From dgeuenic@tu-bs.de Tue Jun 23 02:52:38 1998 Received: from rzcomm1.rz.tu-bs.de (root@rzcomm1.rz.tu-bs.de [134.169.9.107]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA07851 Tue, 23 Jun 1998 02:52:33 -0400 (EDT) Received: from rzab0.rz.tu-bs.de (daemon@rzab0.rz.tu-bs.de [134.169.9.28]) by rzcomm1.rz.tu-bs.de (8.8.6/8.8.6) with ESMTP id IAA07669 for ; Tue, 23 Jun 1998 08:52:17 +0200 (METDST) Received: from tu-bs.de (ppp343.ts.rz.tu-bs.de) by rzab0.rz.tu-bs.de with ESMTP (1.37.109.24/15.6) id AA018954727; Tue, 23 Jun 1998 08:52:07 +0200 Sender: NetUser1@ws.rz.tu-bs.de Message-Id: <358F6CE7.2D9A5237@tu-bs.de> Date: Tue, 23 Jun 1998 08:52:56 +0000 From: Daniel Geuenich X-Mailer: Mozilla 4.05 [en] (X11; I; Linux 2.0.33 i586) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: Summary:G:3D-grid of current density tensors Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL-lers, Some days ago I asked the following question: > My question concerns the computation of > NMR/magnetic properties under Gaussian 94. > > I am interested in generating a plot of the current density. > When using the NMR=CSGT or NMR=IGAIM keyword, Gaussian 94 > prints only one current density tensor, but what I need is > a calculation of the current density tensor over a > 3-dimensional grid of points. > > Is it possible to do this with Gaussian 94? When not, which > program is capable of doing such a job? Here is the only answer I received: > Dr. Geuenich, > > G94 does not include this capability. I know that some work > by Todd Keith with ProAIMS and the IGAIM option he worked on could > generate this but I don't believe it is in the distributed version of > ProAIM. Thanks to D. J. Fox. From uccanka@ucl.ac.uk Tue Jun 23 10:02:11 1998 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA11625 Tue, 23 Jun 1998 10:02:09 -0400 (EDT) Received: from [128.40.76.24] (actually host chromium.chem.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (XT-PP) with ESMTP; Tue, 23 Jun 1998 15:02:04 +0100 X-Sender: uccanka@pop-server.bcc.ac.uk Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 23 Jun 1998 15:03:30 +0100 To: chemistry@www.ccl.net From: Nik Kaltsoyannis Subject: Quantum BioInorganic Chemistry Meeting Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id KAA11625 QBIC (Quantum BioInorganic Chemistry) Meeting University of Warwick, UK, July 29-31 1999 Preliminary Announcement Introduction We are pleased to extend an invitation to all interested parties to attend this two-day meeting (a satellite of the WATOC'99 Congress) which will focus on the role of computational techniques in bioinorganic chemistry. Among those who have already accepted invitations to speak are D. Case, Scripps Institute, USA T. Clark, University of Erlangen-Nuernberg, Germany M. Hall, Texas A&M University, USA I. Hillier, University of Manchester, UK B. Roos, University of Lund, Sweden A. Warshel, University of Southern California, USA Date and Location The meeting will take place from lunchtime on Thursday July 29th 1999 to lunchtime on Saturday July 31st 1999 at the University of Warwick. The University of Warwick is situated between the towns of Warwick and Coventry in the Midlands of England, close to Stratford-upon-Avon. Accommodation has been reserved in the University's on-site halls of residence. Abstracts Abstracts will be required of all presentations (oral and poster). Further details will be available with the First Circular (September 1998), but it should be noted that the closing date for abstract submission is Friday 15th January 1999. Fees The fees have not yet been finalised, but it is expected that the combined cost of registration, accomodation and food will be of the order of £250 for industrialists, £150 for academics and £95 for students. First Circular The First Circular will be available from September 1998. Anyone wishing to receive the First Circular should contact Dr R.J. Deeth or Dr. N. Kaltsoyannis at the following addresses: Dr R.J. Deeth Inorganic Computational Chemistry Group Department of Chemistry University of Warwick Coventry CV4 7AL e-mail: r.j.deeth@warwick.ac.uk Ph: +44 1203 523187 Fax: +44 1203 524112 Dr N. Kaltsoyannis Centre for Theoretical and Computational Chemistry University College London 20 Gordon Street London WC1H 0AJ e-mail: n.kaltsoyannis@ucl.ac.uk Ph: +44 171 504 4670 Fax: +44 171 380 7463 From robert@pauli.utmb.edu Tue Jun 23 11:41:26 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 LAA13129 Tue, 23 Jun 1998 11:41:25 -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 KAA02680 for <@nmr.utmb.edu:CHEMISTRY@www.ccl.net>; Tue, 23 Jun 1998 10:48:33 -0500 Received: (from robert@localhost) by pauli.utmb.edu (980616/Sun/9.16./980616/Sun_Microsystems) id KAA14553; Tue, 23 Jun 1998 10:42:21 -0500 (CDT) From: "Robert Fraczkiewicz" Message-Id: <9806231042.ZM14551@pauli.utmb.edu> Date: Tue, 23 Jun 1998 10:42:21 -0500 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Uploading PDB files to a CGI script Cc: werner@newton.utmb.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Netters: We would like to start a web service where people would upload atomic coordinates in PDB format through an HTML form (e.g., by pasting them to TEXTAREA, or direct upload of a disk file via tag) and get results back to their browsers. The form and CGI script work wonderfully as long as the PDB data size stays below ~20000 characters, which is insufficient for any practical application. Above this number the server times out without even touching the CGI script. Is there a limit on the amount of data a web client can transfer to a web server through forms? Personally, I don't believe that. I am sure many of you had faced similar problem. Any hints will be greatly appreciated and summarized on the list. With best regards, Robert Fraczkiewicz University of Texas Medical Branch From krys.radacki@ac.rwth-aachen.de Mon Jun 22 10:44:53 1998 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA27577 Mon, 22 Jun 1998 10:44:46 -0400 (EDT) Received: from ac.rwth-aachen.de (pae102.ac.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-10 #30440) with ESMTP id <01IYJLE54SR0000L40@mail.rwth-aachen.de> for CHEMISTRY@www.ccl.net; Mon, 22 Jun 1998 16:45:38 +0200 Date: Mon, 22 Jun 1998 14:44:07 +0000 From: Krzysztof Radacki Subject: Saddle point search with Gaussian Sender: root@mail.rwth-aachen.de To: CCL Message-id: <358E6DB6.D177CFDB@ac.rwth-aachen.de> Organization: Inst.Inorg.Chem., RWTH Aachen, Germany MIME-version: 1.0 X-Mailer: Mozilla 4.05 [en] (X11; I; Linux 2.1.99 i586) Content-type: multipart/alternative; boundary="------------9B1FF6B2B40C83E565892DFF" --------------9B1FF6B2B40C83E565892DFF Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, I tried to find TS between two minima with Gaussian 94. All standard ways like OPT=TS or QST2 or QST3 failed. When I did 'manual' search for changing one angle which realy differs both structure - opening of 3-membered ring (it means OPT=Z-MATRIX and then in variables deklaration: a1=90.0 S 10 0.01) I found value for witch energii was the highest. FREQ calculations shows for this structure two negative frequencies. When I started for the same input OPT=(saddle=2) I became in log-file: "Optimization stopped. -- Wrong number of Negative eigenvalues: Desiered= 2 Actual= 0 -- Flag reset to prevent archiving." So my question: What are this eigenvalues? I've expected after IR-calculation, that I should be near saddle point or minima. And second: Is there any other way to find TS or saddle point? thanks in advance Krzys Radacki _________________________---------------------------------------------------- ------------------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ----------------------------------------------------------------------------- --------------9B1FF6B2B40C83E565892DFF Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers,
I tried to find TS between two minima with Gaussian 94.  All standard ways like
OPT=TS  or QST2  or QST3 failed.  When I did 'manual' search for changing one
angle which realy differs both structure - opening of 3-membered ring (it means
OPT=Z-MATRIX and then in variables deklaration: a1=90.0 S 10 0.01) I found value
for witch energii was the highest. FREQ calculations shows for this structure
two negative frequencies. When I started for the same input OPT=(saddle=2)
I became in log-file:
"Optimization stopped.
  -- Wrong number of Negative eigenvalues: Desiered=  2  Actual=  0
  -- Flag reset to prevent archiving."

So my question: What are this eigenvalues? I've expected after IR-calculation,
that I should be near saddle point or minima. And second: Is there any other
way to find TS or saddle point?

thanks in advance 

 
       Krzys Radacki
 _________________________----------------------------------------------------
 -------------------------   e-mail:       Krys.Radacki@ac.RWTH-Aachen.DE  ---
 -----------------------------------------------------------------------------
  --------------9B1FF6B2B40C83E565892DFF-- From eugene@liposome.genebee.msu.su Mon Jun 22 14:02:20 1998 Received: from liposome.genebee.msu.su (eugene@liposome.genebee.msu.su [158.250.34.92]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA00570 Mon, 22 Jun 1998 14:02:13 -0400 (EDT) Received: (from eugene@localhost) by liposome.genebee.msu.su (8.8.5/8.8.5) id WAA06057; Mon, 22 Jun 1998 22:05:23 +0400 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Date: Mon, 22 Jun 1998 22:05:20 +0400 (MSD) To: CHEMISTRY@www.ccl.net Subject: CCL:Is SGI O2/150 much faster than PII/233? In-Reply-To: <358BD0FE.96E2DEB@guomai.sh.cn> References: <358BD0FE.96E2DEB@guomai.sh.cn> X-Mailer: VM 6.43 under 20.4 "Emerald" XEmacs Lucid Message-ID: <13710.39721.2250.588392@liposome.genebee.msu.su> 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? > > Thank you very much > > Y. Fan Five minutes ago I visited http://www.amd.com/news/prodpr/9849.html which said, among other things: With its SIMD-style instructions and dual register execution pipelines, the AMD-K6-2 processor can deliver up to four floating point results per clock cycle. The AMD-K6-2/333 has a peak floating point performance of 1.333 Gigaflops, significantly greater than the 0.333-Gigaflop peak performance of a Pentium II 333, or the 0.4-Gigaflop peak performance of a Pentium II 400. The AMD-K6-2/300 has a peak floating point performance of 1.2 Gigaflops, or four times the 3D processing power of a Pentium II 300, rated at peak performance of 0.3 Gigaflops. Pricing and Availability The AMD-K6-2 processor is available now. The AMD-K6-2/333 is priced at $369; the AMD-K6-2/300 at $281; and the AMD-K6-2/266 at $185, each in 1,000-unit quantities. AMD expects to offer a 350-MHz version in the third quarter and a 400-MHz version in the fourth quarter of 1998. Naturally, as mdbnch.f claims for K6/200 512 kBytes 2nd cache/64 MByte SDRAM equal performance as PPro 200/256 kBytes 2nd, I'm interested in seeing according figures (even in absence of gcc optimization for the K6-2). Any preliminary figures? Thanks, Eugene Leitl From bear@ellington.Pharmacy.arizona.edu Mon Jun 22 14:48:04 1998 Received: from ellington.Pharmacy.arizona.edu (ellington.Pharmacy.Arizona.EDU [128.196.140.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA01098 Mon, 22 Jun 1998 14:48:03 -0400 (EDT) Received: (from bear@localhost) by ellington.Pharmacy.arizona.edu (8.8.5/8.8.5) id LAA29878 for chemistry@www.ccl.net; Mon, 22 Jun 1998 11:48:05 -0700 (MST) Date: Mon, 22 Jun 1998 11:48:05 -0700 (MST) From: Soaring Bear Message-Id: <199806221848.LAA29878@ellington.Pharmacy.arizona.edu> To: chemistry@www.ccl.net Subject: cobalt enzymes Hello: Despite the physiological importance of vitamin B12 (cobalamine) and the growing structural data about a dozen cobalt containing enzymes, I have only been able to locate 4 studies that have ventured into molecular dynamics of such things, and they only very crudely. Would anyone who has considered Co parameters please email me? thankyou, bear@pharmacy.arizona.edu SOARING BEAR PhD bear@pharmacy.arizona.edu Computational Medicinal Chemistry; Molecular Modeling; Pharmacognosy Protein & DNA Structural Biology; Cancer Biochemistry; Informatics; QSAR http://ellington.pharmacy.arizona.edu/~bear/resume.html currently seeking employment From fgonzale@lauca.usach.cl Mon Jun 22 16:49:48 1998 Received: from ralun.usach.cl (ralun.usach.cl [158.170.64.21]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA02318 Mon, 22 Jun 1998 16:49:45 -0400 (EDT) Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.8.5/8.8.8) with ESMTP id QAA08939 for ; Mon, 22 Jun 1998 16:49:41 -0400 (CST) Received: from lauca.usach.cl (kekule.usach.cl [158.170.16.6]) by lauca.usach.cl (8.6.12/8.6.12) with ESMTP id QAA11141 for ; Mon, 22 Jun 1998 16:58:34 -0400 Message-ID: <358EC232.C31F4403@lauca.usach.cl> Date: Mon, 22 Jun 1998 16:44:34 -0400 From: Danilo Gonzalez Organization: Universidad de Santiago de Chile X-Mailer: Mozilla 4.04 [en] (WinNT; I) MIME-Version: 1.0 To: "chemistry@www.ccl.net" Subject: Solvation Free Energy Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi all! I looking information about solvation free energy of organic molecules. Anybody have any reference or internet site, where I can look this datas? Thanks a lot! Danilo González Nilo University of Santiago de Chile, Faculty of Chemistry and Biology, Computational Chemistry Lab. Casilla 40, Correo 33, Santiago-CHILE Phone: (562) 681 2575-Anexo:799 ; Fax: (562) 681 2108 URL : http://quimbio.usach.cl/~danilo/ E-mail: fgonzale@lauca.usach.cl =================================================================== From yubofan@guomai.sh.cn Sat Jun 20 11:10:13 1998 Received: from guomai.sh.cn ([202.96.206.69]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA20540 Sat, 20 Jun 1998 11:09:59 -0400 (EDT) Received: from guomai.sh.cn ([202.96.225.203]) by guomai.sh.cn (8.8.8/8.8.8) with ESMTP id XAA00744 for ; Sat, 20 Jun 1998 23:07:49 +0900 (CDT) Message-ID: <358BD0FE.96E2DEB@guomai.sh.cn> Date: Sat, 20 Jun 1998 23:10:54 +0800 From: Yubo Fan Reply-To: yubofan@guomai.sh.cn X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Is SGI O2/150 much faster than PII/233? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, 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? Thank you very much Y. Fan -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab yubofan@fudan.edu.cn The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China ============================================================= From krys.radacki@ac.rwth-aachen.de Mon Jun 22 10:44:53 1998 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA27577 Mon, 22 Jun 1998 10:44:46 -0400 (EDT) Received: from ac.rwth-aachen.de (pae102.ac.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-10 #30440) with ESMTP id <01IYJLE54SR0000L40@mail.rwth-aachen.de> for CHEMISTRY@www.ccl.net; Mon, 22 Jun 1998 16:45:38 +0200 Date: Mon, 22 Jun 1998 14:44:07 +0000 From: Krzysztof Radacki Subject: Saddle point search with Gaussian Sender: root@mail.rwth-aachen.de To: CCL Message-id: <358E6DB6.D177CFDB@ac.rwth-aachen.de> Organization: Inst.Inorg.Chem., RWTH Aachen, Germany MIME-version: 1.0 X-Mailer: Mozilla 4.05 [en] (X11; I; Linux 2.1.99 i586) Content-type: multipart/alternative; boundary="------------9B1FF6B2B40C83E565892DFF" --------------9B1FF6B2B40C83E565892DFF Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, I tried to find TS between two minima with Gaussian 94. All standard ways like OPT=TS or QST2 or QST3 failed. When I did 'manual' search for changing one angle which realy differs both structure - opening of 3-membered ring (it means OPT=Z-MATRIX and then in variables deklaration: a1=90.0 S 10 0.01) I found value for witch energii was the highest. FREQ calculations shows for this structure two negative frequencies. When I started for the same input OPT=(saddle=2) I became in log-file: "Optimization stopped. -- Wrong number of Negative eigenvalues: Desiered= 2 Actual= 0 -- Flag reset to prevent archiving." So my question: What are this eigenvalues? I've expected after IR-calculation, that I should be near saddle point or minima. And second: Is there any other way to find TS or saddle point? thanks in advance Krzys Radacki _________________________---------------------------------------------------- ------------------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ----------------------------------------------------------------------------- --------------9B1FF6B2B40C83E565892DFF Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers,
I tried to find TS between two minima with Gaussian 94.  All standard ways like
OPT=TS  or QST2  or QST3 failed.  When I did 'manual' search for changing one
angle which realy differs both structure - opening of 3-membered ring (it means
OPT=Z-MATRIX and then in variables deklaration: a1=90.0 S 10 0.01) I found value
for witch energii was the highest. FREQ calculations shows for this structure
two negative frequencies. When I started for the same input OPT=(saddle=2)
I became in log-file:
"Optimization stopped.
  -- Wrong number of Negative eigenvalues: Desiered=  2  Actual=  0
  -- Flag reset to prevent archiving."

So my question: What are this eigenvalues? I've expected after IR-calculation,
that I should be near saddle point or minima. And second: Is there any other
way to find TS or saddle point?

thanks in advance 

 
       Krzys Radacki
 _________________________----------------------------------------------------
 -------------------------   e-mail:       Krys.Radacki@ac.RWTH-Aachen.DE  ---
 -----------------------------------------------------------------------------
  --------------9B1FF6B2B40C83E565892DFF-- From eugene@liposome.genebee.msu.su Mon Jun 22 14:02:20 1998 Received: from liposome.genebee.msu.su (eugene@liposome.genebee.msu.su [158.250.34.92]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA00570 Mon, 22 Jun 1998 14:02:13 -0400 (EDT) Received: (from eugene@localhost) by liposome.genebee.msu.su (8.8.5/8.8.5) id WAA06057; Mon, 22 Jun 1998 22:05:23 +0400 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Date: Mon, 22 Jun 1998 22:05:20 +0400 (MSD) To: yubofan@guomai.sh.cn Cc: CHEMISTRY@www.ccl.net Subject: CCL:Is SGI O2/150 much faster than PII/233? In-Reply-To: <358BD0FE.96E2DEB@guomai.sh.cn> References: <358BD0FE.96E2DEB@guomai.sh.cn> X-Mailer: VM 6.43 under 20.4 "Emerald" XEmacs Lucid Message-ID: <13710.39721.2250.588392@liposome.genebee.msu.su> 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? > > Thank you very much > > Y. Fan Five minutes ago I visited http://www.amd.com/news/prodpr/9849.html which said, among other things: With its SIMD-style instructions and dual register execution pipelines, the AMD-K6-2 processor can deliver up to four floating point results per clock cycle. The AMD-K6-2/333 has a peak floating point performance of 1.333 Gigaflops, significantly greater than the 0.333-Gigaflop peak performance of a Pentium II 333, or the 0.4-Gigaflop peak performance of a Pentium II 400. The AMD-K6-2/300 has a peak floating point performance of 1.2 Gigaflops, or four times the 3D processing power of a Pentium II 300, rated at peak performance of 0.3 Gigaflops. Pricing and Availability The AMD-K6-2 processor is available now. The AMD-K6-2/333 is priced at $369; the AMD-K6-2/300 at $281; and the AMD-K6-2/266 at $185, each in 1,000-unit quantities. AMD expects to offer a 350-MHz version in the third quarter and a 400-MHz version in the fourth quarter of 1998. Naturally, as mdbnch.f claims for K6/200 512 kBytes 2nd cache/64 MByte SDRAM equal performance as PPro 200/256 kBytes 2nd, I'm interested in seeing according figures (even in absence of gcc optimization for the K6-2). Any preliminary figures? Thanks, Eugene Leitl From bear@ellington.Pharmacy.arizona.edu Mon Jun 22 14:48:04 1998 Received: from ellington.Pharmacy.arizona.edu (ellington.Pharmacy.Arizona.EDU [128.196.140.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA01098 Mon, 22 Jun 1998 14:48:03 -0400 (EDT) Received: (from bear@localhost) by ellington.Pharmacy.arizona.edu (8.8.5/8.8.5) id LAA29878 for chemistry@www.ccl.net; Mon, 22 Jun 1998 11:48:05 -0700 (MST) Date: Mon, 22 Jun 1998 11:48:05 -0700 (MST) From: Soaring Bear Message-Id: <199806221848.LAA29878@ellington.Pharmacy.arizona.edu> To: chemistry@www.ccl.net Subject: cobalt enzymes Hello: Despite the physiological importance of vitamin B12 (cobalamine) and the growing structural data about a dozen cobalt containing enzymes, I have only been able to locate 4 studies that have ventured into molecular dynamics of such things, and they only very crudely. Would anyone who has considered Co parameters please email me? thankyou, bear@pharmacy.arizona.edu SOARING BEAR PhD bear@pharmacy.arizona.edu Computational Medicinal Chemistry; Molecular Modeling; Pharmacognosy Protein & DNA Structural Biology; Cancer Biochemistry; Informatics; QSAR http://ellington.pharmacy.arizona.edu/~bear/resume.html currently seeking employment From fgonzale@lauca.usach.cl Mon Jun 22 16:49:48 1998 Received: from ralun.usach.cl (ralun.usach.cl [158.170.64.21]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA02318 Mon, 22 Jun 1998 16:49:45 -0400 (EDT) Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.8.5/8.8.8) with ESMTP id QAA08939 for ; Mon, 22 Jun 1998 16:49:41 -0400 (CST) Received: from lauca.usach.cl (kekule.usach.cl [158.170.16.6]) by lauca.usach.cl (8.6.12/8.6.12) with ESMTP id QAA11141 for ; Mon, 22 Jun 1998 16:58:34 -0400 Message-ID: <358EC232.C31F4403@lauca.usach.cl> Date: Mon, 22 Jun 1998 16:44:34 -0400 From: Danilo Gonzalez Organization: Universidad de Santiago de Chile X-Mailer: Mozilla 4.04 [en] (WinNT; I) MIME-Version: 1.0 To: "chemistry@www.ccl.net" Subject: Solvation Free Energy Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi all! I looking information about solvation free energy of organic molecules. Anybody have any reference or internet site, where I can look this datas? Thanks a lot! Danilo González Nilo University of Santiago de Chile, Faculty of Chemistry and Biology, Computational Chemistry Lab. Casilla 40, Correo 33, Santiago-CHILE Phone: (562) 681 2575-Anexo:799 ; Fax: (562) 681 2108 URL : http://quimbio.usach.cl/~danilo/ E-mail: fgonzale@lauca.usach.cl =================================================================== From mn1@helix.nih.gov Tue Jun 23 16:53:54 1998 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA19301 Tue, 23 Jun 1998 16:53:53 -0400 (EDT) Received: (from mn1@localhost) by helix.nih.gov (8.8.5/8.8.5) id QAA01584; Tue, 23 Jun 1998 16:53:51 -0400 (EDT) Date: Tue, 23 Jun 1998 16:53:51 -0400 (EDT) From: "M. Nicklaus" Message-Id: <199806232053.QAA01584@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 Sat, 20 Jun 1998 23:10:54, Yubo Fan wrote: > 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? 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. Hope this helps. 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 billings@helix.nih.gov Tue Jun 23 18:00:11 1998 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA20560 Tue, 23 Jun 1998 18:00:10 -0400 (EDT) Received: (from billings@localhost) by helix.nih.gov (8.8.5/8.8.5) id SAA15194; Tue, 23 Jun 1998 18:00:08 -0400 (EDT) Date: Tue, 23 Jun 1998 18:00:08 -0400 (EDT) From: Eric Billings To: "M. Nicklaus" cc: CHEMISTRY@www.ccl.net Subject: G94 build script In-Reply-To: <199806232053.QAA01584@helix.nih.gov> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Marc - I recently got an email asking how to build G94 on a Linux box. Do you have this handy or could I direct the person to you for some help ? Thanks, - Eric From patchkov@acs.ucalgary.ca Tue Jun 23 18:51:08 1998 Received: from ds11.acs.ucalgary.ca (root@ds11.acs.ucalgary.ca [136.159.244.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id SAA21138 Tue, 23 Jun 1998 18:51:07 -0400 (EDT) Received: by acs1.acs.ucalgary.ca (AIX 4.1/UCB 5.64/4.03) id AA117246; Tue, 23 Jun 1998 16:49:28 -0600 Message-Id: <9806232249.AA117246@acs1.acs.ucalgary.ca> Subject: Re: CCL:G:Is SGI O2/150 much faster than PII/233? To: mn1@helix.nih.gov (M. Nicklaus) Date: Tue, 23 Jun 98 16:49:27 MDT From: "Serguei Patchkovskii" Cc: CHEMISTRY@www.ccl.net, mn1@helix.nih.gov In-Reply-To: <199806232053.QAA01584@helix.nih.gov>; from "M. Nicklaus" at Jun 23, 1998 4:53 pm X-Mailer: ELM [version 2.3 PL11K] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit > 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. The memory substems of O2 and Origin 200 are also very different, and are designed with different uses in mind. The O2 memory subsystem is not intended for heavy scientific number crunching (it is optimized for 3D graphics work), and does not perform quite as well for these tasks as the Origin's memory. You can get the detailed technical characteristics of R5k O2 and Origin 200 along with some benchmarks for these machines from the SGI web site at http://www.sgi.com if you wish. The basic conclusion is that 150MHz R5k O2 is not going to perform anywhere close to 195 MHz R10k Origin 200 for number-crunching programs like Gaussian. If I'll hazard a guess, I would say that this O2 is going to be at least factor of four slower than this particular Origin on direct SCF jobs, with larger factors for more memory-intensive jobs (e.g. MP2). The O2 is definitly NOT going to be faster than the PII machine mentioned in your post - simply because it is not suited well for the task you are trying to give it. Regards, /Serge.P