From ross@cgl.ucsf.EDU Mon Oct 5 15:01:17 1992 Date: Mon, 5 Oct 92 22:01:17 -0700 From: ross@cgl.ucsf.edu (Bill Ross) To: chemistry@ccl.net Subject: electronic publishing The following is the first evidence I have seen of a major journal and organization planning to move from protons to electrons. >From the (paper) journal, _Communications_of_the_ACM_ (Assoc for ...membership...has been gradually declining from a high of 82,000 several years ago. Stepped-up membership recruitment campaigns have produced fewer new members than drop out, and 35% of the new ones drop out at their first renewal. ...It is plainly time for a change. ... ACM must establish an influential presence in cyberspace; it is now largely unnoticed there. A large subset of the following actions can be realized by 1995: o Use the new ACM network host, `acm.org', to conduct ACM business... o Cooperate with the Electronic Frontier Foundation [& others, in network publishing] o Cooperate w/ digital library projects... o Establish an electronic refereed journal ... w/ filters that deliver sections to individual subscribers according to their preferences... o Experiment with the production of an on-line multimedia magazine... o Establish an on-line repository of collected algorithms... ... Bill Ross PS - vis-a-vis my earlier mention of the FBI seeking wiretap abilities on _all_ computer networks, someone told me that that stuff gets discussed a lot on the Electronic Frontier Foundation reflector: eff-request@eff.org to join. From oosten@rulhm1.LeidenUniv.nl Tue Oct 6 11:52:20 1992 Date: Tue, 6 Oct 92 10:52:20 +0100 From: oosten@rulhm1.LeidenUniv.nl (A.B. van Oosten) To: CHEMISTRY@ccl.net Subject: barbie talk Assuming that the barbie story is not some kind of joke: Whether the barbie doll is the root of the problem of math-phobia or just an expression of it is an interesting but rather academic question. What's important is that it is very much *part* of the problem, and of a of a few other problems I can think of. The latest version of the doll will no doubt have a harmful effect on children and I feel that the (American) scientific community should take action here. +---------------------------------------+-----------------------------------+ | Tony van Oosten | Huygens Laboratory | | | University of Leiden | | Ab initio cluster calculations | PO Box 9504, 2300 RA Leiden, | | on Defects in Semiconductors | The Netherlands | | | Phone: (+31) 71 275908 | | | Fax: (+31) 71 275819 | +---------------------------------------+-----------------------------------+ | Network : | +---------------------------------------------------------------------------+ From lrellick@magnus.acs.ohio-state.edu Tue Oct 6 03:35:03 1992 Date: Tue, 6 Oct 92 7:35:03 EDT From: Lorraine M Rellick To: chemistry@ccl.net Subject: who "belongs" in science How nice of Joe to tell us who "belongs" in science. Obviously concerned parents, or just those of us who are concerned about the future of research (i.e., the quality of science education) don't belong. Great additude Joe! From curtis@sagi.wistar.upenn.edu Tue Oct 6 06:56:38 1992 Date: Tue, 6 Oct 92 10:56:38 EDT From: curtis@sagi.wistar.upenn.edu (curtis wahlgren) Subject: Ribbons v2.0 To: SHAUN%JASON.DECNET@relay.the.net Shawn Where does one obtain a copy of Ribbons? It sounds like something we could use on our Iris workstations too. I thank you in advance for your kindness. -- Curtis Wahlgren curtis@sagi.wistar.upenn.edu From ravishan@swan.wesleyan.edu Tue Oct 6 05:37:29 1992 Date: Tue, 6 Oct 92 09:37:29 -0400 From: G. Ravishanker To: u5949@sn2011.plk.af.mil Subject: MO visualization Andy One of the public domain renderers you may want to consider is RASTER3D. We use it for most of our rendering. It is pretty good and simple. You just need to prepare a list of primitives (which include sphere, triangles, flat-ended and rounded cylinders) with the appropriate coordinate list, any additional geometrical parameters (such as radius), and color. I easily modified the program to incorporate ellipses to draw thermal ellipsoid and adding other primitives involves solving some parametric equations for the primitive and coding it in following the code for other primitives. I picked up the raster3d distribution via anon. ftp >from xray0.bchem.washigton.edu. I am not sure if it is still available there. One thing nice about raster3d is it is pretty much system independent. The default code is written to output the bitmap produced to be compatible with Iris, but you can always change it (The original program was written to run under a VAX and produce a bitmap file, which was then viewed elsewhere, I think...). The other one you may want to look at is called rayview from Columbia. I was not too thrilled by the quality of the pictures. These involve some work and are not ready to go fo ryour purposes, but I thought you should know about these. Ravi From jkl@ccl.net Tue Oct 6 07:05:54 1992 From: jkl@ccl.net (Jan Labanowski) Date: Tue, 6 Oct 1992 11:05:54 -0400 To: chemistry@ccl.net Subject: Barbie-Doll Dear netters... I am trying very hard to be very flexible. However, chemistry@ccl.net is a Computational Chemistry forum. If there are enough people who are interested, I can set up another reflector barbie-doll@ccl.net where you can finish your discussion. If you are seriously interested in this option, please contact me. To repudiate labels of my insensitivity to the problem, please be informed that I am also a father --- I simply do not buy toys which I consider inappropriate. Jan Labanowski jkl@ccl.net From ravishan@swan.wesleyan.edu Tue Oct 6 07:06:56 1992 Date: Tue, 6 Oct 92 11:06:56 -0400 From: G. Ravishanker To: chemistry@ccl.net Subject: Presidential Election and Research Grants Folks I was listening to parts of Bill Clinton's interview with Larry King on CNN last night and one question and its answer interested me very much and thought people in this list may be interested in discussing about it. Someone called in with a question to Clinton as to what his strategy is towards basic research in academic instituions. The question also mentioned that Clinton plan proposes to cut budget for such research. His explanation was that he does not intend to cut budget for research per se, but plans to cut the adminstrative cost associated with the grants (I guess he was referring to indirect costs) and funnel most of it back to research grants. Therefore, he claims that his plan actually will funnel more money back into research. On the surface this looks great, however, how can the Govt. control indirect costs, except to say that we will not give beyond a certain percent of the direct costs to you. Will the Adminstrators of the academia agree to such proposal? (Since the indirect costs can run as high as 70% in some cases, the savings from reducing this may be significant...) What do people in this newsgroup think of this idea? Ravi From riddle@nersc.gov Tue Oct 6 02:31:23 1992 Date: Tue, 6 Oct 92 09:31:23 PDT From: riddle@nersc.gov (Alan Riddle) To: chemistry@ccl.net Subject: Barbie dolls of the world unite! So Barbie thinks math is hard. Well, it is. So some people think that this doll will prevent a generation of little girls from becoming scientists. Come on, it is only a toy. If you are concerned about children and science, then VOTE! Build more schools, and hire teachers for them. Tax the billions spent on live entertainment (sports, concerts, movies). Build a couple fewer stealth bombers and spend the money on education. Come on, education is very important. Lets not trivialize the fight to educate our children. Leave Barbie alone and do something worth while. Alan Riddle The opinions are mine, my bosses don't know I have them. From tripos!metis!matt@uunet.UU.NET Mon Oct 5 11:23:54 1992 From: tripos!metis!matt@uunet.UU.NET (Matt Clark) To: uunet!ccl.net!chemistry@uunet.UU.NET Subject: Re: Wavetracer bites the dust Date: Mon, 05 Oct 92 15:23:54 EDT - -------- Is there really a big market for limited-purpose attached processors? The number of fast workstations being developed seems to indicate that a general purpose computer is more cost effective for the majority of scientists and engineers. For the price of the Zephyr you could afford an RS6000 that can run all kinds of generally available software with little or no modification. From d3f012@gator.pnl.gov Tue Oct 6 03:26:01 1992 Date: Tue, 6 Oct 92 10:26:01 PDT From: d3f012@gator.pnl.gov Subject: musings on rotational variations To: chemistry@ccl.net Jimmy Stewart writes: >>As far as rotational invariance is concerned, great care has >>been taken to ensure that all calculations are rotationally >>invariant. Over the past nine years, I have received several >>papers to review in which the authors claim to have corrected >>faults in MOPAC which had caused loss of rotational invariance. >>In each case I have recommended against publication unless the >>authors could demonstrate that rotational invariance was lost. Would it be possible to find out what the causes of the rotational variations were in some of those calculations... were they ever documented? The concerns raised were not with possible rotational variations in MOPAC, or any other program, but rather the inherant rotational variance that may exist in the MNDO-family of methods themselves (ie. MNDO, AM1, PM3). For what it's worth, using MNDO, AM1, and PM3, as implemented in Argus, (as well as MOPAC), gives no evidence of rotational variations for the cases I have examined, employing static geometry energy calculations. However, I am still exploring this issue. I am concerned with the solution of the two-electron integrals using truncated multipole expansions. When one takes derivatives of these expressions, then basis functions of higher angular momentum number, or higher multipoles in the classical expansion, must be considered. It is not clear to me that this is addressed in any of the MNDO-family literature. As I have not seen the MOPAC or AMPAC source code, can anyone shed any light on whether this issue is addressed? If this is the case, then I could see a possible inconsistency in the way derivatives are done with these multipole expansions, and the net result of this <> be that slightly different geometries, energies. etc. are obtained if different starting orientations (but same internal geometry) are used. I <> that this would not be a problem for small systems. However, large systems with C1 symmetry (which I am most interested in) might be a problem. Has anyone else ever thought about these issues? I have the highest regard for the positive impact these methods have had on chemistry. Please keep in mind that I am merely searching for a deeper understanding at this point. ************************************************************************** Mark A. Thompson email: d3f012@pnlg.pnl.gov Sr. Research Scientist voice: 509-375-6734 Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory PO Box 999, Mail Stop K1-90 Richland, WA. 99352 ************************************************************************** From evi@tiberius.tc.cornell.edu Tue Oct 6 10:06:09 1992 To: chemistry@ccl.net Subject: chemistry & Barbie dolls Date: Tue, 06 Oct 92 14:06:09 EDT From: Evi Goldfield The idea that anyone who would "listen" to a Barbie doll doesn't belong in science is a good example of the subtle and not-so-subtle messages that discourage girls from going into science. Many little girls play with Barbie dolls. If the Barbie doll talks, they may even "listen" to it. So now we not only have Barbie telling the little girls that math is hard, but we have male scientists reinforcing the message that science is not for them. Evi Goldfield Senior Research Scientist Cornell Theory Center From zjtg05@nap.amoco.com Tue Oct 6 08:38:22 1992 Date: Tue, 6 Oct 1992 13:38:22 -0500 From: zjtg05@nap.amoco.com To: chemistry@ccl.net Subject: Issues of importance to Computational Chemistry In my original post, I simply meant that if a person's choice to either enter science or some other field would be determined by a talking Barbie, then I do not think that person belongs in science. I still believe that. Now, please enough flames; my poor machine is all 'coked' up. :-) :Joe jtgolab@nap.amoco.com 06-Oct-92 From jkl@ccl.net Tue Oct 6 13:57:05 1992 From: jkl@ccl.net (Jan Labanowski) Date: Tue, 6 Oct 1992 17:57:05 -0400 To: chemistry@ccl.net Subject: Program to animate normal vibrations from G90 Dear Netters We got a nice gift from Milan Hadoscek (in TeX: Milan Hado\v{s}\v{c}ek}. His xvibs program will: 1. extract normal modes from G9X input. 2. create an Xmol input file for animation. 3. You now can use Xmol to see animation of normal vibrations calculated by G9X by reading the file to Xmol (XYZ format) and clicking on Extras, then Animation. Xmol is available from anonymous ftp at ftp.msc.edu in /pub/xmol. Consult postings about Xmol in our archives: 92/06/03, 92/06/12. You can obtain xvibs.c and readme file from anonymous ftp on www.ccl.net in /pub/chemistry/xvibs: ftp www.ccl.net Login: anonymous Password: Your_e-mail_address ftp> ascii ftp> cd pub/chemistry/xvibs ftp> get xvibs.c ftp> get readme ftp> quit You can also get these files by sending a message: send ./xvibs/xvibs.c from chemistry send ./xvibs/readme from chemistry to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET Below, the comments from the xvibs.c program header. Jan Labanowski jkl@ccl.net /********************************************************** Program extracts normal modes from Gaussian output file. It writes separate files, one simple cosine trajectory for particular normal mode. Output is in Xmol XYZ format. (Click Animate button and enjoy!) Compiling: cc -o xvibs xvibs.c -lm Running: xvibs mymolecule.out {all|1-(3*N-6)} Example: g90 benzene.out (or equivalent) xvibs benzene.out all Output files are named benzene.{1-30} or xvibs benzene.out 15 for mode 15 only. Output will be benzene.15 ------------------------------------------- Written in 1990 by Milan Hodoscek Institute of Chemistry, Ljubljana, Slovenia Modified for XMOL 1992 @NIH, Bethesda, MD Bug report to: milan@helix.nih.gov -------------------------------------------