From Patrick.Bultinck@rug.ac.be Mon Sep 1 10:21:31 1997 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.8.3/950822.1) id JAA25720; Mon, 1 Sep 1997 09:56:29 -0400 (EDT) Received: from hartree1.rug.ac.be by mserv.rug.ac.be with SMTP id AA29644 (5.67b/IDA-1.5 for ); Mon, 1 Sep 1997 15:53:23 +0200 Received: by hartree1.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA09168; Mon, 1 Sep 1997 15:52:48 +0200 Date: Mon, 1 Sep 1997 15:52:47 +0200 (DFT) From: Patrick Bultinck To: CCL Subject: MM2 (92) atom type list Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear, I am looking for the atom type list of the MM2 program, more specifically a release around 1992. I have a MM3 copy, and have found relevant articles describing mol. mech. parameters. These are given in a table with reference to atom types of MM2. The atom type list has changed over the years, and to use the parameters, I need to exactly know what MM2 atom corresponds to what MM3 atom type. Hope somebody can help with this simple matter, Patrick ***************************************************************************** Patrick Bultinck Ph. D. Student Quantum Chemistry Dept. Inorganic & Physical Chemistry System/Network Administrator University of Ghent Tel. Int'l code/32/9/264.44.44 Krijgslaan 281 (S-3) Fax. Int'l code/32/9/264.49.83 9000 Gent E-mail : Patrick.Bultinck@rug.ac.be Belgium http://allserv.rug.ac.be/~pbultink/ ***************************************************************************** From longo@NPD.UFPE.BR Mon Sep 1 11:21:28 1997 Received: from NPD1.NPD.UFPE.BR for longo@NPD.UFPE.BR by www.ccl.net (8.8.3/950822.1) id LAA25994; Mon, 1 Sep 1997 11:07:10 -0400 (EDT) Received: from rlongo1.dqf.ufpe.br by NPD.UFPE.BR (PMDF V5.1-4 #20469) with ESMTP id <01IN4LWKAKV40001EO@NPD.UFPE.BR> for chemistry@www.ccl.net; Mon, 1 Sep 1997 12:04:54 GMT-3 Date: Mon, 01 Sep 1997 12:10:22 -0300 From: Ricardo Longo Subject: GRINDOL Program To: chemistry@www.ccl.net Message-id: <340ADADE.1DC2D5DC@npd.ufpe.br> MIME-version: 1.0 X-Mailer: Mozilla 4.01 [en] (Win95; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Priority: 3 (Normal) Dear CCLers, Does anyone know how to get the GRINDOL program (J. Lipinski, Int. J. Quantum Chem. 34: 423 (1988), 44: 831 (1992); Spectrochimica Acta 51A: 381 (1995); Chem. Phys. Letters 262: 449 (1996)) or get in touch with the author(s) (Jozef Lipinski)? Thanks a lot. Ricardo Longo longo@npd.ufpe.br From gostowskir@apsu01.apsu.edu Mon Sep 1 19:21:30 1997 Received: from apsu02.apsu.edu for gostowskir@apsu01.apsu.edu by www.ccl.net (8.8.3/950822.1) id SAA28350; Mon, 1 Sep 1997 18:30:45 -0400 (EDT) Received: from gostowskir.apsu.edu by APSU02.APSU.EDU (PMDF V5.1-4 #16785) with ESMTP id <01IN4X7UF8VK001QUY@APSU02.APSU.EDU> for chemistry@www.ccl.net; Mon, 1 Sep 1997 17:28:34 CST Date: Mon, 01 Sep 1997 17:31:05 -0500 From: Rudy Gostowski Subject: defining dihedral angles in publications To: chemistry@www.ccl.net Message-id: <01IN4X7UFKXE001QUY@APSU02.APSU.EDU> MIME-version: 1.0 X-Mailer: Microsoft Internet Mail 4.70.1155 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal Would someone please suggest how to define dihedral angles in a manuscript to be submitted to a "non-computational" journal. Is a list of the atom numbers sufficient. thanks, Rudy Gostowski Department of Chemistry Austin Peay State University Box 4547 Clarksville, TN 37044 615-648-7624 FAX 615-648-5996 gostowskir@apsu01.apsu.edu From agiss.com!joelp@agiss.com Thu Aug 28 10:20:36 1997 Received: from resudox.net for agiss.com!joelp@agiss.com by www.ccl.net (8.8.3/950822.1) id JAA06522; Thu, 28 Aug 1997 09:31:51 -0400 (EDT) Received: from agiss.UUCP (uucp@localhost) by resudox.net (8.8.5/8.7.3/resudox) with UUCP id IAA31971; Thu, 28 Aug 1997 08:05:15 -0400 Received: from joelpc.agiss.com () by agiss.com (4.1/SMI-4.1) id AA01668; Thu, 28 Aug 97 08:54:38 EDT Received: by joelpc.agiss.com with Microsoft Mail id <01BCB391.95409A00@joelpc.agiss.com>; Thu, 28 Aug 1997 09:05:51 -0400 Message-Id: <01BCB391.95409A00@joelpc.agiss.com> From: Joel Polowin To: CCL , "'Adnan Hazar'" Subject: RE: Problem with HyperNMR Date: Thu, 28 Aug 1997 09:05:50 -0400 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Adnan Hazar writes: > From: Serge Pachkovsky > > In your particular case, there are 64 atoms and 145 orbitals, so the > shilding tensor calculation should need from 2Mb (for a "generous" > implementation) to 93Mb (for a "wasteful" one). Coupling constants > might need from 32Mb to 132Mb, possibly in addition to the shielding > tensor requirements. Keep in mind what these are back-of-the-envelope > estimations, actual requirements may differ by a factor of 2 or four > in either direction, depending on the actual implementations' quality. The problem is not (or should not be) with the calculation of the shielding tensors and coupling constants -- that should be no real problem for a system of this size. (As you noted in your earlier message, this calculation is completed successfully in a couple of minutes.) But the calculation of the spectrum from those values has an (approximately) exponential dependence on the number of spin states. Or so I believe; I have never understood the details of those calculations very well. It is possible to do the first calculation on many atoms, save the results in a file, and then edit that file to reduce the "NMR Atom" set so that the spectrum is calculated only for fewer atoms. This is not a trivial editing job, however, since you would need to remove blocks of arrays of numbers. What HyperNMR really needs is a way of defining a further subset of "NMR Atoms" -- "Spectrum Atoms". I had suggested something like that to the developer, but there wasn't time to implement it before the last software release. Joel Polowin joelp@agiss.com From weyrich@chclu.chemie.uni-konstanz.de Thu Aug 28 07:20:35 1997 Received: from dg10.chemie.uni-konstanz.de for weyrich@chclu.chemie.uni-konstanz.de by www.ccl.net (8.8.3/950822.1) id GAA05747; Thu, 28 Aug 1997 06:24:58 -0400 (EDT) Received: by dg10.chemie.uni-konstanz.de (MX V4.2 AXP) id 1; Thu, 28 Aug 1997 12:21:57 CET Sender: weyrich@chclu.chemie.uni-konstanz.de Date: Thu, 28 Aug 1997 12:21:57 CET From: weyrich@dg10.chemie.uni-konstanz.de Reply-To: weyrich@chclu.chemie.uni-konstanz.de To: chemistry@www.ccl.net CC: weyrich@chclu.chemie.uni-konstanz.de Message-ID: <009B9735.71240219.1@dg10.chemie.uni-konstanz.de> Subject: RE: CCL:G:cache size affecting G94 calcs Dear Dr. Bausch, I think you are right with your guess. In workstation-type computers including well-known SMP machines, the bandwidth to main memory is a serious bottleneck. It slows down any calculation tremendously for which the instructions of a loop plus the data it works on do not fit into the processor cache. An example: A 75 MHz PowerChallenge with R8000 processors has a bandwidth of about 135 MBytes/sec to main memory (provided the other processors do not use the common bus). The scalar product with two floating-point operations between R*8 vector or matrix elements requires the exchange of 32 bytes. Therefore the Mflops drop to 2*135/32 = 8.4 Mflops as soon as the data have to be fetched from and stored back to the main memory -- far below the nominal peak performance of 300 Mflops. By bus interference it can become even worse. That effect has been investigated in detail by John D. McCalpin, and he has introduced the STREAM benchmark, which measures the bandwidth and the resulting Mflops for c(i)=a(i) (COPY), c(i)=d*a(i) (SCALE), c(i)=a(i)+b(i) (ADD) and c(i)=c(i)+a(i)*b(i) (TRIAD). The programs and results are available via anonymous ftp from ftp.cs.virginia.edu in the directory /pub/stream/ (tables Balance.tbl, Bandwidth.tbl, and MFLOPS.tbl in /pub/stream/Tables/standard/). The SPEC_95 benchmarks catch a bit of the memeory-bandwidth effect by using medium- size test programs, whereas earlier SPECs reflect more or less only the cache performance. It would be extremely helpful for the Comp Chem community to agree on a test suite of benchmarks with varying size (say, S, M, L, XL), preferably GAMESS for ab initio because of its free availability and its being part of SPEC_95 and some MD program. Such a test suite would answer the numerous questions we are seeing in the CCL again and again, and the Comp Chem community is commercially important enough to convince all major computer manufacturers to determine and publish the benchmark data already when announcing a product. To all CCL subscribers: It is only a question of our agreement! I would like to see comments (and encouragements). Sincerely yours, Wolf Weyrich (Professor of Physical Chemistry) ----------------------------------------------------------------------------------- From tcg@chem.unipune.ernet.in Sat Aug 30 11:21:01 1997 Received: from relay6.UU.NET for tcg@chem.unipune.ernet.in by www.ccl.net (8.8.3/950822.1) id LAA19131; Sat, 30 Aug 1997 11:02:58 -0400 (EDT) Received: from sangam.ncst.ernet.in by relay6.UU.NET with ESMTP (peer crosschecked as: sangam.ncst.ernet.in [202.41.110.33]) id QQdevs16473; Sat, 30 Aug 1997 11:02:39 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [144.16.31.4]) by sangam.ncst.ernet.in (8.7.5) with SMTP id UAA02005 for ; Sat, 30 Aug 1997 20:42:18 +0530 (GMT+05:30) Received: from unipune.ernet.in by iucaa (5.65v3.2/SMI-4.1) id AA08498; Sat, 30 Aug 1997 20:29:44 +0500 Received: from chem.unipune.ernet.in by unipune.ernet.in (8.8.5/UNIPUNE-MAILHUB(02.04.97)) id UAA13148; Sat, 30 Aug 1997 20:27:59 -0500 (GMT) Received: by chem.unipune.ernet.in (8.7.5/SMI-SVR4) id UAA00492; Sat, 30 Aug 1997 20:38:16 -0500 Date: Sat, 30 Aug 1997 20:38:16 -0500 From: tcg@chem.unipune.ernet.in (Students of Dr. S.R. Gadre) Message-Id: <199708310138.UAA00492@chem.unipune.ernet.in> To: CHEMISTRY@www.ccl.net Dear Sirs and Madams : We have developed an interesting topography based approach for studying Li+ ...hydrocarbon interactions. Are you aware of any such recent theoretical/experimental studies ? Please let us know. Thanks..........................Shridhar Gadre e-mail address gadre@parcom.ernet.in gadre@unipune.ernet.in gadre@chem.unipune.ernet.in