymer Modeling 6. Neural Networks 7. Data Analysis/Curve Fitting Software 8. 2D/3D Structure Searching 9. Data Standards/Data Exchange/Interchange If anyone is interested in this project, please contact me by INTERNET, mail, FAX, or phone: Stephen R. Heller Informatics Project Leader Plant Genome Research Program USDA, ARS, BARC-West Building 005, Room 337 Beltsville, MD 20705-2350 USA Phone: 301-504-6055 FAX: 301-504-6231 INTERNET: SRHELLER@ASRR.ARSUSDA.GOV To initiate the ACS review of any proposed book for this series I will need, at least, a tentative title, outline, list of chapters, and authors. From rbw@msc.edu Tue Feb 8 11:27:39 1994 Received: from mitvma.mit.edu for rbw@msc.edu by www.ccl.net (8.6.4/930601.1506) id LAA15243; Tue, 8 Feb 1994 11:11:18 -0500 Received: from noc.msc.edu by mitvma.mit.edu (IBM VM SMTP V2R2) with TCP; Tue, 08 Feb 94 11:11:21 EST Received: from uh.msc.edu by noc.msc.edu (5.65/MSC/v3.0.1(920324)) id AA19749; Tue, 8 Feb 94 10:10:19 -0600 Received: by uh.msc.edu (5.65/MSC/v3.1r(920220)) id AA21940; Tue, 8 Feb 94 10:10:18 -0600 Date: Tue, 8 Feb 94 10:10:18 -0600 From: rbw@msc.edu (Richard Walsh) Message-Id: <9402081610.AA21940@uh.msc.edu> To: chemistry%ccl.net@MITVMA.MIT.EDU, msennet@watertown-emh1.army.mil Subject: Re: CCL: High Cost of Comp. Chem. Michael, That was a nice summary of the problems individuals and small sized working groups in industry have down stream when a first generation computational chemistry infrastructure begins to age. A dollar spent in upgrading does not buy the same marginal improvment in capability in the second or nth generation. And maintaining currency costs huge amounts of time away from the job one has really been hired to do (even when one has the budget to try to maintain it). These direct costs are further magnified when R&D opportunities are lost as computational chemists perform system administrative functions. In a large general manufacturing company with which I am very familiar which has perhaps a dozen working groups and hundreds of individuals with workstations, these costs explode, but are at the same time are hard to account for. One way to minimize this is to have a tap from ones local resource into an external resource whose sole function is to provide current hardware and software, and which is sustained by income from multiple sources/users. By adding depth to ones resources across a network, the life of the resources available in ones office can be extended and you can reduce the time spent maintaining their currency. The commercial customers that we have use us for precisely these reasons. We upgrade the hardware and maintain the operating system; we get the new versions of GAUSSIAN, MOPAC, or what have you and install them; and we try to maintain as tight a coupling to the office resource as possible with software of our own and third parties. Unlike centralized facilities on the inside, if we don't perform, the customer can go elsewhere. I would not want to suggest that outsourcing is a panacea, but to me it clearly has something to offer on this subject. Richard Walsh Minnesota Supercomputer Center, Inc. Chemistry Applications Support From XIANZ@ASUCHM.LA.ASU.EDU Tue Feb 8 14:20:44 1994 Received: from ASUCHM.LA.ASU.EDU for XIANZ@ASUCHM.LA.ASU.EDU by www.ccl.net (8.6.4/930601.1506) id NAA16841; Tue, 8 Feb 1994 13:43:38 -0500 From: Date: Tue, 8 Feb 1994 11:43:36 -0700 (MST) To: chemistry@ccl.net Message-Id: <940208114336.8143@ASUCHM.LA.ASU.EDU> Subject: memory/swap problem with SGI Indigo Hi netters, I have memory/swap problem with running my program on Indigo. We have 32Mbytes memory on that machine. The physical requirment of my program is 42.3Mbytes (the result from the command SIZE). Now my question is: can I run this program without increasing memory? If so, how can I do that? If this benefits the net, I'll do summary. Thanks in advance! Xianzhang Gu Department of Chemistry Arizona State University email: Xianz@asuchm.la.asu.edu From h.rzepa@ic.ac.uk Tue Feb 8 14:23:21 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.4/930601.1506) id NAA16787; Tue, 8 Feb 1994 13:35:26 -0500 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <15704-0@punch.ic.ac.uk>; Tue, 8 Feb 1994 18:32:14 +0000 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA26299; Tue, 8 Feb 94 18:34:47 GMT Message-Id: <9402081834.AA26299@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: Tue, 8 Feb 1994 18:35:11 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Re: High Cost of Comp. Chem. Perhaps as a chemical community we should learn from the Maths, Physics, and Biology communities. Is my perception correct that much more HIGH QUALITY free software is available in these areas for a variety of platforms? More importantly, the ethos that "we can only use well supported software" (at a significant annual maintenance charge!) may not apply so much as it does in chemistry. As the object orientation becomes stronger, so maintenance might just become less of a problem. As for the hardware, it has become a fact of life that every 4-5 years, a sea change occurs in the machine flavour of the year, and a lemming like migration occurs. In my time (which I have to confess goes back to paper tapes, Hollerith cards, etc etc) I have seen about five flavours come (and perhaps go) in chemistry, especially in graphics! In university, we of course survive because the turnover of graduate students occurs on a similar time scale; they don't notice, only the harassed project supervisors who neve quite understand the latest operating systems do! Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.01, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From June '94: (44) 171 584 5774, Fax: (44) 171 584 5804 http://www.ch.ic.ac.uk/rzepa.html From gerard@scripps.edu Tue Feb 8 18:25:26 1994 Received: from scripps.edu for gerard@scripps.edu by www.ccl.net (8.6.4/930601.1506) id RAA19101; Tue, 8 Feb 1994 17:38:24 -0500 Received: from planti.scripps.edu by scripps.edu (5.61/1.34) id AA18987; Tue, 8 Feb 94 14:38:20 -0800 Received: by planti (920330.SGI/911001.SGI) for @riscsm.scripps.edu:chemistry@ccl.net id AA03909; Tue, 8 Feb 94 12:13:32 -0800 Date: Tue, 8 Feb 94 12:13:32 -0800 From: gerard@scripps.edu (Gerard Jensen) Message-Id: <9402082013.AA03909@planti> To: chemistry@ccl.net Subject: newsletter What has become of the cc newsletter? --------------------------------------------------------------------------------- stereo pair stereo pair Gerard M. Jensen, Ph.D. The Scripps Research Institute-MB8 H H H H Department of Molecular Biology \ | | \ 10666 N. Torrey Pines Road H--C---C--H H---C---C---H La Jolla, California, 92037 / | | / gerard@scripps.edu H H H H Ph: 619-554-4325 Fax: 619-554-6188 --------------------------------------------------------------------------------- From shepard@dirac.tcg.anl.gov Tue Feb 8 18:27:33 1994 Received: from dirac.tcg.anl.gov for shepard@dirac.tcg.anl.gov by www.ccl.net (8.6.4/930601.1506) id SAA19273; Tue, 8 Feb 1994 18:01:44 -0500 Received: by dirac.tcg.anl.gov (4.1/SMI-4.1) id AA08957; Tue, 8 Feb 94 17:01:43 CST Date: Tue, 8 Feb 94 17:01:43 CST From: shepard@dirac.tcg.anl.gov (Ron Shepard) Message-Id: <9402082301.AA08957@dirac.tcg.anl.gov> To: CHEMISTRY@ccl.net Subject: CCL:Re: High Cost of Comp. Chem. Cc: shepard@tcg.anl.gov h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) writes: >Perhaps as a chemical community we should learn from >the Maths, Physics, and Biology communities. Is my perception >correct that much more HIGH QUALITY free software is >available in these areas for a variety of platforms? As one of many authors of free chemistry software, I do not think that this is really the situation. I do think that there might be more commercial software in chemistry than in math and physics (I don't know about biology). One difference however is that there are large-scale organized attempts in these other disciplines to write software that is shared by the community. Look at EISPACK, LINPACK, and LAPACK, all distributed with anonymous ftp. In the USA, the NSF tried this in chemistry in the late '70s with the NRCC, and in my opinion it was very successful at this goal, but chemists do not seem to be of the mindset to support such a large-scale directed effort to develop codes. >More importantly, >the ethos that "we can only use well supported software" >(at a significant annual maintenance charge!) may not apply so >much as it does in chemistry. This is a good point. It might be the size of the codes involved. For example, a mathematician with minimal computing expertise might be more inclined to use someone else's 200-line code to compute PI to 10^8 digits, or to perform a matrix inversion, that would a chemist with minimal computing expertise to download 150K lines of COLUMBUS. But, I don't know the answer to this. Maybe others do? I can work to make COLUMBUS easier to install, and easier to port, and easier to understand, but I can't turn it into a 200-line program. >As the object orientation becomes stronger, >so maintenance might just become less of a problem. Heh, Heh... ;-) >As for the hardware, it has become a fact of life that every 4-5 >years, a sea change occurs in the machine flavour of the year, and >a lemming like migration occurs. In my time (which I have to confess >goes back to paper tapes, Hollerith cards, etc etc) I have seen about >five flavours come (and perhaps go) in chemistry, especially in graphics! In >university, we of course survive because the turnover of graduate >students occurs on a similar time scale; they don't notice, only the >harassed project supervisors who neve quite understand the latest >operating systems do! Another good observation. Part of the answer is that every 4-5 years something really useful and exciting comes along. Display terminals really are easier to use than Hollerith cards after all. However, in order to use this new gizmo of the year, you have to give up what you were doing before. In order to use new RISC workstations, you have to learn unix and give up VMS. In order to use PHIGS, you have to give up fortran and learn C. I have noticed however that this doesn't bother people in computing as much as it does people in science. I think this is related to the maturity of the different disciplines. It could be that our training in science allows us to appreciate more the kind of knowledge that remains useful for decades (or centuries) rather than months or years. $.02 Ron Shepard shepard@tcg.anl.gov From faeder@jila02.Colorado.EDU Tue Feb 8 20:20:53 1994 Received: from jila02.Colorado.EDU for faeder@jila02.Colorado.EDU by www.ccl.net (8.6.4/930601.1506) id TAA19819; Tue, 8 Feb 1994 19:23:09 -0500 Received: by jila02.Colorado.EDU id AA20752 (5.65c+/IDA-1.4.4/CNS-3.2 for CHEMISTRY@ccl.net); Tue, 8 Feb 1994 17:23:09 -0700 Date: Tue, 8 Feb 1994 17:23:09 -0700 From: jim faeder Message-Id: <199402090023.AA20752@jila02.Colorado.EDU> To: CHEMISTRY@ccl.net Subject: Request for Molecular Graphics Software Reply-To: faeder@ccl.net My research group has an Alpha AXP 3000 workstation and we would like molecular graphics software that would allow us to visualize the results of Monte Carlo and molecular dynamics simulations of small clusters (10-100 atoms). We would like to have space-filling models, preferably with some sort of shading, and have the capability of animating multiple frames. Does anyone know of some free (or nearly free) software that might accomplish these objectives? Thanks. --- +----------------------------------------------------------+ | Jim Faeder | | JILA, Campus Box 440 | | University of Colorado | | Boulder, CO 80309 | |----------------------------------------------------------| | | faeder@jila02.colorado.edu | hm. | 303-449-6953 | | email | -or- |-----+---------------| | | faeder@spot.colorado.edu | wk. | 303-492-7803 | +----------------------------------------------------------+