From chemistry-request@www.ccl.net Wed Jan 13 04:55:51 1999 Received: from hartree.chem.kuleuven.ac.be (hartree.quantchem.kuleuven.ac.be [134.58.49.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA15245 Wed, 13 Jan 1999 04:55:45 -0500 (EST) Received: from localhost (steven@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id KAA24164 for ; Wed, 13 Jan 1999 10:55:08 +0100 Date: Wed, 13 Jan 1999 10:55:07 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:Metal Complex Optimization Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, what would be the method of choice for structure optimizations of fairly large transition metal systems (say 50 atoms) of Ti or Zr? I would like to get some feeling of timings and quality. Thanks, Steven -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From chemistry-request@www.ccl.net Wed Jan 13 10:11:49 1999 Received: from sirio.cineca.it (sirio.cineca.it [193.204.121.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA17125 Wed, 13 Jan 1999 10:11:26 -0500 (EST) Received: (from incci000@localhost) by sirio.cineca.it (8.8.5/8.7) id QAA25095; Wed, 13 Jan 1999 16:02:59 +0100 (MET) Date: Wed, 13 Jan 1999 16:02:58 +0100 (MET) From: Sigismondo Boschi To: Fenglou Mao cc: CCL Subject: Re: CCL:ANSI C++ question? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Yes, C++ has been standardized by a committee of standardization ISO/ANSI. the most important name is "Bjarne Stroustrup" (the c++ "creator"), that has recently published a book about the ANSI C++, very nice indeed: "The C++ Programming Language", third edition. I strongly suggest it. STL is now part of the ansi/iso standard of c++. The press release of C++ ISO standard can be found here: http://www.research.att.com/~bs/iso_release.html Here you can find either some interesting links. The ANSI drafts of the standard are not at disposal in any electronic form: they have to be requested directly to "ANSI": From a FAQ: You can get a paper copy of the standard from ANSI. Either send email to Lynn Barra (lbarra@itic.nw.dc.us) or send a letter to the address below, and ask for the latest version of "Draft Proposed American National Standard for Information Systems - Programming Language C++" which is document number CD14882. It is typically shipped 2-day FedEx within the continental US. If you want to order via snail mail, send a letter to X3 Secretariat / 1250 Eye Street NW / Suite 200 / Washington, DC 20005 / 202-626-5738. Finally, reporting from a FAQ: C++ has been standardized by ANSI (The American National Standards Organization), BSI (The British Standards Institute), DIN (The German National Standards Organization), several other national standards bodies, and ISO (The International Standards Organization). The ISO standard has been finalized and adopted by unanimous vote Nov 14, 1997. The ANSI-C++ committee is called "X3J16". The ISO C++ standards group is called "WG21". The major players in the ANSI/ISO C++ standards process includes just about everyone: representatives from Australia, Canada, Denmark, France, Germany, Ireland, Japan, the Netherlands, New Zealand, Sweden, the UK, and the USA, along with representatives from about a hundred companies and many interested individuals. Major players include AT&T, Ericsson, Digital, Borland, Hewlett Packard, IBM, Mentor Graphics, Microsoft, Silicon Graphics, Sun Microsystems, and Siemens. After about 8 years of work, this standard is now complete. On November 14, 1997, the standard was approved by a unanimous vote of the countries that had representatives present in Morristown. Final ratification by two dozen countries is expected by March 1998. --------------------------------------- --------------------------------- |Sigismondo Boschi |tel: +39 51 6171559 | |CINECA (Gruppo Supercalcolo) - INSTM |fax: +39 51 6132198 | |via Magnanelli, 6/3 |e-mail: s.boschi@cineca.it | |40033 Casalecchio di Reno (Bologna) | | |ITALY | | --------------------------------------- --------------------------------- On Tue, 12 Jan 1999, Fenglou Mao wrote: > Dear all, > I am wondering if there is a ANSI C++ standard, and if have one, > where I can find an introduction about it. And how about STL(standard > template library) defined in ANSI C++, and how to find some introduction > about it? > > Sincerely Yours, > > FengLou Mao > ******************************* > ADD:Mr. FengLou Mao > Peking University > BeiJing > P.R.China > Tel:86-10-62751490 > Fax:86-10-62751725 > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: mao@csb0.IPC.PKU.EDU.CN > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From chemistry-request@www.ccl.net Wed Jan 13 10:44:25 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA17676 Wed, 13 Jan 1999 10:44:19 -0500 (EST) Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id QAA12596; Wed, 13 Jan 1999 16:43:33 +0100 From: Jochen Kuepper Organization: Heinrich-Heine-Universitaet To: Ferenc Csizmadia , chemistry@www.ccl.net Subject: Re: CCL:New ideas for chemistry software Date: Sat, 19 Feb 2135 23:03:00 +0100 X-Mailer: KMail [version 1.0.11] Content-Type: text/plain References: <3697B311.E8D65392@chemaxon.com> MIME-Version: 1.0 Message-Id: <99011316433300.10662@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id KAA17677 Regarding the summary of new ideas: Dear All, please keep in mind that PC does not mean Microsoft ! There have been several statements that want to get programs ported to Windows to be able to run them on "cheap" PC-hardware. Since there are many OSs that run these programs on exactly that cheap hardware, I would not see this urgent need for porting but would like the programs to be enhanced in functionality ! PS: I know at least 10 OSs of very different flavour running on exactly this PC hardware, of which MS_DOS(+Win3.1+Win9x) and Windows NT are only two, and will be only one really soon, since the DOS branch is declared death already by Microsoft. Moreover basically all of this can be installed in parallel on the same machine. So I would strongly suggest to work on the science part of the programs, not the operating system topics. Greetings, Jochen ----------------------------------------------------------------------- Jochen K"upper Heinrich-Heine-Universit"at D"usseldorf jochen@uni-duesseldorf.de Institut f"ur Physikalische Chemie I Universit"atsstr. 1, Geb 26.43 Raum 02.29 phone ++49-211-8113681 40225 D"usseldorf fax ++49-211-8115195 Germany http://www-public.rz.uni-duesseldorf.de/~jochen ----------------------------------------------------------------------- From chemistry-request@www.ccl.net Wed Jan 13 11:01:53 1999 Received: from sg2.csrsrc.mi.cnr.it (sg2.csrsrc.mi.cnr.it [155.253.3.253]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA18057 Wed, 13 Jan 1999 11:01:36 -0500 (EST) Received: from localhost by sg2.csrsrc.mi.cnr.it via SMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) for id RAA13130; Wed, 13 Jan 1999 17:05:14 -0800 Date: Wed, 13 Jan 1999 17:05:12 -0800 From: Alessandra Villa To: chemistry@www.ccl.net Subject: ab initio calculation: NMR shielding tensor Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I wonder if someone have performed ab initio NMR shielding tensor calculations on paramagnetic compounds by means of GIAO or CSGT methods. Could you point me some paper concerning the argument? or could you write me your knowledge about the reliability of GIAO and CSGT NMR shielding tensor calculations on paramagnetic molecules? I will summary all the answers. Thank you Alessandra ******************************************************************************* Alessandra Villa ale@sg2.csrsrc.mi.cnr.it PhD-Student Dipartimento di Chimica Fisica ed Elettrochimica Universtita' degli Studi di Milano via Golgi 19 20133 Milano-Italy ******************************************************************************* From chemistry-request@www.ccl.net Wed Jan 13 12:12:07 1999 Received: from wavefun.com (wave-fw.wavefun.com [209.125.133.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id MAA20235 Wed, 13 Jan 1999 12:12:06 -0500 (EST) From: Date: Wed, 13 Jan 1999 09:11:24 -0800 Message-Id: <9901130911.ZM28405@wavefun.com > In-Reply-To: Steven Creve "CCL:Metal Complex Optimization" (Jan 13, 10:55am) References: X-Mailer: Z-Mail-SGI (3.2S.3 08feb96 MediaMail) To: Steven Creve Subject: Re: CCL:Metal Complex Optimization Cc: CHEMISTRY@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Jan 13, 10:55am, Steven Creve wrote: > Subject: CCL:Metal Complex Optimization > > > Hi all, > > > what would be the method of choice for structure optimizations of fairly > large transition metal systems (say 50 atoms) of Ti or Zr? I would like to > get some feeling of timings and quality. > > Thanks, > > Steven > > > -------------------------------------------------------------------------- > Steven Creve steven.creve@chem.kuleuven.ac.be > Labo Quantumchemie > Celestijnenlaan 200F > 3001-HEVERLEE tel: (32) (16) 32 73 93 > BELGIUM fax: (32) (16) 32 79 92 > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: Steven.Creve@chem.kuleuven.ac.be > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html >-- End of excerpt from Steven Creve PM3(TM) in our SPARTAN can calculate Ti and Zr compounds. The method is a semi-emperical one, and have no problem to optimize 50 atom systems by today's computer. The results of geometry optimizations with PM3(TM) are pretty good. Jianguo Yu -- +-----------------------+------------------+-------------------------+ |Jianguo Yu, Ph.D. | ______________ | E-Mail: yu@wavefun.com | |Computational Chemist | \ _________ / | Phone: (949)955-2120 | |Wavefunction Inc. | \ \\\\\\\\/ | Fax: (949)955-2118 | |18401 Von Karman | \ \\\\\/ | "The doctrines observe | |Suite 370 | \ \\/ | nature" | |Irvine, CA 92612 | \/ | Lao-tzu (604-531 B.C.)| +----------------------http://www.wavefun.com------------------------+ From chemistry-request@www.ccl.net Wed Jan 13 19:54:47 1999 Received: from sungod.ccs.yorku.ca (zK9EYroKA9hZYuK4LlDFTP8sBV+RopV1@sungod.ccs.yorku.ca [130.63.236.104]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA22078 Wed, 13 Jan 1999 19:54:46 -0500 (EST) Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sungod.ccs.yorku.ca (8.8.7/8.6.11) with SMTP id TAA08621 for <@mailrelay.yorku.ca:chemistry@www.ccl.net>; Wed, 13 Jan 1999 19:54:46 -0500 (EST) Received: by curl.gkcl.yorku.ca (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id TAA03709; Wed, 13 Jan 1999 19:56:34 -0500 From: chan@curl.gkcl.yorku.ca (Wai-To-Chan) Message-Id: <199901140056.TAA03709@curl.gkcl.yorku.ca> Subject: Re: CCL:G:SUMMARY OF RATE/ACTIVATION ENERGY To: chemistry@www.ccl.net Date: Wed, 13 Jan 1999 19:56:33 -0500 (EST) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Having read Dr Topper's information about POLYRATE I realize I should take back my remarks about the program being inappropriate for isomerisation reaction rate calculation. In writing my previous message I had in mind that it is not always neccessary to apply unimolecular rate theory rigorously using a package as sophiscated as POLYRATE. One can estimate rate constants using a calculator merely by substitution of thermodynamic quantities readily obtained from ab initio MO calculations into the Arrhenius rate equation, K = A * exp(-E/RT). Evaluation of the rate constant this way is not strictly valid as E is the high-pressure- -activation-energy which is not equivalent to the barrier height obtained from ab initio calculation. Nonetheless the ab initio barrier height should approximate E reasonably well and I would not recommend one going through the trouble of calculating it using RRKM method. My opinion is that applying RRKM method safely requires a better than casual understanding of the background theory which happened to be a difficult learning experience to me. However I should have presented my thoughts on using POLYRATE, which I never used, more carefully. Finally I should point out I mistakenly referred to Q the "partition function" from the Arrhenius rate equation as the "entropy" in my early comments. My apology for the blunder. Wai-To Chan Research Associate Department of Chemistry York University Toronto, Canada From chemistry-request@www.ccl.net Wed Jan 13 21:43:04 1999 Received: from mail-03.telis.org (mail-03.telis.org [204.71.76.231]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA22635 Wed, 13 Jan 1999 21:43:03 -0500 (EST) Received: from [207.49.123.49] (s06-pm42.snaustel.campuscwix.net [207.49.123.49]) by mail-03.telis.org (8.9.0/8.8.8) with ESMTP id SAA15007 for ; Wed, 13 Jan 1999 18:37:30 -0800 (PST) X-Sender: gammadas@mail.telis.org Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 13 Jan 1999 20:38:36 -0600 To: chemistry@www.ccl.net From: Goutam Das Subject: complex geom calc protocol Here are two more responses to my originial questions which goes as follows: A very big thank you to everyone who responded. "I wonder whether there are protocols (besides MD sim) for calculating geometries (ab initio/semiempiric/molmech) of minima's and finally glob minimas for pairs of simple molecules. If there are, I would deeply appreciate if anyone could kindly point me to good references. Normally I optimize geom's of both mol's, then freeze the crd's of each and then move one relative to another and then relax all constraints, guessing inital geoms by intuition--I am sure I miss a lot of conf's and maybe certainly the glob min (although I understand that there is no guarantee that any particular method could give the global min). However, there should be a much better & efficient subroutine." Date: Tue, 05 Jan 1999 09:13:07 -0600 From: "Mark A. Zottola" X-Accept-Language: en MIME-Version: 1.0 To: Goutam Das Subject: Global Minima Dear Dr. Das, I do not have the reference on hand, but I do know that in the late 80's Dr. Scheraga published a paper on an algorithm for finding the global minimum for a geometry by manipulating the dimensionality of the problem. I believe instead of working in n-space and doing a geometry minimization (which is almost guaranteed to NOT find the global minimum), Scheraga's approach (I believe, check the paper) works on starting with a low dimensionality then adding complexity, the idea being that if you approach the problem from the downside, the first point you should hit would be the global minimum... Good luck finding the reference. If I manage to run across it I will send it to you. Best of luck in your research! -- ********* Mark A. Zottola Alabama Research and Education Network 119 Rust Research Center Nichols Research Corporation University of Alabama-Birmingham VOICE: (205) 934-3893 Birmingham, AL 35294 EMAIL: asnmaz01@csimail.asc.edu From: ross@cgl.ucsf.EDU Date: Mon, 4 Jan 1999 20:57:55 -0800 (PST) To: gammadas@telis.org Subject: Re: CCL:complex geom calcn protocol You might find 'molecular silverware' by people at Rohm-Haas (Hass?) of interest. It was written up in J. Comp. Chem. a few years ago. Bill Ross GOUTAM DAS, Ph.D BETZDEARBORN (A division of Hercules) PO BOX 4300, 9669 GROGANS MILL ROAD THE WOODLANDS, TX 77387-4300 # 281.367.6201 xt 425///email:gammadas@telis.org From chemistry-request@www.ccl.net Wed Jan 13 22:17:34 1999 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id WAA22740 Wed, 13 Jan 1999 22:17:27 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA24526; Thu, 14 Jan 99 11:15:50 -0800 Date: Thu, 14 Jan 1999 11:15:50 -0800 (PST) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" Subject: fasta3 build question. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, Did anyone build fasta3 in linux(egcs)? When I built it, it had some problem in thread? Did anyone have\ experience about it? Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725