From katagiri@nrim.go.jp Wed Jun 24 02:23:26 1998 Received: from kugane.nrim.go.jp (kugane.nrim.go.jp [144.213.2.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA25309 Wed, 24 Jun 1998 02:23:25 -0400 (EDT) Received: from hana.nrim.go.jp ([144.213.34.128]) by kugane.nrim.go.jp (8.8.8+2.7Wbeta7/NRIMSep-97) with SMTP id PAA03536 for ; Wed, 24 Jun 1998 15:23:23 +0900 (JST) Received: from hana (localhost [127.0.0.1]) by hana.nrim.go.jp (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id PAA02434 for ; Wed, 24 Jun 1998 15:23:20 +1000 Sender: katagiri@nrim.go.jp Message-ID: <35908D48.167E@nrim.go.jp> Date: Wed, 24 Jun 1998 15:23:20 +1000 From: katagiri Organization: National Research Institute for Metals X-Mailer: Mozilla 3.01SGoldC-SGI [ja_euc] (X11; I; IRIX64 6.4 IP30) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: pseudopot for rare earth elements Content-Type: text/plain; charset=iso-2022-jp Content-Transfer-Encoding: 7bit Dear My colleagues, I would like to construct pseudopotentials for rare earth elements. Does anyone know any package? Any information will be appreciated. Regards, -Masa Katagiri -- ----------------------------------------------------------------------- Masa Katagiri E-mail:katagiri@nrim.go.jp http://www.nrim.go.jp (Office) National Research Institute for Metals (NRIM) Sengen 1-2-1, Tsukuba, Ibaraki 305, Japan ----------------------------------------------------------------------- From ep7@dent.okayama-u.ac.jp Wed Jun 24 03:40:17 1998 Received: from deews1.dent.okayama-u.ac.jp (deews1.dent.okayama-u.ac.jp [150.46.202.36]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA26065 Wed, 24 Jun 1998 03:40:12 -0400 (EDT) From: ep7@dent.okayama-u.ac.jp Received: from [150.46.140.80] (yobou2.dent.okayama-u.ac.jp [150.46.140.80]) by deews1.dent.okayama-u.ac.jp (8.8.8/3.6W) with SMTP id QAA10264 for ; Wed, 24 Jun 1998 16:41:29 +0900 (JST) Message-Id: <199806240741.QAA10264@deews1.dent.okayama-u.ac.jp> Date: Wed, 24 Jun 1998 16:57:45 +0900 To: CHEMISTRY@www.ccl.net Subject: (H2O)2 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Sir: I would like to ask about paper for interaction energy of water dimer corrected BSSE. Thank you. Masao Masamura Preventive Dentistry Okayama University Dental School Shikata-cho, 2-5-1 Okayama 700 Japan FAX: 81-86-235-6714 e-mail: ep7@dent.okayama-u.ac.jp From manettif@unisi.it Wed Jun 24 07:17:06 1998 Received: from sivax.unisi.it (sivax.unisi.it [193.205.4.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA27740 Wed, 24 Jun 1998 07:17:04 -0400 (EDT) Received: from unisi.it ([193.205.4.77]) by sivax.unisi.it with SMTP; Wed, 24 Jun 1998 13:16:19 +0200 (MET-DST) Sender: fabrizio@www.ccl.net Message-ID: <3590E00E.C4030D7E@unisi.it> Date: Wed, 24 Jun 1998 13:16:30 +0200 From: "Dr. Fabrizio Manetti" Organization: Universita' degli Studi di Siena X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Sulfonate params Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netters, I'm working with some naphthalene sulfonates. Does anyone know where I can find any references? Does anyone have force field parameters for these types of functional groups? I'll summarize to the list. Thanks in advance for your help. Cheers, Fabrizio ******************************** Dr. Fabrizio Manetti Dip. Farmaco Chimico Tecnologico Universita' degli Studi di Siena Banchi di Sotto 55 53100 Siena, Italy Phone: ++39 577 298 359 ******************************** From svedung@phc.chalmers.se Wed Jun 24 08:57:34 1998 Received: from idun.phc.chalmers.se (idun.phc.chalmers.se [129.16.97.44]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA28762 Wed, 24 Jun 1998 08:57:33 -0400 (EDT) Received: from fkrs2.phc.chalmers.se (fkrs2.phc.chalmers.se [129.16.97.48]) by idun.phc.chalmers.se (8.8.8/8.8.7) with ESMTP id OAA12144 for ; Wed, 24 Jun 1998 14:57:33 +0200 Received: (from svedung@localhost) by fkrs2.phc.chalmers.se (8.8.8/8.8.8) id OAA16201; Wed, 24 Jun 1998 14:57:33 +0200 Date: Wed, 24 Jun 1998 14:57:32 +0200 (MDT) From: Harald Svedung To: CHEMISTRY@www.ccl.net Subject: propane Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I would like to know if there are any good intramolecular potential functions for propane arround, preferrably reproducing the 27 normal mode frequenzies and having fair dissociation energies. Any pointer is welcome! thanks in advance yours /Harald Harald Svedung (M.Sc.) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone: +46-31-240897 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden www.che.chalmers.se/~svedung/ From jdillen@msi.com Wed Jun 24 09:36:39 1998 Received: from vishnu.msicam.co.uk (vishnu.msicam.co.uk [192.190.183.28]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA29233 Wed, 24 Jun 1998 09:36:38 -0400 (EDT) Received: from manu (manu.msicam.co.uk [192.190.183.130]) by vishnu.msicam.co.uk (8.8.8/8.8.8) with SMTP id OAA20679; Wed, 24 Jun 1998 14:29:58 +0100 (BST) Received: by localhost with Microsoft MAPI; Wed, 24 Jun 1998 14:29:44 +0100 Message-ID: <01BD9F7C.87FB33F0.jdillen@msi.com> From: Jan Dillen Reply-To: "jdillen@msi.com" To: "'Harald Svedung'" Cc: "CHEMISTRY@www.ccl.net" Subject: RE: propane Date: Wed, 24 Jun 1998 14:29:43 +0100 Organization: Molecular Simulations X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit On Wednesday, June 24, 1998 13:58, Harald Svedung [SMTP:svedung@phc.chalmers.se] wrote: > Dear CCLers, > > I would like to know if there are any good intramolecular potential > functions for propane arround, preferrably reproducing the 27 normal mode > frequenzies and having fair dissociation energies. Any pointer is > welcome! > If you are willing to accept heat of formation as a negative dissociation energy: EFF93 - J. Comput. Chem., 16 (1995), 595-609 MM4 - J. Comput. Chem. , 17 (1996) 642-668 --- Jan Dillen From EILMES@Trurl.ch.uj.edu.pl Wed Jun 24 09:55:07 1998 Received: from if.uj.edu.pl (root@jetta.if.uj.edu.pl [149.156.64.210]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA29526 Wed, 24 Jun 1998 09:55:04 -0400 (EDT) Received: from Trurl.ch.uj.edu.pl (trurl.ch.uj.edu.pl [149.156.71.254]) by if.uj.edu.pl (8.8.7/8.7.1) with ESMTP id QAA25661 for ; Wed, 24 Jun 1998 16:05:45 +0200 (MET DST) Received: from TRURL/MAILQUEUE by Trurl.ch.uj.edu.pl (Mercury 1.40); 24 Jun 98 15:52:10 GMT+2 Received: from MAILQUEUE by TRURL (Mercury 1.40); 24 Jun 98 15:52:05 GMT+2 From: "Andrzej Eilmes" Organization: Faculty of Chemistry, UJ To: chemistry@www.ccl.net Date: Wed, 24 Jun 1998 15:52:04 MET+2 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Quadruple precision HQRII.F Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: Dear CCLers, Is anyone of you aware of a quadruple precision (real*16) Fortran version of the diagonalisation routine HQRII.F ? F90 compiler for Digital Unix allows to use real*16 variables, however, there are some constants in the routine which are machine-precision dependent (and some which *probably* are, although this is not explicitly stated) therefore I wonder whether anyone has tried to adjust these constants for higher accuracy calculations and tested the program. I would be grateful for any information. Andrzej Eilmes ---------------------------------------------------------------- Dr Andrzej Eilmes eilmes@trurl.ch.uj.edu.pl Faculty of Chemistry, Jagiellonian University, Cracow, Poland Phone: (48-12) 6336377 ext. 213 Fax: (48-12) 6340515 ---------------------------------------------------------------- From elewars@alchemy.chem.utoronto.ca Wed Jun 24 11:51:26 1998 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA01158 Wed, 24 Jun 1998 11:51:26 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id LAA01870 for chemistry@www.ccl.net; Wed, 24 Jun 1998 11:51:25 -0400 (EDT) Date: Wed, 24 Jun 1998 11:51:25 -0400 (EDT) From: "E. Lewars" Message-Id: <199806241551.LAA01870@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: REFS TO WATER DIMER, BSSE 1998 June 24, Wed Masao Masamura asked for refs to the water dimer and BSSE. J Phys Chem 1992, 96, 5019-5029 J Chem Phys 1992, 97, 6649-6662 J Phys Chem 1995, 99, 8091-8107 J Phys Chem 1996, 100, 2993-2997 Accounts of Chemical Research 1996, 29, 536-543 Water hexamer: Chem Phys Letters 1991, 176, 41-45 ======================== E. Lewars ====================== From tapas@risky3.thchem.siu.edu Wed Jun 24 12:16:31 1998 Received: from risky3.thchem.siu.edu (risky3.thchem.siu.edu [131.230.89.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA01527 Wed, 24 Jun 1998 12:16:30 -0400 (EDT) Received: (from tapas@localhost) by risky3.thchem.siu.edu (AIX4.2/UCB 8.7/8.7) id LAA21636; Wed, 24 Jun 1998 11:21:37 -0500 (CDT) Date: Wed, 24 Jun 1998 11:21:33 -0500 (CDT) From: Tapas Kar To: ep7@dent.okayama-u.ac.jp cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:(H2O)2 In-Reply-To: <199806240741.QAA10264@deews1.dent.okayama-u.ac.jp> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Here is a good reference for you. "Hydrogen Bonding, A theoretical perspective" by Steve Scheiner, Oxford Univ. Press. ISBN 0-19-509011-x On Wed, 24 Jun 1998 ep7@dent.okayama-u.ac.jp wrote: > Date: Wed, 24 Jun 1998 16:57:45 +0900 > From: ep7@dent.okayama-u.ac.jp > To: CHEMISTRY@www.ccl.net > Subject: CCL:(H2O)2 > > Dear Sir: > > I would like to ask about paper for interaction energy of water > dimer corrected BSSE. > > Thank you. > > Masao Masamura > Preventive Dentistry > Okayama University Dental School > Shikata-cho, 2-5-1 > Okayama 700 > Japan > FAX: 81-86-235-6714 > e-mail: ep7@dent.okayama-u.ac.jp > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: ep7@dent.okayama-u.ac.jp > -- Original Sender From: Address: ep7@dent.okayama-u.ac.jp > 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 > > ----------------- Tapas Kar, Ph. D Asst. Scientist Department of Chemistry Southern Illinois University at Carbondale Illinois 62901-4409 Fax: (618) 453 6408 Tel: (618) 453 6433 From Bernd.Hartke@RUS.Uni-Stuttgart.DE Wed Jun 24 13:21:57 1998 Received: from artemis.rus.uni-stuttgart.de (artemis.rus.uni-stuttgart.de [129.69.18.28]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA02772 Wed, 24 Jun 1998 13:21:48 -0400 (EDT) Received: from servus02.rus.uni-stuttgart.de (servus02-fd.rus.uni-stuttgart.de [129.69.18.202]) by artemis.rus.uni-stuttgart.de (8.8.7/8.8.7) with SMTP id TAA25888 for ; Wed, 24 Jun 1998 19:21:42 +0200 (MET DST) env-from (itcbernd@servus.rus.uni-stuttgart.de) Received: from servint2.rus.uni-stuttgart.de by servus02.rus.uni-stuttgart.de (AIX 4.1/UCB 5.64/SERVus-1.2) id AA42608; Wed, 24 Jun 1998 19:21:42 +0200 Received: by servint2.rus.uni-stuttgart.de (AIX 4.1/UCB 5.64/4.03) id AA38116; Wed, 24 Jun 1998 19:21:41 +0200 From: Bernd.Hartke@RUS.Uni-Stuttgart.DE (Bernd Hartke) Message-Id: <9806241721.AA38116@servint2.rus.uni-stuttgart.de> Subject: CCL: more recent water dimer (and hexamer) refs To: chemistry@www.ccl.net Date: Wed, 24 Jun 1998 19:21:41 +0200 (MES) X-Mailer: ELM [version 2.4 PL25 PGP6] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit In reply to a question by Masao Masamura, for refs to the water dimer and BSSE, E.Lewars supplied some dimer references. I would like to add the following to his list: M.Schuetz et al., J.Chem.Phys. 107 (1997) 4597. This study treats the dimer at the MP2 level with _very_ large basis sets and explicitly discusses the influence of BSSE and other errors. E.Lewars also pointed to a reference on the water hexamer (Chem Phys Letters 1991, 176, 41-45). This work is by now slightly outdated, in particular it arrives at a proposed global minimum that is qualitatively different from later work using higher-level calculations (MP2 instead of HF-SCF), e.g. - C.J.Tsai and K.D.Jordan, Chem.Phys.Lett. 213 (1993) 181. - D.C.Clary et al., Nature 381 (1996) 501; J.Phys.Chem. 100 (1996) 18014. Note that recent experimental work seems to be in agreement with the cage structure found in these theoretical studies: - Saykally et al., J.Phys.Chem. A 101 (1997) 8995. I should also mention that M.Schuetz, Prof. H.-J.Werner and myself have just developed an improved NEMO potential that reproduces ab-initio MP2 energies of all the important pentamer and hexamer minimum structures perfectly (including the cage). A paper on these results will be submitted in a few weeks. Bernd Hartke -- PD Dr. Bernd Hartke e-mail: hartke@theochem.uni-stuttgart.de Dep. of Theoretical Chemistry e-mail: bernd.hartke@rus.uni-stuttgart.de University of Stuttgart http://www.theochem.uni-stuttgart.de/~hartke Pfaffenwaldring 55 Phone: +49-711-685-4409 70569 Stuttgart FAX: +49-711-685-4442 GERMANY From dew01@xray5.chem.louisville.edu Tue Jun 23 10:35:17 1998 Received: from xray5.chem.louisville.edu (xray5.chem.louisville.edu [136.165.12.18]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id KAA12161 Tue, 23 Jun 1998 10:35:16 -0400 (EDT) Received: (from dew01@localhost) by xray5.chem.louisville.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id KAA01745 for CHEMISTRY@www.ccl.net; Tue, 23 Jun 1998 10:38:30 -0400 From: "Donald E. Williams" Message-Id: <9806231038.ZM1743@xray5.chem.louisville.edu> Date: Tue, 23 Jun 1998 10:38:29 -0400 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Molecular packing and force field development Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii I have created a web page describing my molecular packing and force field development programs. The programs are: mpa - Molecular Packing Analysis mpg - Molecular Packing Graphics pdm97- Potential-Derived Multipoles nbp - Non-Bonded Parameters The address is http://www.louisville.edu/~dewill01 -- Dr. Donald E. Williams email:dew01@xray5.chem.louisville.edu Department of Chemistry University of Louisville phone:502-852-5975 Louisville, KY 40292 fax: 502-852-8149 From andrew@info.combichem.com Tue Jun 23 11:45:51 1998 Received: from hermes.combichem.com (hermes.combichem.com [207.158.48.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA13207 Tue, 23 Jun 1998 11:45:50 -0400 (EDT) Received: from info.combichem.com ([207.158.46.99]) by hermes.combichem.com (Post.Office MTA v3.1.2 release (PO205-101c) ID# 0-49457U200L100S0) with ESMTP id AAA336 for ; Tue, 23 Jun 1998 08:42:09 -0700 Message-ID: <358FCD05.6505A4A5@info.combichem.com> Date: Tue, 23 Jun 1998 08:43:01 -0700 From: Andrew Smellie X-Mailer: Mozilla 4.04 [en] (WinNT; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: First call for papers: Anaheim ACS, session on Conformational Analysis Content-Type: multipart/alternative; boundary="------------EF55EC2A617E15111CB238A9" --------------EF55EC2A617E15111CB238A9 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All, I'm organizing a session at the Anaheim ACS in April '98 devoted to conformational analysis (CA). It's time there was session on this subject, since CA forms the basis of so many compuational chemistry problems (hypothesis and pharmacophore generation, database searching, docking etc). I'd like to make this a lively session that focuses not only on CA algorithms, but also examines the problem domain and identifies the problems to be solved, the metrics used to measure success and future directions. If you are interested in participating, please send me an email describing your proposed talk. Below is the short abstract I submitted to the ACS recently, and I very much look forward to your participation in this session. I will be out of the office on vacation from 6/29 to 7/12, but will respond asap. Session Title: Conformational Analysis: Stepping up to the new challenges. The interest in processing millions of compounds from high-throughput screening and combinatorial or virtual libraries has placed new demands on the ability to conformationally analyze large numbers of molecules. Often the generation of good low-energy conformations for these large datasets is the major bottleneck in deducing 3D information from these molecules. This session focuses on models, tools and techniques for deriving 3D information from large numbers of molecules. Andrew Smellie. (650)-842-0560 asmellie@combichem.com --------------EF55EC2A617E15111CB238A9 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit

Dear All,

I'm organizing a session at the Anaheim ACS in April '98 devoted to conformational analysis (CA).
It's time there was session on this subject, since CA forms the basis of so many compuational
chemistry problems (hypothesis and pharmacophore generation, database searching, docking etc).

I'd like to make this a lively session that focuses not only on CA algorithms, but also examines
the problem domain and identifies the problems to be solved, the metrics used to measure
success and future directions.

If you are interested in participating, please send me an email describing your proposed talk.

Below is the short abstract I submitted to the ACS recently, and I very much look forward
to your participation in this session.

I will be out of the office on vacation from 6/29 to 7/12, but will respond asap.

Session Title: Conformational Analysis: Stepping up to the new challenges.
The interest in processing millions of compounds from high-throughput screening and combinatorial
or virtual libraries has placed new demands on the ability to conformationally analyze large
numbers of molecules. Often the generation of good low-energy conformations for these large
datasets is the major bottleneck in deducing 3D information from these molecules. This session
focuses on models, tools and techniques for deriving 3D information from large numbers of molecules.
 

Andrew Smellie.
(650)-842-0560
asmellie@combichem.com --------------EF55EC2A617E15111CB238A9-- From bernhold@npac.syr.edu Tue Jun 23 15:19:34 1998 Received: from snake.npac.syr.edu (snake.npac.syr.edu [128.230.162.60]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id PAA16604 Tue, 23 Jun 1998 15:19:33 -0400 (EDT) Received: from localhost (bernhold@localhost) by snake.npac.syr.edu (950413.SGI.8.6.12/8.6.6) with SMTP id PAA12486; Tue, 23 Jun 1998 15:18:38 -0400 Message-Id: <199806231918.PAA12486@snake.npac.syr.edu> X-Authentication-Warning: snake.npac.syr.edu: Host localhost didn't use HELO protocol Reply-to: bernhold@npac.syr.edu To: CHEMISTRY@www.ccl.net Subject: Re: CCL:CCL:Is SGI O2/150 much faster than PII/233? In-reply-to: <13710.39721.2250.588392@liposome.genebee.msu.su> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-ID: <12483.898629518.1@snake.npac.syr.edu> Date: Tue, 23 Jun 1998 15:18:38 -0400 From: "David E. Bernholdt" I don't know about any specific comparisons between the R5000 or R10000 in an O2 and the PII or AMD-K6-2, but... It is important to remember increasingly, system components other than the CPU can strongly effect the performance for "real" applications. With memory busses at 66 or 100 MHz, it can be quite hard to feed the CPU fast enough to get the peak performance, unless everything is coming out of cache. And the utility of the cache will depend strongly on the applications and algorithms involved. Balance may be more important than raw CPU performance. On Mon, 22 Jun 1998 22:05:20 +0400 (MSD) Eugene Leitl wrote: > Yubo Fan writes: > > > Recently, someone told me that SGI O2/150 workstation could run G94 much > > faster than G94W run on PII/233? Is it true? Could you please give some > > advice? > > [...] The AMD-K6-2/333 has a peak floating point performance of > 1.333 Gigaflops... -- 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 ccl@www.ccl.net Tue Jun 23 15:54:02 1998 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA17162 Tue, 23 Jun 1998 15:54:01 -0400 (EDT) Received: from ETSU.ETSU.EDU (ETSU.etsu.edu [151.141.4.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id PAA15506 for ; Tue, 23 Jun 1998 15:53:58 -0400 (EDT) Message-Id: <199806231953.PAA15506@ccl.net> Received: from ETSU.ETSU.EDU by ETSU.ETSU.EDU (IBM VM SMTP V2R2) with BSMTP id 2958; Tue, 23 Jun 98 15:52:49 EDT Received: from ETSU.ETSU.Edu (NJE origin R29CLOSE@ETSU) by ETSU.ETSU.EDU (LMail V1.2c/1.8c) with BSMTP id 5406; Tue, 23 Jun 1998 15:52:49 -0400 Date: Tue, 23 Jun 98 15:44:32 EDT From: Dave Close Organization: East Tennessee State University Subject: Linux -malign-double? To: chemistry@ccl.net Dear CCL Users: Recently I posted a LINUX makefile for installing G94 on a Pentium running RedHat Linux. Milan Hodoscek wrote me to say that I had omitted the -malign-double compiler option. In fact I recalled his posting of this several months ago. When we tried it here there was hardly any difference in runtime. Milan has written me again to say this option could make a large difference in run time on a Pentium. My question is does anyone know about this option? Is it now a default setting so now it is not important? Or have I done something wrong? To see what we used go to: http://physweb,etsu.edu/c_r_g94_linux.html Regards, Dave Close. From robert@pauli.utmb.edu Tue Jun 23 19:26:47 1998 Received: from nmr.utmb.edu (dggin1.utmb.edu [129.109.73.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id TAA21543 Tue, 23 Jun 1998 19:26:46 -0400 (EDT) Received: from pauli.utmb.edu (pauli.utmb.edu [129.109.73.25]) by nmr.utmb.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id SAA03705 for <@nmr.utmb.edu:CHEMISTRY@www.ccl.net>; Tue, 23 Jun 1998 18:34:13 -0500 Received: (from robert@localhost) by pauli.utmb.edu (980616/Sun/9.16./980616/Sun_Microsystems) id SAA16803 for CHEMISTRY@www.ccl.net; Tue, 23 Jun 1998 18:27:45 -0500 (CDT) From: "Robert Fraczkiewicz" Message-Id: <9806231827.ZM16801@pauli.utmb.edu> Date: Tue, 23 Jun 1998 18:27:45 -0500 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: CCL:Uploading PDB files to a CGI script Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Netters: Thanks to all who replied to my inquiry. In my original posting I have reported a web server timing out when large files are uploaded via an HTML form. After some wrestling with the script I have figured out that the web server is basically OK and can accept data of any size. The problem is with Netscape browsers: server times out because browsers cannot handle large amounts of data from CGI programs. Let me present an example: This simple HTML form will let you upload any readable disk file into a CGI program: Simple form

Enter PDB file name:

The CGI program I used takes the data and returns it to the browser as plain text (compile it and replace "your_CGI_script" by the executable pathname): #include #include main() { unsigned long i, n=0; char *cl; printf("Content-type:text/plain\n\n"); cl=getenv("CONTENT_LENGTH"); if(cl) n=atoi(cl); for(i=0; i Message-Id: <199806241817.OAA01368@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: Re: Is SGI O2/150 much faster than PII/233? Cc: mn1@helix.nih.gov On Tue, 23 Jun 98 16:49:27, Serguei Patchkovskii wrote: > > I don't have benchmark results for either exactly an SGI O2/150 or for G94W > > run on PII/233. However, in the context of extensive benchmarking of G94 on > > a range of computers--from Cray J90 to Alpha and Pentium II/Pro systems-- > > (paper forthcoming in J. Chem. Inf. Comput. Sci.), we have obtained results > > for two systems that are close enough that they might allow extrapolation to > > the computers you're looking at. > > > > Aggregate job cpu times (sec) for G94 test jobs 1, 28, 94, 155, 194, 296, 302: > > SGI Origin 200, R10000 195 MHz CPU, 64 MB RAM: 923 sec > > Pentium II 300 MHz CPU, 64 MB RAM, Windows NT: 1283 sec > > > > So I would venture to guess that an SGI O2/150 workstation would run G94 > > faster than G94W run on PII/233, but not "much faster". I'd expect on the > > order of 50% more CPU time on the PII/233 compared to SGI O2/150. > > Sorry, Marc, but this estimation is not valid. R5k is a very different CPU > from R10k. In particular, the R5k was optimized for single precision floating > point. It does not perform well for double precision, which is that Gaussian > is going to excersize. It is also an in-order CPU, and does not tolerate > memory latencies well. The R10k, on the other hand, is super-scalar out-of- > order processor, and has been optimized for double precision floating point. > At the same clock speed, R10k may easily be four times faster for double- > precision floating point than R5k. [snip] I agree. I had overlooked the fact that the SGI O2/*150* is (may be? --see below) not an R10k machine like the newer R10k@250MHz and R10k@195MHz O2's. This indeed would invalidate my comparison. (The original question didn't mention CPU type.) But then, HUMBEL Stephane wrote: > Hi, as I am going to buy an Origin 200 and I have an O2, I did the same > benchmark as patchkov, here are the results > > > Aggregate job cpu times (sec) for G94 test jobs 1, 28, 94, 155, 194, 296, 302: > > SGI Origin 200, R10000 195 MHz CPU, 64 MB RAM: 923 sec > > Pentium II 300 MHz CPU, 64 MB RAM, Windows NT: 1283 sec > SGI O2 R10000 150 Mhz CPU, 320MB RAM: 1418 sec =====?? > if you are aware of better O2 results I'd like to know that. I am not very > happy with my mips4 compilation. (G94 rev E.2, this bench was with another > job running on the same machine, but it should not matter for cpu results > as I do have enough memory). Carlos Simmerling pointed out to me that there is no such thing as a *195*MHz R10k Origin 200, but only a 180MHz version. The machine on which the above G94 timing was obtained had indeed an R10k 195MHz CPU, but was an Indigo2 system. (I got confused because the machine with the same hostname is *now* an Origin 200 but was an Indigo2 at the time of the benchmarking.) Also, these small test jobs are not always a good indicator for the performance of a system for larger 'real-life' G94 jobs. We've clearly seen this in our benchmarking, where we also timed larger DFT jobs. However, the two machines I mentioned were unfortunately not included in the DFT part of our comparison. I apologize for the confusion that my posting may have created. I guess I should have stuck to the numbers we've actually measured and not tried to guess benchmark outcomes :-\ Finally, lest my posting may create the impression that I was basically trying to say "these commodity-type computers such as PII systems cannot do real serious (G94) work", let me assure you that the exact opposite is true (as our benchmark study clearly showed.) Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 37 Convent Dr, MSC 4255 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute, & Center for Molecular Modeling, Ctr. for Information Technology, NIH ------------------------------------------------------------------------ From shenkin@still3.chem.columbia.edu Wed Jun 24 15:56:39 1998 Received: from mailrelay1.cc.columbia.edu (cu41754@mailrelay1.cc.columbia.edu [128.59.35.143]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA05409 Wed, 24 Jun 1998 15:56:38 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id PAA19922; Wed, 24 Jun 1998 15:56:29 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id PAA14359; Wed, 24 Jun 1998 15:56:27 -0400 From: "Peter Shenkin" Message-Id: <9806241556.ZM14357@still3.chem.columbia.edu> Date: Wed, 24 Jun 1998 15:56:27 -0400 In-Reply-To: "M. Nicklaus" "CCL:G:Is SGI O2/150 much faster than PII/233?" (Jun 24, 2:17pm) References: <199806241817.OAA01368@helix.nih.gov> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: "M. Nicklaus" , CHEMISTRY@www.ccl.net Subject: Re: CCL:G:Is SGI O2/150 much faster than PII/233? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Jun 24, 2:17pm, M. Nicklaus wrote: > Subject: CCL:G:Is SGI O2/150 much faster than PII/233? > ... these small test jobs are not always a good indicator for the performance > of a system for larger 'real-life' G94 jobs. We've clearly seen this in our > benchmarking, where we also timed larger DFT jobs. However, the two machines > I mentioned were unfortunately not included in the DFT part of our comparison. I'm glad someone finally said this. For CPU bound jobs, it's clear that Pentium II will be faster than O2 and it's to its credit that it's competitive with R10000. But many large Gaussian jobs are IO bound, and here a Pentium II with a conventional architecture will probably suffer. -P. -- *********** How can we have ethnic music without ethnic hatred? *********** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From dspellmeyer@combichem.com Wed Jun 24 17:47:18 1998 Received: from hermes.combichem.com (hermes.combichem.com [207.158.48.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA07187 Wed, 24 Jun 1998 17:47:17 -0400 (EDT) Received: from karpo.info.combichem.com ([207.158.46.107]) by hermes.combichem.com (Post.Office MTA v3.1.2 release (PO205-101c) ID# 0-49457U200L100S0) with SMTP id AAA325 for ; Wed, 24 Jun 1998 14:43:30 -0700 Message-Id: <3.0.5.32.19980624144927.0080cc60@mail.combichem.com> X-Sender: dspellmeyer@mail.combichem.com X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Wed, 24 Jun 1998 14:49:27 -0700 To: CHEMISTRY@www.ccl.net From: dspellmeyer@combichem.com (David Spellmeyer) Subject: Call for Papers - Anaheim ACS Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" SYMPOSIUM ANNOUNCEMENT AND CALL FOR PAPERS Applications of Computers in Combinatorial Chemistry to be held at the American Chemical Society Meeting in Anaheim, CA March 21-25, 1999 Sponsored by the Division of Computers in Chemistry This symposium will cover all aspects of computational chemistry applied to the field of molecular diversity and combinatorial chemistry. This includes design and analysis of combinatorial libraries, design of conformationally constrained libraries, computational measures of diversity, information-based libraries, coverage-based libraries, and others. New algorithms and applications of existing algorithms are welcome. The due date for 150 word abstracts is November 18, 1998. For planning purposes, however, please let me know if you plan to submit an abstract no later than July 31, 1998. David Spellmeyer CombiChem, Inc. 1804 Embarcadero Road, Suite 201 Palo Alto, CA 94306 (650)-842-0560 ext. 105 (650)-842-0575 FAX dspellmeyer@combichem.com http://www.combichem.com From katagiri@nrim.go.jp Wed Jun 24 23:40:56 1998 Received: from kugane.nrim.go.jp (kugane.nrim.go.jp [144.213.2.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id XAA11096 Wed, 24 Jun 1998 23:40:54 -0400 (EDT) Received: from momokusa.nrim.go.jp ([144.213.240.13]) by kugane.nrim.go.jp (8.8.8+2.7Wbeta7/NRIMSep-97) with ESMTP id MAA17923 for ; Thu, 25 Jun 1998 12:40:52 +0900 (JST) Received: from localhost (momokusa.nrim.go.jp [144.213.240.13]) by momokusa.nrim.go.jp (8.8.7+2.7Wbeta7/3.6Wbeta6) with SMTP id MAA05218 for (); Thu, 25 Jun 1998 12:40:51 +0900 (JST) Date: Thu, 25 Jun 1998 12:40:51 +0900 (JST) From: KATAGIRI Masahiko Message-Id: <199806250340.MAA05218@momokusa.nrim.go.jp> To: chemistry@www.ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp Subject: summary: pseudopotentials for rare earth elements X-Subject: summary: pseudopotentials for rare earth elements X-Mailer: LaMail Dear my colleagues, I posted a question on pseudopotential generation for rare earth elements. This is the summary. I thank you very much for your help. Regards, -Masa Katagiri (question) I would like to construct pseudopotentials for rare earth elements. Does anyone know any package? 1. MSI's CASTEP code offers pseudopotentails for all elements of the PSE. Find more info on http://www.msi.com/info/products/modules/CASTEP.html Best regards Klaus Klaus Stark,PhD Application Scientist Molecular Simulations Ltd. 230/250 The Quorum, Barnwell Road Cambridge CB5 8RE England 2. Our group has developed pseudopotentials for the Ln's in conjunction with Walt Stevens @ the Natl. Inst. of Standards & Tech. AUTHOR(s): Cundari, Thomas R. Stevens, Walter J. TITLE(s): Effective core potential methods for the lanthanides. In: The journal of chemical physics. APR 01 1993 v 98 n 7 Page: 5555 An application to the trihalides is described in... AUTHOR(s): Cundari, Thomas R. Sommerer, Shaun O. Tippett, Lynn TITLE(s): Effective core potential studies of lanthanide complexes. In: The journal of chemical physics. OCT 22 1995 v 103 n 16 Page: 7058 Our ECPs are incorporated into the GAMESS program (Iowa State), but I am sure will work w/ any other program. Additionally, a considerable amount of research has been done on the Ln ECPs by the Stuttgart group (refs given in the papers). Additionally, a recent paper by myself & an undergraduate research student compares a variety of methods (pseuopotentials included) for Ln complexes. Cundari, T. R., Saunders, L. C., Modeling Lanthanide Coordination Complexes. Comparison of Semiempirical and Classical Methods, Journal of Chemical Information and Computer Sciences; 1998; 38(3); 523-528. Hope this info is of some use. Tom Cundari Associate Professor of Chemistry Professor Tom Cundari phone:901-678-2629 Department of Chemistry email: tcundari@memphis.edu University of Memphis FAX: 901-678-3447 Memphis, TN 38152-6060 www.chem.memphis.edu/compchem.html Research: Comp inorganic chemistry, artificial intelligence apps in chemistry; catalysis; advanced materials; ab initio, semi- empirical & MM modeling of metal complexes *** Starting Fall '98 @ UofM: PhD w/ concentration in Comp Chem & Comp Research on Materials Institute @ U of Memphis ***