From owner-chemistry@ccl.net Tue Apr 9 05:45:28 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id FAA09924; Tue, 9 Apr 1996 05:44:12 -0400 (EDT) Received: from neumann.sissa.it for demaria@neumann.sissa.it by bedrock.ccl.net (8.7.1/950822.1) id FAA09749; Tue, 9 Apr 1996 05:43:07 -0400 (EDT) Received: (from demaria@localhost) by neumann.sissa.it (8.7.3/8.7.1) id LAA36481; Tue, 9 Apr 1996 11:41:42 +0200 From: Leonardo Demaria Message-Id: <199604090941.LAA36481@neumann.sissa.it> Subject: Exchange series divergency. To: chemistry@ccl.net Date: Tue, 9 Apr 1996 11:41:42 +22311408 (MET_DST) Cc: demaria@neumann.sissa.it (Leonardo Demaria) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Hi everybody, I'm trying to preform CNDO calculations for solids, diamond and graphite in particular. I want to use a large unit cell and only the gamma point for Brillouin zone integrations. On Hartree-Fock calculations for solids the exchange energy diverges for the gamma point. This causes some convergence problems when Brillouin zone integrations are performed using special points and becomes a serious pro- blem when one is trying to do computer simulations using large unit cells and only gamma point sampling. Usually an artificial cut-off for the exchange series is introduced. I know about some ways to efficently handle this divergency when doing calcu- lations with special points (F.Gygi and A.Baldereschi works) but I've not been able to find anything different from the cut-off trick for calculations with a large unit cell. CNDO, being an approximate Hartree-Fock scheme, inherits this exchange series divergency problems. Does anyone know how to handle this problem without using a cut-off? If don't then, does anyone know where to find useful information about how to choose the cut-off ? I'll summarize the answers. Thank you in advance, Leonardo De Maria Ph.D. student Universita di Trieste Dipartimento di Fisica Teorica Strada Costiera 11 Miramare-Grignano I-34014 - Trieste tel: +39 40 224265 fax: 224601 e-mail : demaria@vstst0.ts.infn.it (also demaria@neumann.sissa.it can be used) From toukie@zui.unizh.ch Tue Apr 9 08:45:30 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.7.1/950822.1) id IAA11381; Tue, 9 Apr 1996 08:27:38 -0400 (EDT) Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA29492; Tue, 9 Apr 96 14:27:37 +0200 X-Nupop-Charset: Swiss Date: Tue, 9 Apr 1996 14:28:33 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <52113.toukie@zui.unizh.ch> To: chemistry@www.ccl.net Subject: Is RasWin 2.6 availble? Dear Colleagues; I have been using RasWin 2.6 beta, with the expectation that the full implementation of RasWin 2.6 would be available very shortly. Has the full implementation of RasWin 2.6 in fact been deposited in an FTP site? If so, please send details [incl. address, subdirectory site, and file name(s)]. Kindly do NOT send WWW sites, as I cannot download from them yet. Thanks in advance to all responders. Sincerely, S. Shapiro ZH toukie@zui.unizh.ch From bernhold@oldnova.npac.syr.edu Tue Apr 9 10:45:37 1996 Received: from postoffice.npac.syr.edu for bernhold@oldnova.npac.syr.edu by www.ccl.net (8.7.1/950822.1) id KAA12784; Tue, 9 Apr 1996 10:13:40 -0400 (EDT) Received: from oldnova.npac.syr.edu (root@oldnova.npac.syr.edu [128.230.7.4]) by postoffice.npac.syr.edu (8.7.5/8.7.1) with ESMTP id KAA29537 for ; Tue, 9 Apr 1996 10:13:36 -0400 (EDT) Received: from nova.npac.syr.edu (bernhold@nova.npac.syr.edu [128.230.7.2]) by oldnova.npac.syr.edu (8.7.1/8.7.1) with SMTP id KAA10539 for chemistry@www.ccl.net; Tue, 9 Apr 1996 10:13:35 -0400 (EDT) From: "David E. Bernholdt" Message-Id: <199604091413.KAA10539@oldnova.npac.syr.edu> X-Authentication-Warning: oldnova.npac.syr.edu: Host bernhold@nova.npac.syr.edu [128.230.7.2] didn't use HELO protocol To: chemistry@www.ccl.net (CCL) Subject: Re: CCL:WWW developments In-reply-to: Message from tj ODonnell of "Mon, 08 Apr 96 13:55:42 CDT." <199604081855.NAA07631@ernie.eecs.uic.edu> Date: Tue, 09 Apr 96 10:13:34 -0400 > but what we really want to know is whether the CONTENT > of a requested applet is identical to the content of one in cache, > regardless of the name (URL) of the applet. To do an exhaustive > comparison, we'd have to get the remote applet anyway, so this is > not a viable alternative. What I'm suggesting is some unique > way of identifying an applet, independent of its URL. Actually, this is not technically hard, and is related to issues of code/data integrity and security which are becoming increasingly important concerns on "the net". (see also encryption, digital signatures, PGP, ...) In this case, you could apply a secure one-way hash (aka digital signature, such as MD5) to the data and compare the signatures. The signature is a short (16 or 32 digit?) hexadecimal number, so it is quick to transmit and MD5 is not too hard to compute. I believe chance of identical MD5 signatures arising from different inputs is 2^-64 (5e-20), which ought to satisfy most uses. I'm not aware of any browsers which do this now, but its probably coming. -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu From weber@xhost2.tripos.com Tue Apr 9 10:52:54 1996 Received: from gatekeeper.tripos.com for weber@xhost2.tripos.com by www.ccl.net (8.7.1/950822.1) id KAA13011; Tue, 9 Apr 1996 10:34:25 -0400 (EDT) Received: (from news@localhost) by gatekeeper.tripos.com (8.6.12/8.6.12) id JAA25096 for ; Tue, 9 Apr 1996 09:34:27 -0500 Received: from tripos.tripos.com(192.160.145.1) by gatekeeper.tripos.com via smap (V1.3) id sma025094; Tue Apr 9 09:34:10 1996 Received: from xhost2.tripos (xhost2.tripos.com [192.160.145.213]) by tripos.tripos.com (8.6.12/8.6.12) with ESMTP id JAA16839 for ; Tue, 9 Apr 1996 09:31:43 -0500 Received: by xhost2.tripos (940816.SGI.8.6.9/5.6) id JAA13498; Tue, 9 Apr 1996 09:31:34 -0500 From: "Paul Weber" Message-Id: <9604090931.ZM13496@xhost2.tripos.com> Date: Tue, 9 Apr 1996 09:31:34 -0500 X-Mailer: Z-Mail (3.2.0 06sep94) To: chemistry@www.ccl.net Subject: Java and other WWW developments Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, First, I'm glad that Steve Bachrach and others have been impressed with the recent web developments for chemistry, including the Java-based "Sketch and Fetch" tool we created here. From my research, it is clear that chemistry users are among the growing population of computer users who are finding that Browsers and Java make distributed computing a heck of a lot easier than copying files over ftp. Silicon Graphic's recent announcement of Molecular Inventor (now in beta) is another indicator of how computational chemistry is about to change very much, and very quickly. (And you can use Molecular Inventor with SYBYL as well -- Steve only mentioned SGI and MSI and hey, I hate being overlooked!). For more information about Molecular Inventor, see the SGI homepage (check under "News") at www.sgi.com. I'm also surprised to see the attention focused just on Java -- if all you want to do is look at a molecule, you might consider VRML as well as Molecular Inventor for getting a much improved display quality. VRML and MI formats are pretty easy to write too, so general support in the future seems to be a good bet. Now about Java - The download times are a drawback that many have noted, and many are working on. Downloading the classes once and storing locally is probably the best bet, as long as the application remembers to check to see if it is still up to date. I don't think anyone should lose sleep or waste time worrying about the multitude of Java Applets that could be coming available. Having many Java applets out there is NOT the issue. First, writing an applet to rotate a molecule is **pretty darn easy** (see the example in the Sun Java release). But more important, I see Java and Web technology as the ultimate integrator -- you will be able to construct web pages for your work, where you could mix and match applets from different vendors. Thus, a "plug and play" of applications. The real issue then is will there be a common data format to drag and drop between applets? Again, I think the Molecular Inventor format from SGI comes the closest to what we could use (and Tripos is using it, as well as MSI and probably other vendors, too). A common vision is to think of the Browser as the new desktop, or GUI to your work. You might, in the not too distant future, get a chemistry version of "plug and play" where a molecule sketched in a Tripos applet is used to pull out compounds from an MDL database, some of which are then minimized using the Merck FF, all on the same page (which could then be stored or "registered" as a notebook page that could be searched later). I think that it is a good time for the community to search for acceptable standards, such as SGI's Molecular Inventor, Tripos's SLN, DayLight's SMILES, or the PDB (yuck). The chemistry community could then promote the use of these standard formats by all software producers, whether garage-shop, grad student, or public company. Watch the Web for more big developments soon! -- --------------------------------------------------------------------- Paul L. Weber, Ph. D. Vice President, Product Development Phone: 314 647 1099 Tripos, Inc. Fax: 314 647 9241 1699 S. Hanley Rd St. Louis MO 63144 USA Email: weber@tripos.com --------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Apr 9 14:45:33 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id OAA18884; Tue, 9 Apr 1996 14:35:00 -0400 (EDT) Received: from bilbo.bio.purdue.edu for gsoriano@bilbo.bio.purdue.edu by bedrock.ccl.net (8.7.1/950822.1) id OAA18863; Tue, 9 Apr 1996 14:34:56 -0400 (EDT) Received: (from gsoriano@localhost) by bilbo.bio.purdue.edu (8.7.3/8.7.1) id NAA33980 for chemistry@ccl.net; Tue, 9 Apr 1996 13:34:48 -0500 Message-Id: <199604091834.NAA33980@bilbo.bio.purdue.edu> Subject: biosym To: chemistry@ccl.net Date: Tue, 9 Apr 1996 13:34:47 -0500 (EST) From: "Glenda Soriano" X-Mailer: ELM [version 2.4 PL24] Content-Type: text i am trying to do a calculation of electron transfer pathways using the greenpath program written in UCSD. the problem is that the program requires connectivity info for the protein. one way of doing this is to run the protein inside InsightII which has biosym. would anyone be familiar with Insight???? Glenda M Soriano gsoriano@bilbo.bio.purdue.edu From boyd@chem.iupui.edu Tue Apr 9 15:45:35 1996 Received: from indyvax.iupui.edu for boyd@chem.iupui.edu by www.ccl.net (8.7.1/950822.1) id PAA20083; Tue, 9 Apr 1996 15:37:43 -0400 (EDT) Received: from macgw.chem.iupui.edu by INDYVAX.IUPUI.EDU (PMDF V5.0-5 #5862) id <01I3C9SDVAHC00CN7J@INDYVAX.IUPUI.EDU> for chemistry@www.ccl.net; Tue, 09 Apr 1996 14:13:57 -0500 Date: Tue, 09 Apr 1996 14:07:37 -0500 From: Boyd Subject: Reviews in Computational Chemistry To: OSC CCL Message-id: X-Mailer: Mail*Link SMTP-MS 3.0.2 Content-transfer-encoding: 7BIT Dear Colleagues: I looking for 1995 journal articles that cite "Reviews in Computational Chemistry." Please send me your reprints by snail mail. I need them by May 1. Thanks, Don Donald B. Boyd, Ph.D. Research Professor of Chemistry Co-editor, REVIEWS IN COMPUTATIONAL CHEMISTRY Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Internet boyd@chem.iupui.edu REVIEWS IN COMPUTATIONAL CHEMISTRY Home Page on the World Wide Web URL http://chem.iupui.edu/~boyd/rcc.html