From klein@quantix.u-strasbg.fr Thu Jan 12 04:35:58 1995 Received: from quantix.u-strasbg.fr for klein@quantix.u-strasbg.fr by www.ccl.net (8.6.9/930601.1506) id EAA11542; Thu, 12 Jan 1995 04:03:42 -0500 From: Received: by quantix.u-strasbg.fr (AIX 3.2/UCB 5.64/4.03) id AA34440; Thu, 12 Jan 1995 10:04:29 +0100 Date: Thu, 12 Jan 1995 10:04:29 +0100 Message-Id: <9501120904.AA34440@quantix.u-strasbg.fr> To: chemistry@ccl.net Subject: summary about geom. opt. Cc: klein@quantix.u-strasbg.fr I asked for a couple of days for generl references about geometry optimization. Thank you very much for your answers. Here is a summary of them, I hope it will be useful for those who are interested in. A. "Optimization Methods in Computational Chemistry" by Tamar Schlick in "Reviews in Computational Chemistry," volume 3, edited by Kenny Lipkowitz and Don Boyd. B. Practical Methods of Optimization (vol.1 Unconstrained Optimization) R.Fletcher, John Wiley & Sons 1980 C. Introduction to Optimization E.M.L.Beale, John Wiley & Sons 1988 D. T.H.Fischer and J. Almlof, J. Phys. Chem.,96,9768,(1992) E. H.B.Schlegel ``Optimization of equilibrium geometries and transition states structures'' (p. 249) in Ab initio methods in quantum chemistry Part. I -Advances in chemical physics Vol. LXVII (John Wiley and sons) 1987. F. H.B.Schlegel, Adv. Chem. Phys. 67, 249 (1987) G. An introduction to computation chemistry. Tim Clarke H. Analytic derivatives methods and geometry optimisation in modern quantum chemistry, p437, by Szabo & Ostlund From delaney@jh01sg.demon.co.uk Thu Jan 12 06:35:57 1995 Received: from gate.demon.co.uk for delaney@jh01sg.demon.co.uk by www.ccl.net (8.6.9/930601.1506) id GAA12506; Thu, 12 Jan 1995 06:33:08 -0500 Received: from post.demon.co.uk by gate.demon.co.uk id aa01368; 12 Jan 95 11:24 GMT Received: from jh01sg.demon.co.uk by post.demon.co.uk id aa15095; 12 Jan 95 11:23 GMT Received: by JH01SG (931110.SGI/zeneca.jf.gwm.3Nov94) for delaney id AA21736; Thu, 12 Jan 95 09:45:34 GMT From: john delaney Message-Id: <9501120945.AA21736@JH01SG> Subject: Shannon-Weaver Diversity Index To: chemistry@ccl.net Date: Thu, 12 Jan 1995 09:45:33 +0000 (GMT) Cc: john delaney X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 261 Can anyoune tell me what the Shannon-Weaver diversity index is ? Are their any recognised methods for measuring chemical diversity ? I get the impression that diversity is relative rather than absolute. Ta. John Delaney Zeneca AgChem delaney@jh01sg.demon.co.uk From darryl@om3.ch.umist.ac.uk Thu Jan 12 06:58:36 1995 Received: from nessie.mcc.ac.uk for darryl@om3.ch.umist.ac.uk by www.ccl.net (8.6.9/930601.1506) id GAA12483; Thu, 12 Jan 1995 06:30:09 -0500 Received: from om3.ch.umist.ac.uk (actually trigger.ch.umist.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Thu, 12 Jan 1995 11:29:00 +0000 Received: by om3.ch.umist.ac.uk (940406.SGI/) for chemistry%ccl.net@nessie.mcc.ac.uk id AA10987; Thu, 12 Jan 95 11:40:32 GMT Date: Thu, 12 Jan 1995 11:40:31 +0000 (GMT) From: Darryl Ellson Subject: Tyrosine To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I'd like to thank all the people who have provided most useful references and data concearning my query. Many Thanks ..... Darryl Ellson. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Darryl A. Ellson - Dept. Chemistry, UMIST, Manchester. M60 1QD Tel: 061-236-3311 x4476 Fax: 061-236-7677 E-mail: darryl@trigger.ch.umist.ac.uk ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From noy@tci002.uibk.ac.at Thu Jan 12 07:36:06 1995 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.9/930601.1506) id HAA12999; Thu, 12 Jan 1995 07:24:56 -0500 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA03699 (5.65c/IDA-1.4.4 for ); Thu, 12 Jan 1995 13:24:46 +0100 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA35132; Thu, 12 Jan 1995 13:24:45 +0100 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9501121224.AA35132@tci002.uibk.ac.at> Subject: Summary: what makes Gaussian fast ? To: chemistry@ccl.net Date: Thu, 12 Jan 1995 13:24:44 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 8469 Dear netters, Thank you very much for your response. I have learned a lot from you responses. Now, I can answer myself somehow why Gaussian is faster than the other. I have attached those I have received at the end of this mail. take care, Teerakiat ------------------------------ original question -------------------------- Dear cyber-chemists, I have experienced using both GAMESS and Gaussian 92 on AIX platform. Gaussian 92 always runs faster than GAMESS in most case. I have found on a review article where written Gaussian spend the computation at the cost of N**2.7 not N**4 as conventional Hartree-Fock scheme (N = no. of Gaussian primitives). Which special algorithms are tailored into Gaussian ? Could somebody point me out a hint or direct me the the proper references I could read through in more detail. Thanks a lot for any responses. take care, Teerakiat PS. The energy obtained from GAMESS is always lower than from Gaussian. Therefore, I believe that the speed is gained at the sacrifice of some precision. ------------------------- compilation of responses ------------------------- From: mei@atlas.rc.m-kasei.co.jp (Akinori MURAKAMI) >> Dear cyber-chemists, ??? >> I have experienced using both GAMESS and Gaussian 92 on >> AIX platform. Gaussian 92 always runs faster than GAMESS in >> most case. I have found on a review article where written Gaussian >> spend the computation at the cost of N**2.7 not N**4 as >> conventional Hartree-Fock scheme (N = no. of Gaussian primitives). That is not true for conventional method. There are only small amount of nonzero integrals(greater than 10**(-10)) and number of those scale as N**(2-3). N**4 is formal scaling not real time computation. cf. R. Ahlichs, Theor. Chim. Acta. vol 33, p157, (1974) >> Which special algorithms are tailored into Gaussian ? Most integral are evaluated by HP(axis rotation method) in both Gaussian and HONDO(GAMESS). Some integrals are evaluated by HGP and PRISM in Gaussian is faster than Rys method in HONDO(GAMESS0. I think that is not main difference. Gaussian seems clever selection for integral evaluation. I don't know the paper. You can imagine from the original paper on direct SCF, J. Almolef, K. Faegri, K. Korsell, J. Comput. Chem. vol 3. p385 (1982). >> PS. The energy obtained from GAMESS is always lower than from >> Gaussian. Therefore, I believe that the speed is gained >> at the sacrifice of some precision. I think your mention about one point calculation. Gaussian use loose conversion threshold, 10**(-4). We get same energy on Gaussian and GAMESS(HONDO). Best regards. Akinori Murakami Mitsubishi Chemical Corporation ----------------------------------------------------------------------- From: c72417@u1.uibk.ac.at (Michael Probst) Hi, Noy ! No reasonable Hartree-Fock program scales with N^4. The power of 2-3 comes from the way in which calculation of near-0 integrals is avoided: The programs get always smarter in this. For large chemical systems the power becomes 2 for a ' perfect program' or even smaller if tricks like FMM are used. I think Gamess has a bit old integral routines that make it slower than Gaussian. Btw, for example turbomole is normally faster than Gaussian. The results of both programs must really be the same up to at least 6 digits after the comma otherwise (1) there are different tresholds or hidden differences in coordinates or so or (2) there is a real bug. Greetings ! How is life going ? Michael ------------------------------------------------------------------------ From: "Dr. Rene Fournier" Hi ; One reason why Gaussian is very fast is because of its efficient calculation of integrals which is very well described in: P. M. W. Gill, Adv. Quantum Chem. 25, 143 (1994). Rene Fournier fournie@ned1.sims.nrc.ca ------------------------------------------------------------------------ From: David Heisterberg >most case. I have found on a review article where written Gaussian >spend the computation at the cost of N**2.7 not N**4 as That's an observed scaling, and all codes behave similarly. The rate-limiting step for most SCF runs is generation and/or subsequent reading of the two-electron integrals, which theoretically grow as N^4. However, in generating them one typically "screens out" integrals that will be small because the centers involved are far apart. These are simply not computed and considered 0. If you throw away integrals for which the appropriate centers are greater than a distance, R, apart, and consider a molecule to be roughly spherical, then the number of centers within distance R of a given one only grows as N^3 rather an N^4. > Which special algorithms are tailored into Gaussian ? Gaussian does have a very fast integral program. The Gaussian manual lists references for the important papers. The PRISM algorithm is pretty smart about choosing the best way to evaluate integrals given the angular momentum and length of contraction. But ultimately they are done based on the recurrence relations of King, Dupuis, and Rys or those of McMurchie and Davidson. > PS. The energy obtained from GAMESS is always lower than from Gaussian has somewhat looser criteria for discarding integrals that Gamess, but you can change this and get the same result >from both codes. > Gaussian. Therefore, I believe that the speed is gained > at the sacrifice of some precision. Yes! -- David J. Heisterberg (djh@ccl.net) Gee, it's so beautiful, I gotta The Ohio Supercomputer Center give somebody a sock in the jaw. Columbus, Ohio -- Little Skippy (Percy Crosby) ------------------------------------------------------------------------- From: Bob Zellmer Are you talking about a single point calculation or a geometry optimization? I believe that when a geom. opt. is done using G92 the threshold for throwing integrals out (treating them as equal to zero) is lower in the early part of the opt. when far away from the optimized geometry. This may also be true for single points depending on how the calculation is done (incore, direct, etc.). There is some limited control over the threshold for keeping integrals. This is why G92 would both be faster than GAMESS and less precise (slightly higher energy). I believe it does mention this in the manual, but I don't remember where. I hope this helps a little bit. Robert Zellmer Chemistry Dept. The Ohio State University Columbus, OH 43017 zellmer@sodium.mps.ohio-state.edu -------------------------------------------------------------------------- From: husuter Dear Mr. Kerdchar, the time difference between G92 and GAMESS is mainly due to other integral routines. The GAMESS/HONDO uses the old Rys-Dupuis routines and some of the G80 routines, look for example at the papers of the group of M. Dupuis, J.Chem.Phys. 65(1976)111 and J.Comp.Phys 21 (1976) 144. The integral routines of the G92++ series are of newer date and you may find them with the reference M. Head-Gordon and J.A. Pople, J.Chem.Phys. 89 (1988) 5777. There is a quite good introduction of the problems of integral evaluation in the last Advances of Quantum Chemistry, from P.M.W. Gill. I would recommend you to look at it. I have also observed that the GAMESS is trastically slower than the newer versions of Gaussian, but there are things which you have to consider too. First of all the GAMESS uses 6d functions, and it may be that you compare with 5d functions in G92. The energies will be different! Secondly the default for the integral neglection threshold (that is what finally makes that the n**4 dependence vanisches) is rather conservative in GAMESS and HONDO (10**-12), which is not necessary except you have very diffuse functions. I am also sure that the people of GAMESS-US, will defend their Program, so you may hear something about possible improvements from their side. hope this helps, Hans Ulrich Suter ----------------------------------------------------------------------- From garciae@ucsub.colorado.edu Thu Jan 12 11:36:02 1995 Received: from ucsub.colorado.edu for garciae@ucsub.colorado.edu by www.ccl.net (8.6.9/930601.1506) id LAA16794; Thu, 12 Jan 1995 11:22:32 -0500 Received: (from garciae@localhost) by ucsub.colorado.edu (8.6.9/8.6.9/CNS-3.5) id JAA13555; Thu, 12 Jan 1995 09:22:27 -0700 Date: Thu, 12 Jan 1995 09:22:27 -0700 (MST) From: Garcia Edgardo To: chemistry@ccl.net Subject: CCL: Optical properties Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I would appreciate some references & programs (shareware or not) about how to calculate optical (linear and non-linear) properties of organic molecules like polarizabilities, hyper-polariz., exited-state dipoles, etc. Thanks in advance. Edgardo Garcia Cristol Chem. & Biochem. Univ. of Colorado at BOULDER From srheller@probe.nalusda.gov Thu Jan 12 12:36:04 1995 Received: from cliff.nalusda.gov for srheller@probe.nalusda.gov by www.ccl.net (8.6.9/930601.1506) id LAA16987; Thu, 12 Jan 1995 11:38:07 -0500 Received: from probe.nalusda.gov by cliff.nalusda.gov (4.1/SMI-4.1) id AA29698; Thu, 12 Jan 95 11:40:12 EST Received: by probe.nalusda.gov (5.0/SMI-SVR4) id AA21380; Thu, 12 Jan 1995 11:30:51 +0500 Date: Thu, 12 Jan 1995 11:30:50 -0500 (EST) From: Steve Heller Subject: 11th ICCCRE To: jcicshelp , chemistry@ccl.net, chminf-l@iubvm.ucs.indiana.edu, orgchem@extreme.chem.rpi.edu Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1318 ---------- Forwarded message ---------- Date: Thu, 12 Jan 95 16:31 GMT From: Professeur DOUCET Jean-Pierre To: Multiple recipients of list Subject: Subject: XIth INTERNATIONAL CONFERENCE ON COMPUTERS IN CHEMICAL RESEARCH AND EDUCATION The XIth ICCCRE will be held in Paris (France), at Cite Internationale Universitaire, between the 17th and 21st of July 1995. The topic selected for emphasis are: Chemical Information Technology Chemical databases: Data, Information and Knowledge Computer-assisted Structural Elucidation and Spectral Simulation Recent advances in Chemometrics Modelling and Molecular Graphics Drug design and QSAR Synthesis Design, Reaction Prediction Computer in Chemical Education The conference will have invited and contributed speakers. A poster session is also planned. If you would like further information or would like to submit an abstract for a contribution in one of the above sessions then please contact Prof. J.P. Doucet or Prof. A. Panaye at : Institut de Toplogie et de Dynamique des Syst mes University Paris 7- Denis Diderot 1 rue Guy de la Brosse - 75005 Paris - France e-mail doucet@jupiter.itodys.jussieu.fr Fax: 33 1 44 27 68 14 or 33 1 44 27 60 53 Tel: 33 1 44 27 44 12 From MOMOT%UACCIT@Arizona.EDU Thu Jan 12 13:36:02 1995 Received: from Arizona.EDU for MOMOT%UACCIT@Arizona.EDU by www.ccl.net (8.6.9/930601.1506) id MAA18305; Thu, 12 Jan 1995 12:49:22 -0500 From: Received: from Arizonet (MOMOT@UACCIT) by Arizona.EDU (PMDF V4.3-10 #2381) id <01HLR8A79J9SEY5F0Q@Arizona.EDU>; Thu, 12 Jan 1995 10:49:17 -0700 (MST) Date: Thu, 12 Jan 1995 10:49:17 -0700 (MST) Subject: Semiempirical parameterization for porphyrins ? To: chemistry@ccl.net Message-id: <01HLR8A7E38IEY5F0Q@Arizona.EDU> X-VMS-To: TELCOM::IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, I am going to do some semiempirical calculations of Fe(III) porphyrin complexes, and trying to get information on the following two questions: 1) Which of available parameterizations is "the best" ? 2) What commercially available programs have parameterization appropriate for porphyrin complexes, and what is the price of such programs ? I will summarize all replies and post them on this net. Thanks in advance. Konstantin From mizan@engin.umich.edu Thu Jan 12 14:36:03 1995 Received: from dhaka.engin.umich.edu for mizan@engin.umich.edu by www.ccl.net (8.6.9/930601.1506) id OAA20109; Thu, 12 Jan 1995 14:28:55 -0500 Received: (mizan@localhost) by dhaka.engin.umich.edu (8.6.8/8.6.4) id OAA26223 for CHEMISTRY@ccl.net; Thu, 12 Jan 1995 14:28:44 -0500 Date: Thu, 12 Jan 1995 14:28:44 -0500 From: "Tahmid I. Mizan" Message-Id: <199501121928.OAA26223@dhaka.engin.umich.edu> To: CHEMISTRY@ccl.net Subject: Atomic partial charges on open shell species Hi, I would be very obliged if someone could suggest some references for (ESP fitted or otherwise) atomic partial charges on open shell species. Thanks in advance Tahmid Mizan University of Michigan From omni@ufba.br Thu Jan 12 18:36:05 1995 Received: from canudos.ufba.br for omni@ufba.br by www.ccl.net (8.6.9/930601.1506) id SAA24604; Thu, 12 Jan 1995 18:05:18 -0500 Received: by canudos.ufba.br (AIX 3.2/UCB 5.64/4.03) id AA28350; Thu, 12 Jan 1995 21:01:02 -0200 Date: Thu, 12 Jan 1995 21:01:01 -0200 (GRNLNDDT) From: Oswaldo Rodrigues Leite Filho To: chemistry@ccl.net Cc: chminf-l@iubvm.ucs.indiana.edu Subject: CCL: Catalyst for CO removal Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Netters, We are looking for catalysts to be used in a fixed bed reactor to decrease the CO ( carbon monoxide ) content in a Hydrogen feedstock from 30 ppm to < 1 ppm. Any help will be wellcome. Please, reply to TIA, Oswaldo Leite From MMYUSOFF@WSUHUB.UC.TWSU.EDU Thu Jan 12 23:36:09 1995 Received: from WSUHUB.UC.TWSU.EDU for MMYUSOFF@WSUHUB.UC.TWSU.EDU by www.ccl.net (8.6.9/930601.1506) id XAA27263; Thu, 12 Jan 1995 23:34:17 -0500 From: Received: from WSUHUB.UC.TWSU.EDU by WSUHUB.UC.TWSU.EDU (PMDF V4.3-9 #6497) id <01HLRX9A61CW8X5MBJ@WSUHUB.UC.TWSU.EDU>; Thu, 12 Jan 1995 22:35:13 -0600 (CST) Date: Thu, 12 Jan 1995 22:35:13 -0600 (CST) Subject: INFORMATION To: CHEMISTRY@ccl.net Message-id: <01HLRX9A73XU8X5MBJ@WSUHUB.UC.TWSU.EDU> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT PLEASE SEND INFORMATION TO: MASHITAH YUSOFF 1845 N FAIRMOUNT WICHITA KS67260-0051 OR VIA INTERNET. THANKS.