From BARANSKA@Trurl.ch.uj.edu.pl Mon Mar 30 02:21:06 1998 Received: from if.uj.edu.pl for BARANSKA@Trurl.ch.uj.edu.pl by www.ccl.net (8.8.3/950822.1) id BAA23260; Mon, 30 Mar 1998 01:48:29 -0500 (EST) 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 IAA27336 for ; Mon, 30 Mar 1998 08:57:51 +0200 (MET DST) Received: from TRURL/MAILQUEUE by Trurl.ch.uj.edu.pl (Mercury 1.40); 30 Mar 98 07:40:10 GMT+2 Received: from MAILQUEUE by TRURL (Mercury 1.40); 30 Mar 98 07:40:04 GMT+2 From: "Malgorzata Baranska, p.253, tel. 265" Organization: Faculty of Chemistry, UJ To: chemistry@www.ccl.net Date: Mon, 30 Mar 1998 07:40:03 MET+2 Subject: IR spectrum of Cu-complex X-Confirm-Reading-To: "Malgorzata Baranska, p.253, tel. 265" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: <87875A37DA@Trurl.ch.uj.edu.pl> Dear CCLers, I use G94 on Convex station and I've done geometry optimization of some biological, quite big ligands and calculated their IR and Raman spectra.Now I try to do the same with metallocomplexes of these ligands.But I can't overcome some difficulties I met with Cu complex (+2 cation).I used UHF/sto-3g and some other basis (LanL2DZ,...)but I still receive such message: Convergence failure - run terminated Error termination via Lnk 1e Job cpu time:18 hours Signal 11: Segmentation violation. I don't know what I should change to complete calculation. I would be very grateful for any suggestion. Malgorzata Baranska Dep. of Chemistry Jagiellonian University Cracow, Poland From jolanala@main.amu.edu.pl Mon Mar 30 06:21:07 1998 Received: from main.amu.edu.pl for jolanala@main.amu.edu.pl by www.ccl.net (8.8.3/950822.1) id FAA24295; Mon, 30 Mar 1998 05:59:07 -0500 (EST) From: Received: from ppp (pppa205.poznan.tpnet.pl [194.204.178.205]) by main.amu.edu.pl (8.8.8/8.8.8) with SMTP id MAA16703 for ; Mon, 30 Mar 1998 12:58:11 +0200 (MET DST) Message-Id: <199803301058.MAA16703@main.amu.edu.pl> Comments: Authenticated sender is To: CHEMISTRY@www.ccl.net Date: Mon, 30 Mar 1998 12:56:47 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: impact factor Priority: normal X-mailer: Pegasus Mail for Win32 (v2.54) Dear all, I am looking for the impact factors for some physical and chemical journals. Could you help me please? Thanks in advance, Jolanta From mforster@nibsc.ac.uk Mon Mar 30 06:27:28 1998 Received: from nibsc.ac.uk for mforster@nibsc.ac.uk by www.ccl.net (8.8.3/950822.1) id FAA24217; Mon, 30 Mar 1998 05:25:38 -0500 (EST) Received: from chalsig.nibsc.ac.uk by nibsc.ac.uk via ESMTP (951211.SGI.8.6.12.PATCH1502/940406.SGI.1(NIBSC)) for id LAA02040; Mon, 30 Mar 1998 11:25:26 +0100 Received: by chalsig.nibsc.ac.uk (951211.SGI.8.6.12.PATCH1502/client-1.3.1(NIBSC)) id LAA18885; Mon, 30 Mar 1998 11:25:25 +0100 Date: Mon, 30 Mar 1998 11:25:25 +0100 From: mforster@nibsc.ac.uk (mforster) Message-Id: <199803301025.LAA18885@chalsig.nibsc.ac.uk> To: chemistry@www.ccl.net Subject: CCL: other processors Please find enclosed some benchmark timings for Alpha, SGI, Sun, Intel and AMD processors. This shows the AMD K6 to be somewhat slower at floating point work than a pentium MMX with comparable clock rate. UNIX (native C compilers) and PC (GCC compiler under Windows 95) benchmarks for 2D NOE calculations using command line version of NOEMOL. System Time (mins:secs). cpu clock rate (MHz). DEC alphastation 500 approx 34 Alpha 333 SGI indigo2 approx 36 R10000 195 Sun Ultra Ent. 4000 approx 36 Ultrasparc 250 Dell XPS D300 1.30 Pentium II 300 SGI challenge 1:50 R4400 150 Dell XPD D233 1.54 Pentium II 233 Compaq deskpro 2.38 Pentium 166 MMX Clone PC 2.56 AMD K6 200 Compaq deskpro 3:00 Pentium 166 (non MMX) Toshiba 110CS laptop 4.36 Pentium 100 SGI Personal iris 6:15 R3000 30 Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel 01707 654753 FAX 01707 646730 E-mail mforster@nibsc.ac.uk From jamal@sg1503.Chemie.Uni-Marburg.DE Mon Mar 30 08:21:09 1998 Received: from sg1503.chemie.uni-marburg.de for jamal@sg1503.Chemie.Uni-Marburg.DE by www.ccl.net (8.8.3/950822.1) id HAA24646; Mon, 30 Mar 1998 07:36:03 -0500 (EST) Received: from pc15142.chemie.uni-marburg.de (pc15142.Chemie.Uni-Marburg.DE [137.248.151.103]) by sg1503.chemie.uni-marburg.de (8.9.0.Beta3/8.9.0.Beta3/schn) with SMTP id OAA18858; Mon, 30 Mar 1998 14:26:40 +0100 (CET) Message-Id: <199803301326.OAA18858@sg1503.chemie.uni-marburg.de> Comments: Authenticated sender is From: "Md. Jamal Uddin" To: Date: Mon, 30 Mar 1998 14:36:26 MDT Subject: Re: CCL:impact factor CC: CHEMISTRY@www.ccl.net X-Confirm-Reading-To: "Md. Jamal Uddin" X-pmrqc: 1 Return-receipt-to: "Md. Jamal Uddin" Priority: normal X-mailer: Pegasus Mail for Windows (v2.01) Dear Jolanta, Here is a table with the Impact Factors(IF) of year 1996 (Source: Institute of Scientific Information, Philadelphia) Copied from CHEMISTRY, A Europian Journal 1998, 4/1 Editorial Journal IF ----------------- --------------- Chem. Rev. 17.112 Acc. Chem. Res. 10.646 Angew. Chem. Int.(Eng) 8.184 Chem. Soc. Rev. 6.223 J. Am. Chem. Soc. 5.948 Chem. Eur. J. 4.814 Anal. Chem. 4.550 J. Med. Chem 4.453 J. Org. Chem. 3.722 Adv. Mater. 3.630 J. Chem Phys. 3.520 J. Phy. Chem 3.370 Organometallics 3.134 J. Chem. Soc. Chem Comm. 3.107 Inorg. Chem 2.990 Tetrahedron Lett. 2.497 Helv. Chim. Acta. 2.369 Tetrahedron 2.232 J. Chem. Soc. Dalton Trans. 2.200 Chem. Ber. 1.958 New. J. Chem. 1.813 J. Chem Soc. Perkin trans.I 1.799 J. Organomet. Chem. 1.794 Chem. Lett. 1.631 Leibigs Ann. 1.549 Z. Anorg. Allg. Chem 1.159 J. Prakt. Chem. 0.551 Pol. J. Chem. 0.492 ---------------------------------------------------------- Cheers, Jamal Uddin AK Frenking Philipps-Universitaet Marburg Fachbereich Chemie D-35032, Germany From merkle@parc.xerox.com Mon Mar 30 12:21:12 1998 Received: from alpha.xerox.com for merkle@parc.xerox.com by www.ccl.net (8.8.3/950822.1) id LAA26673; Mon, 30 Mar 1998 11:47:19 -0500 (EST) Received: from manarken.parc.xerox.com ([13.2.116.21]) by alpha.xerox.com with SMTP id <52704(4)>; Mon, 30 Mar 1998 08:46:20 PST Received: by manarken.parc.xerox.com id <12181>; Mon, 30 Mar 1998 08:46:11 PST From: Ralph Merkle To: chemistry@www.ccl.net Subject: Re: impact factor Message-Id: <98Mar30.084611pst."12181"@manarken.parc.xerox.com> Date: Mon, 30 Mar 1998 08:46:11 PST The journal Nanotechnology had a 1996 impact factor of 1.881, which placed it at the top of its category in engineering. (see: http://www.ioppublishing.com/Journals/Catalogue/NA) This is remarkably good for a new journal. Phys Rev A (listed in the URL given below) had a 1992 impact factor of 2.157 Impact factors for some physics journals are given at: http://arcadia.tuniv.szczecin.pl/impact.html A brief discussion of the impact factor, along with links to two articles on the subject, is at http://www.isinet.com/guidebk/glossary.html#impact factor From tapas@risky3.thchem.siu.edu Mon Mar 30 13:21:18 1998 Received: from risky3.thchem.siu.edu for tapas@risky3.thchem.siu.edu by www.ccl.net (8.8.3/950822.1) id NAA27109; Mon, 30 Mar 1998 13:09:53 -0500 (EST) Received: (from tapas@localhost) by risky3.thchem.siu.edu (AIX4.2/UCB 8.7/8.7) id MAA24234; Mon, 30 Mar 1998 12:13:11 -0600 (CST) Date: Mon, 30 Mar 1998 12:13:06 -0600 (CST) From: Tapas Kar To: "Malgorzata Baranska, p.253, tel. 265" cc: chemistry@www.ccl.net Subject: Re: CCL:G:IR spectrum of Cu-complex In-Reply-To: <87875A37DA@Trurl.ch.uj.edu.pl> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Try vshift if energy is oscillating or use more iteration steps by increasing scfcycle (iop(5/7=n, by default n is 65). You may reducee the convergence criteria iop(5/6=n, by default n=8). On Mon, 30 Mar 1998, Malgorzata Baranska, p.253, tel. 265 wrote: > Date: Mon, 30 Mar 1998 07:40:03 MET+2 > From: Malgorzata Baranska, p.253, tel. 265 > To: chemistry@www.ccl.net > Subject: CCL:G:IR spectrum of Cu-complex > > Dear CCLers, > I use G94 on Convex station and I've done geometry optimization of > some biological, quite big ligands and calculated their IR and Raman > spectra.Now I try to do the same with metallocomplexes of these > ligands.But I can't overcome some difficulties I met with Cu > complex (+2 cation).I used UHF/sto-3g and some other basis > (LanL2DZ,...)but I still receive such message: > Convergence failure - run terminated > Error termination via Lnk 1e > Job cpu time:18 hours > Signal 11: Segmentation violation. > I don't know what I should change to complete calculation. I would be > very grateful for any suggestion. > > Malgorzata Baranska > Dep. of Chemistry > Jagiellonian University > Cracow, Poland > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: BARANSKA@Trurl.ch.uj.edu.pl > -- Original Sender From: Address: BARANSKA@Trurl.ch.uj.edu.pl > 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 rvenable@deimos.cber.nih.gov Sun Mar 22 14:24:18 1998 Received: from deimos.cber.nih.gov for rvenable@deimos.cber.nih.gov by www.ccl.net (8.8.3/950822.1) id NAA28616; Sun, 22 Mar 1998 13:45:47 -0500 (EST) Received: from localhost by deimos.cber.nih.gov with SMTP (1.37.109.14/16.2) id AA230732195; Sun, 22 Mar 1998 13:43:15 -0500 Date: Sun, 22 Mar 1998 13:43:15 -0500 (EST) From: Rick Venable To: chemistry@www.ccl.net Subject: Re: CCL:Top PC vs. Unix In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 22 Mar 1998, Attila Aranyos wrote: > Does anyone know how fast (or slow :)) is a top PC with all you can get now > (P-II 333 MhZ (may be dual) and tip-top HD contorller ) compared with a > Unix workstation? The real issue is the price/performance ratio; you could probably buy a Unix workstation that might out-perform a top PC, but you would probably spend a good deal more money. The disadvantage of the PC approach (assuming Linux) is that you really have to have someone around who can handle the sysadmin stuff, but it's not much different from dealing with IRIX, HP-UX, AIX, etc. Note that current mother boards will be rate limiting for *parallel* usage of dual 333 MHz processors, and the I/O subsystem will be rate limiting for larger calculations that require the continuous use of the swap partition on the hard disk. If the 333 MHz costs a lot more, I'd buy slightly slower processors and spend the savings on more memory. Linux on a PC is a very cost-effective and viable platform for many computational chemistry codes; with an add-on GL board, it can be an alternative to an SGI in some cases, especially where source code is available. There are good Fortran compilers available, both free (g77 and f2c/gcc) and commercial (AbSoft). By "good", I mean that MD and QM codes written to (mostly) the Fortran 77 standard compile, and produce executables which run efficiently and give correct (or equivalent) answers. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov | \ / |=| position of the FDA; for that, http://nmr1.cber.nih.gov/ \/ |=| see http://www.fda.gov ) http://www.erols.com/rvenable From ccl@www.ccl.net Mon Mar 23 01:19:38 1998 Received: from ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id BAA01734; Mon, 23 Mar 1998 01:18:29 -0500 (EST) Received: from auric.chem.csiro.au (auric.chem.CSIRO.AU [138.194.44.10]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id BAA14150 for ; Mon, 23 Mar 1998 01:18:26 -0500 (EST) Received: from [138.194.46.107] (cpr-46107.chem.csiro.au) by auric.chem.csiro.au with SMTP id AA27152 (5.67b/IDA-1.5 for chemistry@ccl.net); Mon, 23 Mar 1998 17:17:53 +1100 X-Sender: win097@auric.chem.csiro.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 23 Mar 1998 17:17:53 +1000 To: chemistry@ccl.net From: "Dr. Dave Winkler" Subject: Gasteiger-Marsili charge calculations Dear e-folk Gasteiger-Marsili methods are widely used for quick charge calculations. However, the method uses an iterative 'ansatz', as a damping factor. This is essentially multiplying each iteration of the calculation by a factor of 2^-n, where n is the number of iterations. As the final charge calculated by this method is quite dependent on the choice of this factor, has anyone seen a justification for this? Cheers, Dave Dr. David A. Winkler Email: dave.winkler@molsci.csiro.au Senior Principal Research Scientist Voice: 61-3-9545-2477 CSIRO Division of Molecular Science Fax: 61-3-9545-2446 Private Bag 10,Clayton South MDC, http://www.csiro.au Clayton 3169, Australia http://www.molsci.csiro.au From jig@qorg1.unizar.es Mon Mar 23 12:19:44 1998 Received: from qorg1.unizar.es for jig@qorg1.unizar.es by www.ccl.net (8.8.3/950822.1) id MAA05824; Mon, 23 Mar 1998 12:17:26 -0500 (EST) Received: from qorg1.unizar.es (localhost [127.0.0.1]) by qorg1.unizar.es with ESMTP (8.7.1/8.7.1) id SAA08420 for ; Mon, 23 Mar 1998 18:11:00 +0100 (MET) Sender: jig@qorg1.unizar.es Message-ID: <351697A3.19333FC7@qorg1.unizar.es> Date: Mon, 23 Mar 1998 18:10:59 +0100 From: Jose Ignacio Garcia Organization: ICMA-Quimica Organica X-Mailer: Mozilla 4.04 [en] (X11; I; -t B.10.20 9000/780) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: EPR basis sets Content-Type: multipart/alternative; boundary="------------6617CA04418A948A130E288B" --------------6617CA04418A948A130E288B Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I am looking for the EPR-II and EPR-III basis sets. The original reference for these basis sets is: V. Barone, in "Recent Advances in Density Functional Methods"; D. P. Chong, Ed., World Scientific Publishing, Singapore, 1995. Unfortunately, I do not have this book. I would acknowledge any help to locate this specialized basis sets. Regards. Jose I. Garcia -- -------------------------------------------------------------------------------- Dr. Jose Ignacio Garcia-Laureiro Phone : 34-976762077 Departamento de Quimica Organica 976761210 Instituto de Ciencia de Materiales de Aragon Fax : 34-976762077 C.S.I.C.-Universidad de Zaragoza e-mail: jig@qorg1.unizar.es E-50009 ZARAGOZA (SPAIN) jig@posta.unizar.es -------------------------------------------------------------------------------- "And all this science I don't understand it's just my job five days a week..." ELTON JOHN - Rocket man -------------------------------------------------------------------------------- --------------6617CA04418A948A130E288B Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers,

I am looking for the EPR-II and EPR-III basis sets. The original reference for these basis
sets is: V. Barone, in "Recent Advances in Density Functional Methods"; D. P. Chong, Ed.,
World Scientific Publishing, Singapore, 1995. Unfortunately, I do not have this book.
I would acknowledge any help to locate this specialized basis sets.
Regards.

Jose I. Garcia 

-- 
--------------------------------------------------------------------------------
Dr. Jose Ignacio Garcia-Laureiro                     Phone : 34-976762077
Departamento de Quimica Organica                                976761210
Instituto de Ciencia de Materiales de Aragon         Fax   : 34-976762077
C.S.I.C.-Universidad de Zaragoza                     e-mail: jig@qorg1.unizar.es
E-50009 ZARAGOZA (SPAIN)                                     jig@posta.unizar.es
--------------------------------------------------------------------------------
"And all this science I don't understand it's just my job five days a week..."
                                               ELTON JOHN - Rocket man
--------------------------------------------------------------------------------
  --------------6617CA04418A948A130E288B-- From jig@qorg1.unizar.es Mon Mar 23 12:19:44 1998 Received: from qorg1.unizar.es for jig@qorg1.unizar.es by www.ccl.net (8.8.3/950822.1) id MAA05824; Mon, 23 Mar 1998 12:17:26 -0500 (EST) Received: from qorg1.unizar.es (localhost [127.0.0.1]) by qorg1.unizar.es with ESMTP (8.7.1/8.7.1) id SAA08420 for ; Mon, 23 Mar 1998 18:11:00 +0100 (MET) Sender: jig@qorg1.unizar.es Message-ID: <351697A3.19333FC7@qorg1.unizar.es> Date: Mon, 23 Mar 1998 18:10:59 +0100 From: Jose Ignacio Garcia Organization: ICMA-Quimica Organica X-Mailer: Mozilla 4.04 [en] (X11; I; -t B.10.20 9000/780) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: EPR basis sets Content-Type: multipart/alternative; boundary="------------6617CA04418A948A130E288B" --------------6617CA04418A948A130E288B Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I am looking for the EPR-II and EPR-III basis sets. The original reference for these basis sets is: V. Barone, in "Recent Advances in Density Functional Methods"; D. P. Chong, Ed., World Scientific Publishing, Singapore, 1995. Unfortunately, I do not have this book. I would acknowledge any help to locate this specialized basis sets. Regards. Jose I. Garcia -- -------------------------------------------------------------------------------- Dr. Jose Ignacio Garcia-Laureiro Phone : 34-976762077 Departamento de Quimica Organica 976761210 Instituto de Ciencia de Materiales de Aragon Fax : 34-976762077 C.S.I.C.-Universidad de Zaragoza e-mail: jig@qorg1.unizar.es E-50009 ZARAGOZA (SPAIN) jig@posta.unizar.es -------------------------------------------------------------------------------- "And all this science I don't understand it's just my job five days a week..." ELTON JOHN - Rocket man -------------------------------------------------------------------------------- --------------6617CA04418A948A130E288B Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers,

I am looking for the EPR-II and EPR-III basis sets. The original reference for these basis
sets is: V. Barone, in "Recent Advances in Density Functional Methods"; D. P. Chong, Ed.,
World Scientific Publishing, Singapore, 1995. Unfortunately, I do not have this book.
I would acknowledge any help to locate this specialized basis sets.
Regards.

Jose I. Garcia 

-- 
--------------------------------------------------------------------------------
Dr. Jose Ignacio Garcia-Laureiro                     Phone : 34-976762077
Departamento de Quimica Organica                                976761210
Instituto de Ciencia de Materiales de Aragon         Fax   : 34-976762077
C.S.I.C.-Universidad de Zaragoza                     e-mail: jig@qorg1.unizar.es
E-50009 ZARAGOZA (SPAIN)                                     jig@posta.unizar.es
--------------------------------------------------------------------------------
"And all this science I don't understand it's just my job five days a week..."
                                               ELTON JOHN - Rocket man
--------------------------------------------------------------------------------
  --------------6617CA04418A948A130E288B-- From srk@engpub1.bu.edu Mon Mar 23 12:19:54 1998 Received: from engpub1.bu.edu for srk@engpub1.bu.edu by www.ccl.net (8.8.3/950822.1) id MAA05739; Mon, 23 Mar 1998 12:07:57 -0500 (EST) Received: (from srk@localhost) by engpub1.bu.edu (8.8.5/8.8.5/(BU-S-02/10/97-v1.0)) id MAA11091; Mon, 23 Mar 1998 12:07:56 -0500 (EST) From: "S. Roy Kimura" Message-Id: <199803231707.MAA11091@engpub1.bu.edu> Subject: summary: electrostatics using MD vs FDPB To: chemistry@www.ccl.net Date: Mon, 23 Mar 1998 12:07:55 -0500 (EST) Cc: srk@engpub1.bu.edu (S. Roy Kimura) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, Here is a summary of responses to the question I posted a few weeks ago concerning electrostatic calculations using MD versus continuum methods. I appreciate all of your responses and comments. Thank you very much. Roy ----- S. Roy Kimura Molecular Engineering Research Laboratory Department of Biomedical Engineering email: srk@bu.edu Boston Univesrity phone: (617)353-4726 ---------------------- original question ----------------------------- I have a question regarding electrostatic calculations in proteins relating to issues such as solvation, salt-bridge stability, or binding energies. I have read that different workers have had varying success in calculating electrostatic energies using the Finite-Difference Poisson-Boltzman method. However, this method suffers from the ambiguity of the dielectric constant of the protein interior which, strictly speaking, shouldn't be considered a homogeneous dielectric continuum in the first place. I was wondering if anyone has made any progress in electrostatic calculations by the full inclusion of solute motion, for instance by conducting molecular dynamics or all-atom Monte Carlo simulations. I realize that such a method will still neglect electronic polarization but will at least correctly treat the inhomogeneity of the protein interior, if it is possible to run long enough to adequately sample the full electrostatic response. Moreover, I was thinking that electronic polarization may still have a chance to be described by a dielectric constant (eps = 2 to 4) superimposed on top of the explicit solute motion which takes care of reorientational polarization. I would appreciate if anyone could point me to some papers that considers electrostatic calculations by averaging the response in MD or MC simulations. I am interested specifically in the feasibility of such calculations which must include solvent in some form (either explicitly or implicitly). I have read some of the works by Warshel, Aqvist, and King who seem to have ideas along this line; however, they chose to describe the solute and solvent through a set of variable dipoles on a grid. I am interested in knowing if it is possible to capture reorientational polarization through explicit consideration of solute atom motion. -------------------------- reply 1 ------------------------------- These two papers might be of help: M. K. Gilson and B. Honig, Biopolymers 25, 2097-2119 (1986) T. Simonson, D. Perahia and A. T. Brunger, Biophys. J. 59, 670-690 (1991) Good luck! Gary -------------------------- reply 2 ------------------------------- The work of Warshel an coworkers offers more than the semimicroscopic PDLD method that treats the solvent as polarizable Langevin dipoles. His program package ENZYMIX includes an all-atom MD program that treats the solvent molecules explicitly (rigid 3-point water model, similar to TIP3P). One difference to other MD programs is that you can chose to include induced dipoles and/or induced forces in the calculations (see F. Lee et al. J.Comp.Chem. (1993)). Depending on what you are interested in you can use Free Energy Perturbation or Linear Response Approximation methods to calculate binding affinites, pKa-valaues, redox potentials or solvation energies. Especially the linear response approximation is conceptually and practically capable of quantifying reorientational (reorganizational) effects. Nevertheless, the PDLD method is also able to deal with these effects, introducing a scalaing constant epsilon that must not be confused with a true dielectric constant but is merely a scaling factor that stands for the contributions to the free energy that are not explicitly taken into account (e.g., induced dipoles, the effect of change in water penetration upon complex formation). As it turnes out, the PDLD results are much more stable than the microscopic ones and for practical purposes this is often the method of choice. Note also the recently published incorporation of the Langevin dipole solvation model as an alternative to TOMASI in Gaussian. A new program package ChemSol1.0 by Jan FLorian and Arieh Warshel calculates solvation energies of compounds with partial charges calculated with Gaussian (Florian & Warshel, J.Phys.Chem. B 1997). For more recent papers on LRA, binding, redox, pka, reorganization of Warshels group, please see for instance: F. Lee et al. Prot.Eng. (1992) F. Lee et al. J.Comp.Chem. (1993) I Muegge et al. Structure (1996) YY Sham et al. J.Phys.Chem. B (1997) A Warshel et al. J.Biol.Inorg.Chem. (1997) I Muegge et al. J.Phys.Chem. B (1997) I Muegge et al. Prot.Eng. (12/1997) (should be out next month) I Muegge et al. Proteins (3/1998) (should be out next month) YY Sham et al. Biophysical J. (4/1998) (nshould be out in 2 month) Best regards, Ingo -- Ingo Muegge D-47E, AP10 2fl Abbott Laboratories 100 Abbott Park Road Abbott Park, IL 60064-3500 Phone: 847 935-4659 FAX: 847 937-2625 ingo.mugge@abbott.com -------------------------- reply 3 ------------------------------- In addition to the names you mentioned, I know that Mike K Gilson at NIST has been considering these issues. Bear ^[[7m^[[5mSOARING BEAR^[[0m bear@pharmacy.arizona.edu O-topoisomerase Computational Medicinal Chemistry 5'*: :*.* Cancer Biochemistry & Drug Design |'*. .*'| | Protein & DNA Structural Biology | | *.,* | | | currently seeking employment 3'*.DNA helix| * http://ellington.pharm.arizona.edu/~bear '***' '**' -------------------------- reply 4 ------------------------------- Dear Dr. Kirma, MD using FDPB solvent has been done and partially reported by Mike Gilson and myself. Initial results were reported in J. Comp. Chem. in 1996. Additional results are current being written. If you have further questions please send them to me. The calculations you want to do can be done using the program UHBD. Best Regards, Jeffry Department of Biochemistry & Chemistry Duquesne University 600 Forbes Ave. Pittsburgh, PA 15282-1530 Phone: (412) 396-4129 FAX: (412) 396-5683 e-mail: madura@mail.cc.duq.edu -------------------------- reply 5 ------------------------------- Dear Roy, maybe the following paper is of interest for you: Loeffler, Schreiber and Steinhauser; Calculation of the Dielectric Properties of a Protein and its Solvent: Theory and Case Study. J Mol Biol 270, 520-534 (1997). A recent paper about salt-link studies by MDS is: Lounnas and Wade, Biochemistry (1997). Regards, Roger -- Roger Abseher, PhD EMBL, Meyerhofstrasse 1 D-69117 Heidelberg, Germany Room No.: V115 Email: abseher@nmr.embl-heidelberg.de Voice: +49 6221 387 305 Fax: +49 6221 387 517 -------------------------- reply 6 ------------------------------- See works by Toshiko Ichiye et al. over the last 7 years (Biophys J.,Biochemistry, Proteins) where we calculated electrostatic potentials at redox site in Fe-S proteins using simple coulombic representations (vis-a-vis Warshel) but without limiting solvent to grid-based dipoles. Swartz, Beck, Ichiye (1996) Dec. Biophys. J. Yelle, Park, Ichiye (1993,1995) Proteins. Swartz, Ichiye (1996,1997) Biochemistry. -Brian -- ============================================================== | Brian W. Beck |E-mail Address: beck@uh.edu | | Dept. Chemistry | | | Univ. of Houston |URL: | | 220 Fleming |http://www.chem.uh.edu/www/pettitt/beck | | Houston, TX, USA |VOICE (713) 743-3264 | | 77204-5641 |FAX (713) 743-2709 | ============================================================== -------------------------- reply 7 ------------------------------- I have also to point out that Warshel has an All Atom model that includes this effect. You can look at: Polarization Constraints in Molecular Dynamics Simulation of Aqueous Solutions: the Surface Constraint All Atom Solvent (SCAAS) Model, A. Warshel and G. King, Chem. Phys. Lett. 121, 124 (1985) or Microscopic Models for Quantum Mechanical Calculations of Chemical Processes in Solutions: LD/AMPAC and SCAAS/AMPAC Calculations of Solvation Energies. V. Luzhkov and A. Warshel, J. Comp. Chem. 13, 199 (1992) With my best wishes, Jordi -- Jordi Villa Department of Chemistry University of Minnesota 207 Pleasant St. SE 55455 Minneapolis MN Tlf: 612-625-53 11 Fax: 612-626-9390 http://klingon.uab.es/jordi e-mail: jordi@klingon.uab.es From seabra@NPD.UFPE.BR Mon Mar 23 14:19:44 1998 Received: from NPD1.NPD.UFPE.BR for seabra@NPD.UFPE.BR by www.ccl.net (8.8.3/950822.1) id NAA06460; Mon, 23 Mar 1998 13:58:34 -0500 (EST) Received: from danon ([150.161.5.125]) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with SMTP id <01IV0F78P74G000M7L@NPD.UFPE.BR> for chemistry@www.ccl.net; Mon, 23 Mar 1998 15:57:40 GMT-3 Date: Mon, 23 Mar 1998 16:08:11 -0300 From: Gustavo de Miranda Seabra Subject: Elastic constants To: Computational Chemistry List Reply-to: Gustavo de Miranda Seabra Message-id: <001001bd568f$067ab8e0$7d05a196@danon.dqf.ufpe.br> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 4.72.2106.4 Content-type: multipart/alternative; boundary="----=_NextPart_000_000D_01BD5675.E0D68740" X-Priority: 3 X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 This is a multi-part message in MIME format. ------=_NextPart_000_000D_01BD5675.E0D68740 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, Does anyone have references about calculating elastic constants of = ionic materials by means of quantum chemical calculations? Thanks very much, Gustavo Seabra seabra@npd.ufpe.br ------=_NextPart_000_000D_01BD5675.E0D68740 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all,
 
    Does = anyone have=20 references about calculating elastic constants of ionic materials by = means of=20 quantum chemical calculations?
 
    = Thanks very=20 much,
 
     Gustavo=20 Seabra
    seabra@npd.ufpe.br
 
------=_NextPart_000_000D_01BD5675.E0D68740-- From bernhold@npac.syr.edu Tue Mar 24 17:19:58 1998 Received: from snake.npac.syr.edu for bernhold@npac.syr.edu by www.ccl.net (8.8.3/950822.1) id QAA15279; Tue, 24 Mar 1998 16:52:48 -0500 (EST) Received: from localhost (bernhold@localhost) by snake.npac.syr.edu (950413.SGI.8.6.12/8.6.6) with SMTP id QAA14814; Tue, 24 Mar 1998 16:53:59 -0500 Message-Id: <199803242153.QAA14814@snake.npac.syr.edu> X-Authentication-Warning: snake.npac.syr.edu: Host localhost didn't use HELO protocol Reply-to: bernhold@postoffice.npac.syr.edu To: chemistry@www.ccl.net cc: bernhold@postoffice.npac.syr.edu Subject: Workshop in OO methods for scientific computing MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-ID: <14811.890776439.1@snake.npac.syr.edu> Date: Tue, 24 Mar 1998 16:53:59 -0500 From: "David E. Bernholdt" Given previous discussions here about object oriented programming, CORBA, and related ideas, this workshop might be interesting to some on this list. I am just passing along info seenon another mailing list -- I have no affiliation with this meeting. From: Mike Henderson Date: Wed, 18 Mar 98 12:31:24 EST Subject: Workshop on Object Oriented Methods for Scientific Computing SIAM Workshop on Object Oriented Methods for Inter-operable Scientific and Engineering Computing October 21-23, 1998 IBM Research Yorktown Heights, New York Background: There is a growing awareness in the universities, and industrial and governmental labs, that object oriented methods have the potential for greatly improving the usefulness of computers in science and engineering. There are already many efforts underway to redesign and reimplement large codes that were written in the 70's and 80's to take advantage of the improvement in maintainability and flexibility that OO designs offer. There still remains a large opportunity to improve the amount of reuse within the community. Repositories such as Netlib and indices like GAMS have improved our ability to share code, but making the shared code useful requires widespread agreement about how the code is structured and how scientific and engineering codes should interoperate. The world is changing. It used to be that large companies had their own internal development teams, which implemented techniques from the open literature or developed their own proprietary methods. University researchers looked for methods for new classes of problems, and pushed the limits of problem size. Software companies provided application packages aimed at solving common problems, bundled with everything from front-ends, to mesh generation and back-ends. Now, as many large companies are cutting back on in-house software development, universities and government labs seem to be doing increasingly more software development and software vendors are springing up to provide special purpose codes. What are the new roles for academics, software companies, and industry? Can a university department support a software product? How does a company test and fire-harden research code? How can software companies quickly incorporate new methods into a professional quality product? Who owns what, and who supports what? This interdisciplinary workshop will bring together representatives from academia, software vendors, industry, and government labs, to identify current and future challenges to implementing and using mathematical algorithms in scientific and engineering computing.

Organizing Committee: Mike Henderson, IBM Research Chris Anderson, UCLA Steve Lyons, Mobil Technology Co. Presentations: The workshop will consist of 3 days of contributed and invited presentations and discussions including, not not limited to, the broad topics of: The current state of the art. - Tools that work together well (or poorly). - The environments in which codes are used. - How new techniques make their way to industrial use. Developing interoperable scientific codes. - Packaging codes. - Balancing interoperability with performance. - Maintenance and ownership of codes. Future directions. - Language of the future. - Design techniques. - Standards for the interoperation of mathematical software? Case studies, position papers proposing topics for discussion, and technical talks describing particular approaches are solicited. The organizers are looking for a broad spectrum of participants, including those involved in the development of industrial codes, and industrial end users. How to Contribute: A report will be issued covering the workshop. Participants will be required to submit a document for inclusion in this report. Those wishing to participate should submit an abstract of a case study, position paper or technical talk by July 1, 1998. Abstracts should be sent to mhender@watson.ibm.com. Notifications of acceptance will be sent by July 30, 1998. Important Dates to Remember: July 1, 1998, deadline for submission of extended abstract. July 30, 1998, notification of acceptance. August 31 1998, deadline for submission of final paper. -- 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 EILMES@Trurl.ch.uj.edu.pl Wed Mar 25 04:20:05 1998 Received: from if.uj.edu.pl for EILMES@Trurl.ch.uj.edu.pl by www.ccl.net (8.8.3/950822.1) id DAA17502; Wed, 25 Mar 1998 03:52:45 -0500 (EST) 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 JAA05069 for ; Wed, 25 Mar 1998 09:59:58 +0100 (MET) Received: from TRURL/MAILQUEUE by Trurl.ch.uj.edu.pl (Mercury 1.40); 25 Mar 98 09:42:28 GMT+2 Received: from MAILQUEUE by TRURL (Mercury 1.40); 25 Mar 98 09:42:26 GMT+2 From: "Andrzej Eilmes" Organization: Faculty of Chemistry, UJ To: chemistry@www.ccl.net Date: Wed, 25 Mar 1998 09:42:24 MET+2 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: DEC Alpha 566 vs. 600 MHz Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: <118D0667A8@Trurl.ch.uj.edu.pl> Dear CCL-ers, We are considering purchase of a workstation based on DEC Alpha processor. There is a substantial price difference between 566 MHz and 600 MHz: 7000 $ vs. 8200 $ which is about 17%, while the increase of "nominal" processor speed is 6%. My question is: does anyone know from his own experience what is the actual speed difference between these two procesors in typical theoretical chemistry or solid state physics calculations. I guess that it is larger than simply 6%. In other words I wonder whether it is reasonable to pay 17% more for faster machine - is the gain worth the money? I would be grateful for any suggestions, 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 gadre@chem.unipune.ernet.in Wed Mar 25 07:20:15 1998 Received: from naveen.ncst.ernet.in for gadre@chem.unipune.ernet.in by www.ccl.net (8.8.3/950822.1) id GAA18145; Wed, 25 Mar 1998 06:44:19 -0500 (EST) Received: from unipune.ernet.in (unipune.ernet.in [196.1.114.1]) by naveen.ncst.ernet.in (8.6.12/8.6.6) with ESMTP id RAA07380 for ; Wed, 25 Mar 1998 17:22:57 +0530 Received: from chem.unipune.ernet.in by unipune.ernet.in (8.8.5/UNIPUNE-MAILHUB(02.04.97)) id RAA06136; Wed, 25 Mar 1998 17:06:29 -0500 (GMT) Received: by chem.unipune.ernet.in (8.7.5/SMI-SVR4) id RAA16944; Wed, 25 Mar 1998 17:25:33 -0500 Date: Wed, 25 Mar 1998 17:25:33 -0500 From: gadre@chem.unipune.ernet.in (Prof. Shridhar R. Gadre) Message-Id: <199803252225.RAA16944@chem.unipune.ernet.in> To: CHEMISTRY@www.ccl.net Subject: REQUEST Dear Sirs and Madams, A Referee has asked us to look at some recent references on the 'Importance of polarization in the binding of lithium cation to hydrocarbon or other molecules'. We will be grateful if you kindly let us know such references of your own work as well as works done by other scientists on this topic. Thank you very much. sincerely, Shridhar R. Gadre e-mail gadre@unipune.ernet.in gadre@chem.unipune.ernet.in From mitht@deom.chph.ras.ru Wed Mar 25 08:15:13 1998 Received: from deom.chph.ras.ru for mitht@deom.chph.ras.ru by www.ccl.net (8.8.3/950822.1) id HAA18343; Wed, 25 Mar 1998 07:19:59 -0500 (EST) Received: from deom.chph.ras.ru (root@localhost [127.0.0.1]) by deom.chph.ras.ru (8.8.3/8.8.3) with ESMTP id PAA05639 for ; Wed, 25 Mar 1998 15:19:31 +0300 Message-ID: <3518F5E4.3BACB805@deom.chph.ras.ru> Date: Wed, 25 Mar 1998 15:17:41 +0300 From: platonov X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: The ab-initio scf-convergence problems. Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear collegues! I've run geometry optimization in GAUSSIAN-94 for 1,8-(NO2)2-4,5-(CF2OCF2)-C10H4-molecule in UHF method (basis - 6-31+G**) and recieved following output file: *************************************** Gaussian 94: SGI-G94RevD.1 1-Feb-1996 21-Mar-1998 *************************************** %Mem=32000000 %Nproc=2 This run will use up to 2 processors. %chk=g94.subst01.040.chk ---------------------------------------------------------------------- # UHF/6-31+G** Guess=Huckel FOpt=(Z-Matrix) # Pop=Reg SCF(Conver=10, MaxCyc=200, VShift=200) ---------------------------------------------------------------------- 1/10=7,38=1/1,3; 2/12=2,14=103,17=6,18=5/2; 3/5=1,6=6,7=111,11=2,25=1,30=1/1,2,3; 4/7=2,11=1/1; 5/5=2,6=10,7=200,10=200,38=4/2; 6/28=1/1; 7/29=1/1,2,3,16; 1/10=7/3(1); 99//99; 2//2; 3/5=1,6=6,7=111,11=2,25=1,30=1/1,2,3; 4/5=5,7=2,11=1,16=2/1; 5/5=2,6=10,7=200,10=200,38=4/2; 7//1,2,3,16; 1//3(-5); 2//2; 3/5=1,6=6,7=111,11=2,25=1,30=1,39=1/1,3; 6/28=1/1; 99/9=1/99; ------------------------------------------------------------- Geometry optimization for 1.8-(NO2)2-4.5-(CF2)2O-C10H4 !3-21! ------------------------------------------------------------- Symbolic Z-matrix: Charge =-1 Multiplicity = 2 C1 C2 1 R1 C3 2 R2 1 A1 C4 3 R3 2 A2 1 D1 0 C5 4 R4 3 A3 2 D2 0 C6 5 R5 4 A4 3 D3 0 C7 2 R6 1 A5 5 D4 0 C8 3 R7 2 A6 1 D5 0 C9 4 R8 3 A7 2 D6 0 N10 5 R9 4 A8 3 D7 0 H11 6 R10 5 A9 4 D8 0 H12 1 R11 2 A10 3 D9 0 C13 9 R12 4 A11 3 D10 0 C14 8 R13 3 A12 4 D11 0 N15 9 R14 4 A13 3 D12 0 H16 13 R15 9 A14 4 D13 0 H17 14 R16 8 A15 3 D14 0 C18 8 R17 3 A16 4 D15 0 O19 7 R18 2 A17 1 D16 0 F20 18 R19 8 A18 14 D17 0 F21 18 R20 8 A19 14 D18 0 F22 7 R21 2 A20 1 D19 0 F23 7 R22 2 A21 1 D20 0 O24 15 R23 9 A22 13 D21 0 O25 15 R24 9 A23 13 D22 0 O26 10 R25 5 A24 6 D23 0 O27 10 R26 5 A25 6 D24 0 Variables: R1 1.34887 R2 1.41535 R3 1.40952 R4 1.42049 R5 1.35191 R6 1.50046 R7 1.41431 R8 1.41956 R9 1.45066 R10 1.06732 R11 1.06951 R12 1.35259 R13 1.34899 R14 1.45126 R15 1.06727 R16 1.06941 R17 1.4992 R18 1.38718 R19 1.36084 R20 1.3462 R21 1.34711 R22 1.3605 R23 1.24316 R24 1.23716 R25 1.24312 R26 1.23734 A1 121.1 A2 120.021 A3 116.417 A4 121.707 A5 119.849 A6 119.877 A7 116.51 A8 122.236 A9 118.522 A10 120.709 A11 121.805 A12 121.189 A13 122.291 A14 118.532 A15 120.658 A16 118.554 A17 112.605 A18 110.025 A19 111.086 A20 110.802 A21 110.034 A22 116.38 A23 117.305 A24 116.313 A25 117.371 D1 -0.562 D2 7.869 D3 -9.881 D4 175.907 D5 181.758 D6 -171.628 D7 162.379 D8 -178.176 D9 177.241 D10 -7.6 D11 -0.763 D12 163.778 D13 -179.307 D14 180.16 D15 177.619 D16 158.38 D17 83.522 D18 -34.535 D19 38.229 D20 -79.472 D21 140.551 D22 -34.223 D23 142.202 D24 -32.63 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Initialization pass. ---------------------------- ! Initial Parameters ! ! (Angstroms and Degrees) ! ---------------------- ---------------------- .......... ------------------------------------------------------------------------ Z-MATRIX (ANGSTROMS AND DEGREES) ........ Z-Matrix orientation: ---------------------------------------------------------- ........ Distance matrix (angstroms): ........ Interatomic angles: ........ Stoichiometry C12H4F4N2O5(1-,2) Framework group C1[X(C12H4F4N2O5)] Deg. of freedom 75 Full point group C1 NOp 1 Largest Abelian subgroup C1 NOp 1 Largest concise Abelian subgroup C1 NOp 1 Standard orientation: ---------------------------------------------------------- ........ ---------------------------------------------------------- Rotational constants (GHZ): 0.4670280 0.2107303 0.1580776 Isotopes: C-12,C-12,C-12,C-12,C-12,C-12,C-12,C-12,C-12,N-14,H-1,H-1,C-12,C-12,N- 14,H-1,H-1,C-12,O-16,F-19,F-19,F-19,F-19,O-16,O-16,O-16,O-16 The smallest eigenvalue of the nuclear repulsion Hessian is 7.13D-01. Standard basis: 6-31+G(d,p) (6D, 7F) There are 457 symmetry adapted basis functions of A symmetry. Crude estimate of integral set expansion from redundant integrals=1.000. Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned on. 457 basis functions 764 primitive gaussians 84 alpha electrons 83 beta electrons nuclear repulsion energy 2084.8643893851 Hartrees. One-electron integrals computed using PRISM. There are 12 eigenvalues of the overlap less than 1.0D-05 The smallest eigenvalue of the overlap matrix is 6.827D-08 Projected Huckel Guess. of initial guess= 0.7500 Requested convergence on RMS density matrix=1.00D-10 within 200 cycles. Requested convergence on MAX density matrix=1.00D-08. Virtual orbitals will be shifted by 0.200 hartree. Integral accuracy reduced to 1.0D-05 until final iterations. Problem detected with inexpensive integrals. Switching to full accuracy and repeating last cycle. Restarting both DIIS and incremental Fock formation. Restarting both DIIS and incremental Fock formation. Restarting both DIIS and incremental Fock formation. Restarting both DIIS and incremental Fock formation. Restarting both DIIS and incremental Fock formation. Restarting both DIIS and incremental Fock formation. ????????????????????????????????????????????????????????????????? Please let me know for what reason the SCF procedure was stopped here (core dumped) and what can I do about it to make SCF proce- dure complete, though at a single point? Almost the same results I have with B3LYP method. Is the extrabasis employment the only way to overcome this prob- lem? Thank you. Sincerely Yours D. Platonov. коооооооооооооооооооооооооооооооооооооооооооооооооооооооооооооооо» є Dmitrii V. Platonov - postgraduate student є є Moscow Lomonosov State Academy of Fine Chemical Technology. є є 117571, Moscow, Russia є є phone: (095)515-24-37 є є e-mail:MITHT@DEOM.CHPH.RAS.RU є йоооооооооооооооооооооооооооооооооооооооооооооооооооооооооооооооој From root@liposome.genebee.msu.su Fri Mar 27 05:08:25 1998 Received: from liposome.genebee.msu.su for root@liposome.genebee.msu.su by www.ccl.net (8.8.3/950822.1) id EAA09773; Fri, 27 Mar 1998 04:18:49 -0500 (EST) Received: (from root@localhost) by liposome.genebee.msu.su (8.8.5/8.8.5) id MAA01973; Fri, 27 Mar 1998 12:27:52 +0300 From: root MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Date: Fri, 27 Mar 1998 12:27:34 +0300 (MSK) To: chemistry@www.ccl.net Cc: pigdog-l@arlington.com Subject: FYI:Re: ASCI BLAS In-Reply-To: <351AD590.60AC@bob.usuf2.usuhs.mil> References: <199803262052.MAA16431@volcanoes.Jpl.Nasa.Gov> <351AD590.60AC@bob.usuf2.usuhs.mil> X-Mailer: VM 6.43 under 20.4 "Emerald" XEmacs Lucid Message-ID: <13595.28837.312706.27604@liposome.genebee.msu.su> Robert Williams writes: > Paul Springer wrote: > > > > The ASCI project has released a very fast BLAS for Linux on Pentiums. > > (See http://www.cs.utk.edu/~ghenry/distrib). They are well worth the > > wait. For multiplying together two double precision matrices of > > size 512 x 512, I clocked a rate of 152 MFlops/s on one of our Beowulf's > > Pentium Pro nodes. Previously the rate had been less than 20. > > Kazushige Goto's assembler dgemm for axp/Linux > (and for alpha-DEC Unix) is now running at 480 MFlops > on a 433 MHz 21164/Linux system (2000x2000), > and 700 MFlops on a 625 MHz 21164 DEC 8400. > DEC is going to 1000 MHz soon and axp/Linux > is very stable on my machine. It might be time > to start thinking along these lines for beowulf. > > -- > Bob Williams, http://bob.usuf2.usuhs.mil/ From Adrian.Mulholland@bristol.ac.uk Fri Mar 27 07:20:36 1998 Received: from dirc.bris.ac.uk for Adrian.Mulholland@bristol.ac.uk by www.ccl.net (8.8.3/950822.1) id HAA10271; Fri, 27 Mar 1998 07:02:56 -0500 (EST) Received: from snow-white (actually host snow-white.chm.bris.ac.uk) by dirc.bris.ac.uk with SMTP-PRIV (PP) with ESMTP; Fri, 27 Mar 1998 12:02:32 +0000 Received: from chth044.chm.bris.ac.uk (chth044.chm.bris.ac.uk [137.222.40.38]) by snow-white.chm.bris.ac.uk (8.8.7/8.8.6) with SMTP id LAA19304 for ; Fri, 27 Mar 1998 11:59:52 GMT From: Adrian Mulholland Sender: Adrian.Mulholland@bristol.ac.uk Reply-To: Adrian.Mulholland@bristol.ac.uk To: CCL Subject: CCL: PhD studentship Message-ID: Date: Fri, 27 Mar 1998 11:55:28 +0000 (GMT) Priority: NORMAL X-Mailer: Simeon for Win32 Version 4.1.2 Build (32) X-Authentication: none MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear CCLers, A PhD position is available in the Department of Chemistry, University of Bristol, UK, in molecular modelling and the simulation of enzyme reactions. Several projects are available, including collaboration with experimental work in the Dept. of Biochemistry. Projects offered include investigation and design of enzyme inhibitors, study of enzyme mechanisms and comparison of enzymes from normal and 'extreme' environments. For more details please see http://www.tlchm.bris.ac.uk/adrian/adrian.html or contact me by e-mail. ---------------------- Adrian Mulholland School of Chemistry Phone: 0117-928-9000, x4279 University of Bristol Fax: 0117-925-1295 Bristol BS8 1TS Adrian.Mulholland@bris.ac.uk From ccl@www.ccl.net Fri Mar 27 11:20:33 1998 Received: from ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA12228; Fri, 27 Mar 1998 10:52:14 -0500 (EST) Received: from cliff.acs.oakland.edu (cliff.acs.oakland.edu [141.210.10.111]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id KAA03964 for ; Fri, 27 Mar 1998 10:52:12 -0500 (EST) Received: from ouchem.chem.oakland.edu (ouchem.chem.oakland.edu [141.210.108.5]) by cliff.acs.oakland.edu (8.8.8/8.8.8) with SMTP id KAA15856 for ; Fri, 27 Mar 1998 10:52:13 -0500 (EST) Received: by ouchem.chem.oakland.edu; id AA07421; Fri, 27 Mar 1998 10:50:01 -0500 From: "Brent H. Besler" Message-Id: <9803271550.AA07421@ouchem.chem.oakland.edu> Subject: A General Statement about Non-Intel x86 Processors To: chemistry@ccl.net Date: Fri, 27 Mar 1998 10:50:01 -0500 (EST) X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit I think it is accurate to make the general statement that the AMD and Cyrix x86 processors cripple the floating point speed to enhance the integer and other instruction speed. If the goal is floating point calculation speed, I would go with a Pentium II. From root@liposome.genebee.msu.su Fri Mar 27 11:26:20 1998 Received: from liposome.genebee.msu.su for root@liposome.genebee.msu.su by www.ccl.net (8.8.3/950822.1) id KAA12143; Fri, 27 Mar 1998 10:45:01 -0500 (EST) Received: (from root@localhost) by liposome.genebee.msu.su (8.8.5/8.8.5) id RAA05393; Fri, 27 Mar 1998 17:38:25 +0300 From: root MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Date: Fri, 27 Mar 1998 17:38:24 +0300 (MSK) To: chemistry@www.ccl.net Subject: CCL:Other Processors In-Reply-To: <004c01bd597f$f98bf6a0$7d05a196@danon.dqf.ufpe.br> References: <004c01bd597f$f98bf6a0$7d05a196@danon.dqf.ufpe.br> X-Mailer: VM 6.43 under 20.4 "Emerald" XEmacs Lucid Message-ID: <13595.46592.828482.515809@liposome.genebee.msu.su> Gustavo de Miranda Seabra writes: > Hi All, > > I would like to know if someone has any experience with desktop > processors other than Intel ones, I mean, AMD-K6 or Cyrix 6x86. What are the > advantages or disadvantages of these processors compared with Pentium or > Pentuim II processors? (At their home pages, the AMD and Cyrix processors > are always comparable to Intel ones.) Current AMD K6 processors are somewhat weaker in concerns to their float performance. This is worsened by the fact that code for the K6 needs to be optimized very differently than for a Pentium (K6 emulates Intel code by a RISC CPU kernel). The bottom line of this is that the K6 delivers (very) roughly half the float performance of Pentium II at the same clock frequency (of course the Pentium also costs significantly more). You would perhaps want to consider the Alpha AXP line of processors. Linux runs on the Alpha, and the egcs compiler makes noticeably better code than gcc. Further improvements are to be expected. If your code does not grab the entire memory bandwidth nother possibility would be a (100baseT-connected cluster of) dual-Pentium II machines running SMP Linux (for that see http://www.beowulf.org ). For K6 info see: http://www.tomshardware.com/k6.html http://www.byte.com/art/9706/sec3/art1.htm also, http://www.amd.com should be helpful. Lots of pdf files there. Regards, Eugene Leitl From jon@sinica.edu.tw Fri Mar 27 21:20:37 1998 Received: from elizium.jon.org for jon@sinica.edu.tw by www.ccl.net (8.8.3/950822.1) id UAA16355; Fri, 27 Mar 1998 20:32:10 -0500 (EST) Received: from nephilim.nmr.ibms.sinica.edu.tw (nephilim [192.168.1.2]) by elizium.jon.org (8.7.5/8.7.3) with SMTP id KAA00909; Sat, 28 Mar 1998 10:02:24 +0800 Message-Id: <3.0.3.32.19980328092828.007bbdb0@192.168.1.3> X-Sender: jon@192.168.1.3 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Sat, 28 Mar 1998 09:28:28 +0800 From: Jon Wright Subject: Re: CCL:Other Processors To: CHEMISTRY@www.ccl.net In-Reply-To: References: <004c01bd597f$f98bf6a0$7d05a196@danon.dqf.ufpe.br> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" At 16:20 27/03/98 +0100, you wrote: >> I would like to know if someone has any experience with desktop >> processors other than Intel ones, I mean, AMD-K6 or Cyrix 6x86. >I know, there are a lot of troubles with Cyrix 6x86. A large >ammount of programs wouldn't like to run. >(I didn't hear anything wrong about AMD-K6.) We have a selection of Cyrix 6x86L/6x86MMX Pentium Pro Pentium II We've found all of them to run Win95 and Linux with no problems at all. However for any serious FP work the Intel are 2-3x faster than the cyrix's. From reports AMD K6 are between cyrix and intel for FP work. If you are going to run Fortran stuff under Linux on a x86 chip it makes good sense to invest in a commercial compiler. We found the Portland Group f77 generated code that ran 3x faster than g77 produced. A few benchmarks are on my web pages: http://www.ibms.sinica.edu.tw/~jon/machines.html Cheers Jon jon@sinica.edu.tw From root@liposome.genebee.msu.su Sat Mar 28 06:20:41 1998 Received: from liposome.genebee.msu.su for root@liposome.genebee.msu.su by www.ccl.net (8.8.3/950822.1) id FAA17505; Sat, 28 Mar 1998 05:41:02 -0500 (EST) Received: (from root@localhost) by liposome.genebee.msu.su (8.8.5/8.8.5) id NAA04230; Sat, 28 Mar 1998 13:48:45 +0300 From: root MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Date: Sat, 28 Mar 1998 13:48:44 +0300 (MSK) To: chemistry@www.ccl.net Subject: CCL:Other Processors In-Reply-To: <199803271909.LAA21585@cagle.emsl.pnl.gov> References: <199803271909.LAA21585@cagle.emsl.pnl.gov> X-Mailer: VM 6.43 under 20.4 "Emerald" XEmacs Lucid Message-ID: <13596.53217.195505.498306@liposome.genebee.msu.su> Ricky A. Kendall writes: > them! I'd also get it in writting!! :) If you want to run additional > OS software such as Linux then you want to stay with the pentium line. Definitely wrong. Early versions of the K6 had _occasional_ problems if 1) you had memory over 32 MBytes AND 2) you ran a taxing task, e.g. a kernel build. All current AMD K6 products are bug-free, and Linux runs great with them. (K6 does not have the F00F bug, for instance). If you want to make sure, look if your CPU is past C stepping, then it's definitely ok. Another thing entirely is float performance. If you want high absolute float performance, go for the Pentium Pro or Pentium II. If you are interested in price/performance ratio, or just integer performance, go for the AMD K6/233. (AMD K6/266 is not very cheap yet). Notice that gcc cannot optimize for the K6 directly yet, this might change in the future. For the price difference, you might also want to purchase a motherboard with 1 MByte 2nd level cache. If you want to build a Beowulf cluster (PVM/MPI code) and your code is is not very memory bandwidth-hungry, you should investigate dual-CPU boards, and Linux SMP. You even don't need a switch for 2-3 node clusters, 2 NICs/machine and 100baseT crossover cable is sufficient. SMP support for Linux is already adequate, and Linus Torvalds (with Transmeta) is currently enhancing it further. In any case there are relatively cheap 200-300 MHz Alphas (0.8-0.9 k$) out there, which run great with Alpha AXP. Use egcs, not gcc for your code then. Compiler support for the Alpha is likely to grow much better in the future. I see possible problems with Compaq's policy to focus on NT-optimized Alpha products for their high-end servers. This might make noncrippled CPUs hard to get in the future. > Cyrix chips have fewer problems with Linux than the AMD but many > people run Linux on all three. There have been lots of problems > reported with the AMD using Linux (look at the linux news groups). I You should have listened closer. This is a public forum, you should have checked twice. > personally would pay the difference to get the pentium based product. Please think things over before you support your favourite monopoly. Forthcoming Merced is purported to suppress free OSses since requiring MDA. Do you really want to face a single-source AND monopoly future? Regards, Eugene Leitl