From chemistry-request@server.ccl.net Fri Jul 30 04:13:43 1999 Received: from stork.EMBL-Heidelberg.DE (stork.EMBL-Heidelberg.DE [192.54.41.54]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA16600 for ; Fri, 30 Jul 1999 04:13:42 -0400 From: Lutz.Ehrlich@EMBL-Heidelberg.de Received: from cuckoo.embl-heidelberg.de (cuckoo.EMBL-Heidelberg.DE [192.54.41.16]) by stork.EMBL-Heidelberg.DE (980427.SGI.8.8.8/8.8.4) with ESMTP id KAA17759; Fri, 30 Jul 1999 10:08:25 +0200 (MDT) Received: by cuckoo.embl-heidelberg.de (8.7.1) id IAA26303; Fri, 30 Jul 1999 08:08:24 GMT MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14241.23927.79533.965661@cuckoo.EMBL-Heidelberg.DE> Date: Fri, 30 Jul 1999 10:08:23 +0200 (MDT) To: daizadeh@nucleus.harvard.edu CC: CHEMISTRY@ccl.net Subject: Re: Python vs. Perl X-Mailer: VM 6.72 under Emacs 19.34.1 > Iraj Daizadeh: > Hello. Perl seems to dominate the > chem(bio)-informatical sciences these > days. An example of such dominance is > descibed on papers describing the BioPerl consortium > http://bio.perl.org (see, e.g., an article in > http://www.bitsjournal.com > Bioperl:Standard perl modules for bioinformatics)... > The question is why...why has python been neglected > from its role in the informatics fields.... > > Your responses would be appreciated...Iraj. Hello Iraj, I think you'll have to note a clear separation here; in the bioinformatics (read sequence analysis as opposed to structure analysis) field, Perl had strong support from the start on. When I speak to bioinfo people here at EMBL, code reuse seems to be the dominant motive for choosing Perl. In my eyes, things are different in the structure-related comp chem field. Right now, I see a lot of projects which use Python in favor of Perl; for example look at Konrad Hinsen's excellent Molecular Modelling Toolkit (http://starship.python.net/crew/hinsen/mmtk.html). Companies like Bioreason or Exelyxis are now looking for people with Python coding experience. People here in NMR at EMBL even dream about developing a next-generation XPLOR as libraries to be used as Python modules. Given Python's excellent CORBA, number crunching and XML support, as well as the Java integration and existing class libraries relevant to the comp chem field, I think it's just a matter of time when Python catches up. Tight integration with web application servers like Zope (http://www.zope.org) could make a big difference in writing web services for the biocomputing community. After having used Perl4 and Perl5 for years, I wonder where people see advantages of Perl in the comp chem field? Comments anybody? Regards, Lutz ______________________________________________________________________ Lutz Ehrlich http://www.embl-heidelberg.de/~ehrlich mailto:lutz.ehrlich@embl-heidelberg.de European Molecular Biology Laboratory phone: +49-6221-387-140 Meyerhofstr. 1 fax : +49-6221-387-517 D-69012 Heidelberg, Germany From chemistry-request@server.ccl.net Fri Jul 30 01:08:12 1999 Received: from deews1.dent.okayama-u.ac.jp ([150.46.140.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA15510 for ; Fri, 30 Jul 1999 01:08:10 -0400 Received: from [150.46.162.72] (liset4.lib.okayama-u.ac.jp [150.46.162.72]) by deews1.dent.okayama-u.ac.jp (8.9.2/3.7Wpl2-oucc-1.0) with SMTP id OAA28757 for ; Fri, 30 Jul 1999 14:02:58 +0900 (JST) Date: Fri, 30 Jul 1999 14:02:58 +0900 (JST) Message-Id: <199907300502.OAA28757@deews1.dent.okayama-u.ac.jp> To: CHEMISTRY@server.ccl.net From: ep7@dent.okayama-u.ac.jp (Masamura) Subject: Re: CCL: Summary of Ion-water clusters MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Sir: More useful answers for my question (Please teach me the recent literatures and reviews of ion-water clusters) were gotten. ************************************************* X-Sender: ss@mail.clemson.edu Content-Type: text/plain; charset="us-ascii" Date: Wed, 28 Jul 1999 09:16:14 -0400 To: ep7@dent.okayama-u.ac.jp (Masamura) From: "Steven J. Stuart" Subject: Re: CCL:Summary of Ion-water clusters X-UIDL: V`Ce9<*H!!nL=!!#lid9 Below are a collection of references concerning ion/water clusters. Most are concerning halide ions in water clusters. Unfortunately, the only good review article I know of is the one by Castleman and Keesee, which is somewhat dated at this point. If your interest is halide and/or chloride ion, I would also be happy to send you a preprint of a recent article of mine that is not yet in print. Best wishes, -Steve Stuart Department of Chemistry Clemson University Clemson, SC 29634 author = "L. X. Dang and D. E. Smith", title = "Molecular dynamics simulations of aqueous ionic clusters using polarizable water", journal = JCP, volume = "99", pages = "6950-6956", year = 1993} author = "P. Ayotte and C. G. Bailey and G. H. Weddle and M. A. Johnson", title = "Vibrational Spectroscopy of Small {B}r$^{-}$\cdot(H$_{2}$O)$_{n}$ and {I}$^{-}$\cdot(H$_{2}$O)$_{n}$ Clusters: {I}nfrared Characterization of the Ionic Hydrogen Bond", journal = JPCA, volume = "102", pages = "3067-3071", year = 1998} author = "P. Ayotte and G. H. Weddle and J. Kim and J. Kelley and M. A. Johnson", title = "A Cluster Study of Anionic Hydration: {S}pectroscopic Characterization of the {I}$^{-}$\cdot{W}$_{n}$, $1 \le n \le 3$, Supramolecular Complexes at the Primary Steps of Solvation", journal = JPCA, volume = "103", pages = "443-447", year = 1999} author = "M. Arshadi and R. Yamdagni and P. Kebarle", title = "Hydration of the Halide Negative Ions in the Gas Phase. {II}. {C}omparison of Hydration Energies for the Alkali Positive and Halide Negative Ions", journal = JPC, volume = "74", pages = "1475-1482", year = 1970} author = "E. Clementi and E. Barsotti", title = "Study of the Structure of Molecular Complexes. {C}oordination Numbers for {L}i$^{+}$, {N}a$^{+}$, {K}$^{+}$, {F}$^{-}$ and {C}l$^{-}$ in Water", journal = CPL, volume = "59", pages = "21--25", year = 1978} author = "J. Caldwell and L. X. Dang and P. A. Kollman", title = "Implementation of Nonadditive Intermolecular Potentials by Use of Molecular Dynamics: {D}evelopment of a Water-Water Potential and Water-Ion Cluster Interactions", journal = JACS, volume = "112", pages = "9144-9147", year = 1990} author = "Castleman, Jr., A. W. and R. G. Keesee", title = "Ionic Clusters", journal = CR, volume = "86", pages = "589-618", year = 1986} author = "J.-H. Choi and K. T. Kuwata and Y.-B. Cao and M. Okumura", title = "Vibrational Spectroscopy of the {C}l$^{-}$(H$_{2}$O)$_{n}$ Anionic Clusters, $n$ = 1 -- 5", journal = JPCA, volume = "102", pages = "503-507", year = 1998} author = "O. M. Cabarcos and C. J. Weinheimer and J. M. Lisy and S. S. Xantheas", title = "Microscopic hydration of the fluoride anion", journal = JCP, volume = "110", pages = "5-8", year = 1999} author = "O. M. Cabarcos and C. J. Weinheimer and T. J. Martinez and J. M. Lisy", title = "The solvation of chloride by methanol --- surface versus interior cluster ion states", journal = JCP, volume = "110", pages = "9516-9526", year = 1999} author = "P. D. Dacre", title = "{SCF} potential surfaces and derived models for {N}a$^{+}$ and {C}l$^{-}$ ions interacting with a water molecule", journal = MP, volume = "51", pages = "633--659", year = 1984} author = "B. T. Gowda and S. W. Benson", title = "Energetics and Structure of the Hydrated Gaseous Halide Anions", journal = JCC, volume = "4", pages = "283--293", year = 1983} author = "K. Hiraoka and S. Mizuse", title = "Gas-phase solvation of {C}l$^{-}$ with {H}$_{2}${O}, {C}{H}$_{3}${O}{H}, {\it i}-{C}$_{3}${H}$_{7}${O}{H}, and {\it t}-{C}$_{4}${H}$_{9}${O}{H}", journal = CP, volume = "118", pages = "457-466", year = 1987} author = "K. Hiraoka and S. Misuze and S. Yamabe", title = "Solvation of Halide Ions with {H}$_{2}${O} and {CH}$_{3}${CN} in the Gas Phase", journal = JPC, volume = "92", pages = "3943-3952", year = 1988} author = "W. L. Jorgensen and D. L. Severance", title = "Limited effects of polarization for {C}l$^{-}$({H}$_{2}${O})$_{n}$ and {N}a$^{+}$({H}$_{2}${O})$_{n}$ clusters", journal = JCP, volume = "99", pages = "4233--4235", year = 1993} author = "R. G. Keesee and Castleman, Jr., A. W.", title = "Gas-phase studies of hydration complexes of {C}l$^{-}$ and {I}$^{-}$ and comparison to electrostatic calculations in the gas phase", journal = CPL, volume = "74", pages = "139-142", year = 1980} author = "H. Kistenmacher and H. Popkie and E. Clementi", title = "Study of the structure of molecular complexes. {V}. {H}eat of formation for the {L}i$^{+}$, {N}a$^{+}$, {K}$^{+}$, {F}$^{-}$, and {C}l$^{-}$ ion complexes with a single water molecule", journal = JCP, volume = "59", pages = "5842-5848", year = 1973} author = "H. Kistenmacher and H. Popkie and E. Clementi", title = "Study of the structure of molecular complexes. {III}. {E}nergy surface of a water molecule in the field of a fluorine or chlorine anion", journal = JCP, volume = "58", pages = "5627-5638", year = 1973} author = "H. Kistenmacher and H. Popkie and E. Clementi", title = "Study of the structure of molecular complexes. {VIII}. {S}mall clusters of water molecules surrounding {L}i$^{+}$, {N}a$^{+}$, {K}$^{+}$, {F}$^{-}$, and {C}l$^{-}$ ions", journal = JCP, volume = "61", pages = "799-815", year = 1974} author = "M. R. Mruzik and F. F. Abraham and D. E. Schreiber", title = "A Monte Carlo study of ion-water clusters", journal = JCP, volume = "64", pages = "481-491", year = 1976} author = "G. Markovich and S. Pollack and R. Giniger and O. Cheshnovsky", title = "Photoelectron spectroscopy of {C}l$^{-}$, {B}r$^{-}$, and {I}$^{-}$ solvated in water clusters", journal = JCP, volume = "101", pages = "9344-9353", year = 1994} author = "L. Perera and M. L. Berkowitz", title = "Many-body effects in molecular dynamics simulations of {N}a$^{+}$({H}$_{2}${O})$_{n}$ and {C}l$^{-}$({H}$_{2}${O})$_{n}$ clusters", journal = JCP, volume = "95", pages = "1954--1963", year = 1991} author = "L. Perera and M. L. Berkowitz", title = "Structure and dynamics of {C}l$^{-}$({H}$_{2}${O})$_{20}$ clusters: \ {T}he effect of the polarizability and the charge of the ion", journal = JCP, volume = "96", pages = "8288-8294", year = 1992} author = "L. Perera and M. L. Berkowitz", title = "Erratum: {M}any-body effects in molecular dynamics simulations of {N}a$^{+}$({H}$_{2}${O})$_{n}$ and {C}l$^{-}$({H}$_{2}${O})$_{n}$ clusters [{J. Chem. Phys.} 95, 1954 (1991)]", journal = JCP, volume = "99", pages = "4236--4237", year = 1993} author = "L. Perera and M. L. Berkowitz", title = "Stabilization energies of {C}l$^{-}$, {B}r$^{-}$, and {I}$^{-}$ ions in water clusters", journal = JCP, volume = "99", pages = "4222--4224", year = 1993} author = "L. Perera and M. Berkowitz", title = "Structures of {C}l$^{-}$({H}$_{2}${O})$_{n}$ and {F}$^{-}$({H}$_{2}${O})$_{n}$ ($n = 2,3,\ldots,15$) clusters. {M}olecular dynamics computer simulations", journal = JCP, volume = "100", pages = "3085--3093", year = 1994} author = "I. Rips and J. Jortner", title = "Ion solvation in clusters", journal = JCP, volume = "97", pages = "536--546", year = 1992} author = "K. G. Spears", title = "Hydration Structures For Halide (-) Ions", journal = JPC, volume = "81", pages = "186", year = "1976"} author = "S. J. Stuart and B. J. Berne", title = "Effects of Polarizability on the Hydration of the Chloride Ion", journal = JPC, volume = "100", pages = "11934--11943", year = 1996} author = "I.-C. Yeh and L. Perera and M. L. Berkowitz", title = "Photodetachment spectra of {C}l$^{-}({H}$_{2}${O})$_{n}$ clusters. {P}redictions and comparisons", journal = CPL, volume = "264", pages = "31-38", year = 1997} author = "X. G. Zhao and A. {G}onzalez-{L}afont and D. G. Truhlar and R. Steckler", title = "Molecular modeling of solvation. {C}l$^{-}$({D}$_{2}${O})", journal = JCP, volume = "94", pages = "5544-5558", year = 1991} author = "X. G. Zhao and D.-H. Lu and Y.-P. Liu and G. C. Lynch and D. G. Truhlar", title = "Use of an improved ion-solvent potential-energy function to calculate the reaction rate and {$\alpha$}-deuterium and microsolvation kinetic isotope effects for the gas-phase {S}$_{N}$2 reaction of {C}l$^{-}$({H}$_{2}${O}) with {CH}$_{3}${C}l", journal = JCP, volume = "97", pages = "6369", year = 1992} @article{ sd94b, author = "D. E. Smith and L. X. Dang", title = "Computer simulations of cesium-water clusters: {D}o ion-water clusters form gas-phase clathrates?", journal = JCP, volume = "101", pages = "7873-7881", year = 1994} @article{ drck91, author = "L. X. Dang and J. E. Rice and J. Caldwell and P. A. Kollman", title = "Ion Solvation in Polarizable Water: {M}olecular Dynamics Simulations", journal = JACS, volume = "113", pages = "2481--2486", year = 1991} @article{ cl96, author = "O. M. Cabarcos and J. M. Lisy", title = "Solvation of ions in the gas-phase: a molecular dynamics simulation", journal = CPL, volume = "257", pages = "265-272", year = 1996} @article{ ckj94, author = "J. E. Combariza and N. R. Kestner and J. Jortner", title = "Energy-structure relationships for microscopic solvation of anions in water clusters", journal = JCP, volume = "100", pages = "2851-2864", year = 1994} ******************************************************** From: "Dr. Ina Hahndorf" To: ep7@dent.okayama-u.ac.jp Date: Tue, 27 Jul 1999 10:40:26 +0200 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: ion water clusters Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01d) X-UIDL: >RPe9?\;e9ll;!!(p[d9 Dear M. Masamura, to get information on protonated water clusters I suggest to have a look in: J. Am. Chem. Soc., 120 (1998) 8777 J. Chem. Phys. 107 (1997) 9695 Chem. Phys. Lett. 289 (1998) 373 and references therein. Yours sincerely Ina Hahndorf please notice the new address: ************************************* Dr. Ina Hahndorf Institut fuer Angewandte Chemie Berlin-Adlershof e.V. Richard-Willstaetter-Str. 12 D-12489 Berlin Germany Tel.: ++49-30-6392-4452 FAX: ++49-30-6392-4454 e-mail: hahndorf@aca-berlin.de ************************************* ****************************************************** *********************************** M. Masamura Department of Preventive Dentistry Okayama University Dental School Shikata-cho 2-5-1, Okayama, 700-8525 Japan *********************************** From chemistry-request@server.ccl.net Fri Jul 30 03:32:58 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA16269 for ; Fri, 30 Jul 1999 03:32:55 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id JAA12043; Fri, 30 Jul 1999 09:27:38 +0200 From: Jochen Kuepper Reply-To: jochen@bacchus.pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: Mehnert Thomas , chemistry@server.ccl.net Subject: Re: CCL:Clustering Date: Mon, 5 Sep 2135 15:51:58 +0200 X-Mailer: KMail [version 1.0.21] Content-Type: text/plain References: <37A01984.DED60457@physik.tu-muenchen.de> MIME-Version: 1.0 Message-Id: <99073009273800.12040@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id DAA16270 On Don, 29 Jul 1999 Mehnert Thomas wrote: >Hi alltogether, > >I investigate clusters normally consisting of two to three molecules. >But sometimes generation of clusters works well and sometimes not >depending on the molecules I use. I think the problem is the process of >creation the clusters during the expansion in the nozzle which depends >probably on the geometry of the nozzle. Does anyone have >an idea with respect to this problem or does anybody know a reference >referring to this? Well, although it is not computational chemistry :-! Have you checked Scoles "Atomic and Molecular" beams book ? There are also paper out that care about expansion conditions and geometries - Lavalle (sp?) geometry, conical geometry, ... If you get any interesting papers, please summarize to the list. If you happen to find someone to build you these nozzles, please tell me so. Btw: Have you asked Neusser ? He should now :-) -- Jochen Heinrich-Heine-Universität Düsseldorf jochen@uni-duesseldorf.de Institut für Physikalische Chemie I phone ++49-211-8113681 Universitätsstr. 26.43.02.29 fax ++49-211-8115195 40225 Düsseldorf, Germany www-public.rz.uni-duesseldorf.de/~jochen From chemistry-request@server.ccl.net Fri Jul 30 03:36:44 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA16291 for ; Fri, 30 Jul 1999 03:36:43 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id JAA12054; Fri, 30 Jul 1999 09:31:18 +0200 From: Jochen Kuepper Reply-To: jochen@bacchus.pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: Iraj Daizadeh , chemistry@ccl.net Subject: Re: CCL:Large matrix diagonalization. Date: Fri, 30 Jul 1999 09:29:56 +0200 X-Mailer: KMail [version 1.0.21] Content-Type: text/plain References: MIME-Version: 1.0 Message-Id: <99073009311801.12040@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id DAA16292 On Don, 29 Jul 1999 Iraj Daizadeh wrote: >For my phd dissertation, we spent quite some time diagonalizing SPARSE >matrices of the order of 1000x1000 or so...The diagonalization process was >performed by a routine called cboris (fortran code): >It is included in the QCPE >This routine is not faster than the diagonalization packages that come >with blas or something or that sort... So why have you used it ? What's it advantage to LAPACK algorithms ? -- Jochen Heinrich-Heine-Universität Düsseldorf jochen@uni-duesseldorf.de Institut für Physikalische Chemie I phone ++49-211-8113681 Universitätsstr. 26.43.02.29 fax ++49-211-8115195 40225 Düsseldorf, Germany www-public.rz.uni-duesseldorf.de/~jochen From chemistry-request@server.ccl.net Fri Jul 30 12:06:32 1999 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA20598 for ; Fri, 30 Jul 1999 12:06:30 -0400 Received: from dwi01.dwi.rwth-aachen.de by mail.rwth-aachen.de (PMDF V5.1-12 #D3869) with ESMTP id <01JE6N7HW47400004K@mail.rwth-aachen.de> for chemistry@ccl.net; Fri, 30 Jul 1999 17:53:31 +0200 Received: from DWI01/SpoolDir by dwi01.dwi.rwth-aachen.de (Mercury 1.44); Fri, 30 Jul 1999 17:53:25 +0000 Received: from SpoolDir by DWI01 (Mercury 1.44); Fri, 30 Jul 1999 17:53:22 +0000 Date: Fri, 30 Jul 1999 17:53:16 +0000 From: JATI KASTANJA Subject: CCL: Levinthal's paradox To: chemistry@ccl.net Message-id: <51C9FF0CF1@dwi01.dwi.rwth-aachen.de> Organization: German Wool Research Institute MIME-version: 1.0 X-Mailer: Pegasus Mail for Windows (v3.01d) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Dear CCLers, does anyone know something about the Levinthal paradox? It deals with the fact that proteins do fold into unique states in seconds. Considering the number of all possible conformations it seems to be quite impossible to do the fold in such a short time. Until now I am unsuccessful in finding out the journal where Cyrus Levinthal first published something about this paradox. I would be very glad to get any advice. Thanks in advance. Regards, Jati ********************************************************************************** Jati Kastanja Phone:+49/241/4469138 German Woolresearch Center Fax:+49/241/4469100 at the University of Technology Aachen email:jkastanja@dwi.rwth-aachen.de Veltmanplatz 8, 52062 Aachen, Germany ********************************************************************************** From chemistry-request@server.ccl.net Fri Jul 30 12:45:45 1999 Received: from postoffice.npac.syr.edu (postoffice.npac.syr.edu [128.230.7.230]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA20861 for ; Fri, 30 Jul 1999 12:45:45 -0400 Received: from snake.npac.syr.edu (snake.npac.syr.edu [128.230.162.60]) by postoffice.npac.syr.edu (8.9.3/8.9.3) with ESMTP id MAA19002; Fri, 30 Jul 1999 12:40:21 -0400 (EDT) Received: from localhost (bernhold@localhost) by snake.npac.syr.edu (8.9.3/8.9.3) with SMTP id MAA04693; Fri, 30 Jul 1999 12:40:08 -0400 (EDT) Message-Id: <199907301640.MAA04693@snake.npac.syr.edu> X-Authentication-Warning: snake.npac.syr.edu: bernhold@localhost didn't use HELO protocol Reply-to: bernhold@npac.syr.edu To: Jochen Kuepper cc: Iraj Daizadeh , chemistry@ccl.net cc: bernhold@npac.syr.edu Subject: Re: CCL:Large matrix diagonalization. In-reply-to: Message from Jochen Kuepper of "Fri, 30 Jul 1999 09:29:56 +0200." <99073009311801.12040@bacchus.pc1.uni-duesseldorf.de> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-ID: <4689.933352804.1@snake.npac.syr.edu> Date: Fri, 30 Jul 1999 12:40:05 -0400 From: "David E. Bernholdt" The LAPACK library deals only with dense matrices, and is a de facto standard library for those operations on uniprocessors. Sparse linear algebra has a great deal of variation across fields and even across different applications, and is a lot less standardized at this point in time. Likewise, parallel dense linear algebra is also a lot less standardized, though that area seems to be consolidating of late. Mounting soapbox... My (humble?) opinion is that chemists (speaking broadly) aren't very smart about solving their linear algbra problems. I think it is getting better, along with the evolution of packages like LAPACK, but historically our track record is pretty poor. Chemists are all too willing to "roll their own" solutions to linear algebra problems, blithly ignoring the fact that there is an entire field of research that devotes itself to such problems. To the extent possible, we should be (well-informed) consumers of the high quality, often highly optimized mainstream linear algebra packages that one can easily obtain from NETLIB or other sites. To be sure, there will be problems that the standard linear algebra tools don't handle well for one reason or another. In that case, my recommendation is to make frieds with a good numerical analyst in the problem area. My experience is that they like new challenges -- it pushes their research & their field along just as chemical challenges do ours, andby virute of their training, they're likely to come up with a better solution than you can working in isolation. The more we chemists expose the numerical analysis community to our unique problems (relative to other fields), the more help we'll get from them, as chemically-derived problems become part of the standard test suites they use when testing new algorithms & libraries. Stepping off soapbox... -- 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 chemistry-request@server.ccl.net Fri Jul 30 14:00:40 1999 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA21394 for ; Fri, 30 Jul 1999 14:00:40 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.9.3/8.9.3) id NAA24321 for chemistry@ccl.net; Fri, 30 Jul 1999 13:55:23 -0400 (EDT) Date: Fri, 30 Jul 1999 13:55:23 -0400 (EDT) From: "E. Lewars" Message-Id: <199907301755.NAA24321@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: STATIC ELECTRON CORRELATION ENERGY 1999 July 30 DYNAMIC AND STATIC ELEC TRON CORRELATION ENERGY Correlation energy is sometimes divided into dynamic and static. Dynamic CE is the deviation from the exact energy caused by not allowing electrons to keep apart properly. It can be calculated ("recovered") by Moller-Plesset (e.g. MP2, MP4) or configuration interaction calculations. Static CE is the deviation from the exact energy caused by trying to represent a wavefunction by just one determinant when at least two are really needed, as with a singlet diradical. QUESTION: Is it true that a common and correct way to handle static CE is with multifererence configuration interaction (MRCI)? Thanks E. Lewars ===================== From chemistry-request@server.ccl.net Fri Jul 30 15:01:54 1999 Received: from ice.lanl.gov (ice.lanl.gov [128.165.22.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA21844 for ; Fri, 30 Jul 1999 15:01:53 -0400 Received: from localhost (localhost [[UNIX: localhost]]) by ice.lanl.gov (8.9.3/8.9.3) id MAA26653; Fri, 30 Jul 1999 12:48:42 -0600 From: Matt Challacombe Reply-To: MChalla@T12.LANL.Gov Organization: Group T-12, Theoretical Chemistry and Molecular Physics To: chemistry@ccl.net Subject: roll your own rant (was Large matrix diagonalization). Date: Fri, 30 Jul 1999 12:42:16 -0600 X-Mailer: KMail [version 1.0.24] Content-Type: text/plain References: <199907301640.MAA04693@snake.npac.syr.edu> Cc: jochen@uni-duesseldorf.de, daizadeh@nucleus.harvard.edu, bernhold@npac.syr.edu MIME-Version: 1.0 Message-Id: <9907301248420C.09427@ice.lanl.gov> Content-Transfer-Encoding: 8bit <> Much of computational chemistry is applied mathematics, and if the field is to move ahead at a reasonable pace, we should not shirk the responsiblilty of pushing the related fields of applied mathematics, computational physics, etc. ourselves. Excellent examples of this spirit is White and Head-Gordon's significant advancement of the Fast Multipole Method and Davidson's method. I've just about completed a parallel sparse atom-blocked linear algebra library for my linear scaling quantum chemistry code MondoSCF. This library allows sparse matrix manipulations with variable sized dense blocks. When I started, I looked carefully at all the available linear algebra software, and talked to many computer scientists and applied mathematicians. The upshot was that nothing like this existed. Moreover, it turns out that parallel methods for sparse matrix multiplies are (were) totally undeveloped! If I'd waited for a numerical analyst to help me, I'd still be waiting ... In my opinion, the CC community is already way to addicted to black box solutions and pre-fab science. To those who do roll their own, I salute you. <> +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ + Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ + + Los Alamos National Laboratory email: mchalla@t12.lanl.gov + + Theoretical Division vmail: (505) 698-4112 + + Group T-12, Mail Stop B268 phone: (505) 665-5905 + + Los Alamos, New Mexico 87545 fax: (505) 665-3909 + + + + "The secret to mountain biking is pretty simple. The slower you go + + the more likely it is you'll crash." -- Julie Furtado + +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ On Fri, 30 Jul 1999, you wrote: > The LAPACK library deals only with dense matrices, and is a de facto > standard library for those operations on uniprocessors. > > Sparse linear algebra has a great deal of variation across fields and > even across different applications, and is a lot less standardized at > this point in time. Likewise, parallel dense linear algebra is also a > lot less standardized, though that area seems to be consolidating of > late. > > Mounting soapbox... > > My (humble?) opinion is that chemists (speaking broadly) aren't very > smart about solving their linear algbra problems. I think it is > getting better, along with the evolution of packages like LAPACK, but > historically our track record is pretty poor. > > Chemists are all too willing to "roll their own" solutions to linear > algebra problems, blithly ignoring the fact that there is an entire > field of research that devotes itself to such problems. To the extent > possible, we should be (well-informed) consumers of the high quality, > often highly optimized mainstream linear algebra packages that one can > easily obtain from NETLIB or other sites. > > To be sure, there will be problems that the standard linear algebra > tools don't handle well for one reason or another. In that case, my > recommendation is to make frieds with a good numerical analyst in the > problem area. My experience is that they like new challenges -- it > pushes their research & their field along just as chemical challenges > do ours, andby virute of their training, they're likely to come up > with a better solution than you can working in isolation. The more we > chemists expose the numerical analysis community to our unique > problems (relative to other fields), the more help we'll get from > them, as chemically-derived problems become part of the standard test > suites they use when testing new algorithms & libraries. > > Stepping off soapbox... > -- > 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 > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- From chemistry-request@server.ccl.net Fri Jul 30 16:01:48 1999 Received: from pscuxc.psc.edu (pscuxc.psc.edu [128.182.73.178]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA22379 for ; Fri, 30 Jul 1999 16:01:48 -0400 Received: from localhost (wymore@localhost) by pscuxc.psc.edu (8.8.7/8.8.7/psc) with ESMTP id PAA18231 for ; Fri, 30 Jul 1999 15:56:31 -0400 (EDT) Date: Fri, 30 Jul 1999 15:56:31 -0400 (EDT) From: Troy Wymore To: chemistry@server.ccl.net Subject: MOPAC excited state energies Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer's I have started using MOPAC to calculate some excited state properties. The molecules are a bit too large to handle with CIS methods in Gaussian. Anyway, I am not sure how to interpret the output I get from the excited state output. It is: STATE ENERGIES EXPECTATION VALUE OF S**2 S FROM S**2=S(S+1) 1 -3.771809 SINGLET 0.00000 0.00000 2 -3.170890 TRIPLET 2.00000 1.00000 3 -2.796270 SINGLET 0.00000 0.00000 4 0.100754 SINGLET 0.00000 0.00000 How do I take this info and calculate the frequency of the transition from the ground state to the excited state? Any help would be much appreciated. Troy Wymore From chemistry-request@server.ccl.net Fri Jul 30 16:44:37 1999 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA22773 for ; Fri, 30 Jul 1999 16:44:35 -0400 Received: from sally.schrodinger.com (sally.schrodinger.com [206.231.140.227]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id NAA10257 for ; Fri, 30 Jul 1999 13:39:16 -0700 Received: from localhost (shenkin@localhost) by sally.schrodinger.com (8.8.5/8.8.5) with ESMTP id QAA11603 for ; Fri, 30 Jul 1999 16:35:46 -0400 X-Authentication-Warning: sally.schrodinger.com: shenkin owned process doing -bs Date: Fri, 30 Jul 1999 16:35:45 -0400 (EDT) From: Peter Shenkin To: chemistry@ccl.net Subject: Re: CCL:Levinthal's paradox In-Reply-To: <51C9FF0CF1@dwi01.dwi.rwth-aachen.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 30 Jul 1999, JATI KASTANJA wrote: > does anyone know something about the Levinthal paradox? ... > Until now I am unsuccessful in finding out the journal where Cyrus ... Hi, If you do find the Journal, you will find that it contains only a passing reference to what has become known as the Levinthal paradox. The idea really derives from a comment Cyrus once made at a meeting. The idea is this. Take a 100-residue protein. Let's suppose each residue can have only, say, 3 conformational states. Then there are 3^100, or about 10^48, possible states. Now suppose the protein can explore a new state with every moleculear vibration. Suppose each vibration takes about a femtosecond. Then exploring all the states would take about 10^48 fs, or 10^33 s. There are about 10^8 s in a year, so exploring all the states would take about 10^25 years. But this is longer than the age of the universe. Now, in order for a protein to fold into its global thermodynamic energy minimum, the folding process has to be ergodic. That is, it has to explore all its states within the time-span of the process. But protein folding takes typically seconds to minutes. So a protein can't be folding into its thermodynamic energetic minimum, since it can't possibly find it in so short a time. Therefore, protein folding must be a kinetically controlled process. I.e., proteins fold to the most accessible minimum, rather than the most stable minimum. In this, protein folding must resemble the kinetically controlled reactions of organic (and bio-) chemistry. The reason it's considered a "paradox" is that most people don't believe it (at least for globular proteins as small as 100 residues). Cyrus didn't believe it either, in fact. But it is fun to think about, and it's great for impressing people at cocktail parties. (You have to go to the right cocktail parties, though. :-) ) -P. -- ********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** From chemistry-request@server.ccl.net Fri Jul 30 17:33:40 1999 Received: from bragg.bio.uci.edu (bragg.bio.uci.edu [128.195.151.87]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA23273 for ; Fri, 30 Jul 1999 17:33:40 -0400 Received: from hemebase.bio.uci.edu (hemebase.bio.uci.edu [128.195.151.52]) by bragg.bio.uci.edu (8.8.8/) with ESMTP id OAA01573 for ; Fri, 30 Jul 1999 14:28:22 -0700 (PDT) From: CS Raman Received: (from raman@localhost) by hemebase.bio.uci.edu (8.8.8/) id VAA13671 for chemistry@ccl.net; Fri, 30 Jul 1999 21:28:22 GMT Message-Id: <199907302128.VAA13671@hemebase.bio.uci.edu> Subject: Re: Levinthal's paradox To: chemistry@ccl.net Date: Fri, 30 Jul 1999 14:28:21 -0700 (PDT) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Jati: {*} does anyone know something about the Levinthal paradox? Well, the list I have provided at the end of this mail should help you track down all the literature pertinent to this problem. {*} Until now I am unsuccessful in finding out the journal where Cyrus {*} Levinthal first published something about this paradox. Cy's article is one of the most MISQUOTED in the literature. His original work was presented in a symposium: Levinthal, C (1969) in Mossbauer Spectroscopy in Biological Systems, (ed) Debrunner, P., & Tsibris, J.C.M., P. 22-24, University of Illinois, Urbana Champaign. How to Fold Graciously. Levinthal also published an article in J. Chim. Phys. (1968) 65: 44-45 entitled "Are there pathways for protein folding?", which is usually quoted as being the source of the paradox. This is incorrect and this article makes no mention of it. 1. Dill KA. Polymer principles and protein folding. Protein Science, 1999 Jun, 8(6):1166-80. 2. Yon JM. Protein folding: concepts and perspectives. Cellular and Molecular Life Sciences, 1997 Jul, 53(7):557-67. 3. Finkelstein, AV; Badretdinov, AY. Physical reason for fast folding of the stable spatial structure of proteins: A solution of the Levinthal paradox. MOLECULAR BIOLOGY, 1997 MAY-JUN, V31 N3:391-398. 4. Shakhnovich EI. Theoretical studies of protein-folding thermodynamics and kinetics. Current Opinion in Structural Biology, 1997 Feb, 7(1):29-40. 5. Dill KA; Chan HS. >From Levinthal to pathways to funnels. Nature Structural Biology, 1997 Jan, 4(1):10-9. 8. Finkelstein AV; Badretdinov AYa. Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold [published erratum appears in Fold Des 1998;3(1):67]. Folding and Design, 1997, 2(2):115-21. 9. Lattman EE. Remembering Cy Levinthal [editorial]. Proteins, 1995 Oct, 23(2):i. 10. Karplus M; Sali A. Theoretical studies of protein folding and unfolding. Current Opinion in Structural Biology, 1995 Feb, 5(1):58-73. 11. Durup, J. On ''Levinthal paradox'' and the theory of protein folding. THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE, 1998 FEB 9, V424 N1-2:157-169. 12. Karplus, M. The Levinthal paradox: yesterday and today. FOLDING & DESIGN, 1997, V2 N4:S69-S75. 13. HONIG B. LEVINTHAL,CYRUS - IN MEMORIAM. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1991, V11 N4:239-241. 14. LATTMAN E. LEVINTHAL,CYRUS MAY 2, 1922 NOVEMBER 4, 1990 - IN MEMORIAM. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1990, V8 N4:R1-R1. I hope this helps. -raman ___________________________________________________________________ C.S.Raman, PhD Tel: (949) 824-1797 University of California Fax: (949) 824-3280 Dept. Molecular Biology & Biochemistry email: craman@uci.edu 3205 Bio Sci II, SH 530 Irvine, CA 92697-3900 ------------------------------------------------------------------- The right to search for truth implies also a duty; one must not conceal any part of what one has recognized to be true. --Albert Einstein ___________________________________________________________________ From chemistry-request@server.ccl.net Fri Jul 30 17:52:32 1999 Received: from mailhost.det.ameritech.net (mpdr0.detroit.mi.ameritech.net [206.141.239.206]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA23420 for ; Fri, 30 Jul 1999 17:52:32 -0400 Received: from kressj.www.ameritech.net ([199.179.190.96]) by mailhost.det.ameritech.net (InterMail v4.01.01.00 201-229-111) with SMTP id <19990730214516.RBIU16694.mailhost.det.ameritech.net@kressj.www.ameritech.net>; Fri, 30 Jul 1999 17:45:16 -0400 Message-ID: <003701bedad4$ce6fade0$60beb3c7@www.ameritech.net> Reply-To: "Jim Kress" From: "Jim Kress" To: "Peter Shenkin" , References: Subject: Re: CCL:Levinthal's paradox Date: Fri, 30 Jul 1999 17:45:13 -0400 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-Mimeole: Produced By Microsoft MimeOLE V5.00.2314.1300 In highly nonlinear systems sudden transitions in states (from one to another) are a well known behavior. Could it be that the 'paradox' is just the result of a simple state change in a protein driven by the highly nonlinear forces that control its configuration? Jim Check out my web site http://www.kressworks.com/ It'll blow your mind (politically), stimulate your senses (artistically) and provide scientific insights that boggle the mind! ----- Original Message ----- From: Peter Shenkin To: Sent: Friday, July 30, 1999 4:35 PM Subject: CCL:Levinthal's paradox > On Fri, 30 Jul 1999, JATI KASTANJA wrote: > > does anyone know something about the Levinthal paradox? > >... > > Until now I am unsuccessful in finding out the journal where Cyrus ... > > Hi, > > If you do find the Journal, you will find that it contains only > a passing reference to what has become known as the Levinthal > paradox. The idea really derives from a comment Cyrus once made at a > meeting. > > The idea is this. Take a 100-residue protein. Let's suppose each > residue can have only, say, 3 conformational states. Then there > are 3^100, or about 10^48, possible states. Now suppose the protein > can explore a new state with every moleculear vibration. Suppose > each vibration takes about a femtosecond. Then exploring all > the states would take about 10^48 fs, or 10^33 s. There are about 10^8 s > in a year, so exploring all the states would take about 10^25 years. > But this is longer than the age of the universe. > > Now, in order for a protein to fold into its global > thermodynamic energy minimum, the folding process has to > be ergodic. That is, it has to explore all its states > within the time-span of the process. But protein folding takes > typically seconds to minutes. So a protein can't be folding > into its thermodynamic energetic minimum, since it can't > possibly find it in so short a time. > > Therefore, protein folding must be a kinetically controlled process. > I.e., proteins fold to the most accessible minimum, rather than the > most stable minimum. In this, protein folding must resemble the > kinetically controlled reactions of organic (and bio-) chemistry. > > The reason it's considered a "paradox" is that most people > don't believe it (at least for globular proteins as small > as 100 residues). Cyrus didn't believe it either, in fact. > But it is fun to think about, and it's great for impressing > people at cocktail parties. (You have to go to the right cocktail > parties, though. :-) ) > > -P. > > -- > ********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* > *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Fri Jul 30 21:06:17 1999 Received: from mailbox.engr.sc.edu (mailbox.engr.sc.edu [129.252.22.203]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA24598 for ; Fri, 30 Jul 1999 21:06:16 -0400 Received: from engr.sc.edu (ch-0304.engr.sc.edu [129.252.27.249]) by mailbox.engr.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2448.0) id 3RMGQ186; Fri, 30 Jul 1999 20:59:19 -0400 Message-ID: <37A24AD7.E9498A89@engr.sc.edu> Date: Fri, 30 Jul 1999 21:01:11 -0400 From: Pedro Derosa X-Mailer: Mozilla 4.04 [en] (WinNT; I) MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Microway Alpha Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I would like to know if there is someone that has run Gaussian 94 in a Microway Alpha system under Digital UNIX. I will appreciate any comments about the preformance and also about any problem you have experienced with this combination. Plase send the answer directed to me, I will summarize if there is any interest. Thank you very much Pedro Derosa -- ******************************** Dr. Pedro A. DEROSA Dept of Chemical Engineering University of South Carolina Off 2A01H Ph. (1-803) 777-0611 FAX (1-803) 777-8265 e-mail: derosa@engr.sc.edu ********************************