From jsl@virgil.ruc.dk Wed Jun 18 04:49:44 1997 Received: from emma.ruc.dk for jsl@virgil.ruc.dk by www.ccl.net (8.8.3/950822.1) id EAA23768; Wed, 18 Jun 1997 04:11:06 -0400 (EDT) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by emma.ruc.dk (8.8.5/8.8.5) with ESMTP id KAA08227; Wed, 18 Jun 1997 10:16:41 +0200 (MET DST) Received: from VIRGIL/MAILQUEUE by virgil.ruc.dk (Mercury 1.21); 18 Jun 97 10:09:53 +0100 Received: from MAILQUEUE by VIRGIL (Mercury 1.21); 18 Jun 97 10:09:50 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry@www.ccl.net, nauss@beryllium.crs.uc.edu Date: Wed, 18 Jun 1997 10:09:49 +0100 Subject: Re: CCL:semantics: molecular modelling Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <256FB925A95@virgil.ruc.dk> CCL: Just one remark. On Tue, 17 Jun 1997, Jeffrey L. Nauss stated - > I have resolved the issue in my own mind as follows. Computational > chemistry would be the application of numerical calculations to the > study of molecular structure. But this is too limited a definition. Chemistry is much more than the study of molecular structure! What with the structure of solids and liquids, and the whole branches of chemical thermodynamics and reaction kinetics? Sure, much can be learned by a study of molecular structure, but this is only part of the story. Computational chemistry might be defined as the application of numerical calculations in the study of chemical problems. Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Department of Chemistry Phone: +45 46757781 + 2710 Roskilde University (RUC) Fax: +45 46757721 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://frederik.ruc.dk/dis/chem/psos =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From kneth@chem.ruc.dk Wed Jun 18 07:49:52 1997 Received: from koala.ruc.dk for kneth@chem.ruc.dk by www.ccl.net (8.8.3/950822.1) id HAA24413; Wed, 18 Jun 1997 07:23:05 -0400 (EDT) Received: from localhost (kneth@localhost) by koala.ruc.dk (8.8.5/8.8.5) with SMTP id NAA01057 for ; Wed, 18 Jun 1997 13:22:55 +0200 Date: Wed, 18 Jun 1997 13:22:55 +0200 (CEST) From: Kenneth Geisshirt X-Sender: kneth@koala.ruc.dk To: chemistry@www.ccl.net Subject: Re: CCL:semantics: molecular modelling In-Reply-To: <256FB925A95@virgil.ruc.dk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 18 Jun 1997, Jens Spanget-Larsen wrote: > Just one remark. On Tue, 17 Jun 1997, Jeffrey L. Nauss stated - > > > I have resolved the issue in my own mind as follows. Computational > > chemistry would be the application of numerical calculations to the > > study of molecular structure. > > But this is too limited a definition. > Computational chemistry might be defined as the application of > numerical calculations in the study of chemical problems. Jens, your definition of computational chemistry is also too limited. I regard the use of artificial intelligence in chemistry as computational chemistry as well. A more appropriate definition could be: Computational chemistry is the application of any computational method in chemistry. Computational method is understood to be any algorithm implemented on a computer. Best wishes Kenneth +-------------------------------------------------------------+ | Kenneth Geisshirt Ph.D.-student | | Dept. of Life Sciences and Chemistry Roskilde University | +-------------------------------------------------------------+ | E-mail: kneth@chem.ruc.dk Phone: +45 4675 7711, ext 2785 | +-------------------------------------------------------------+ From news@franck.pc.Uni-Koeln.DE Wed Jun 18 08:49:44 1997 Received: from franck.pc.Uni-Koeln.DE for news@franck.pc.Uni-Koeln.DE by www.ccl.net (8.8.3/950822.1) id HAA24526; Wed, 18 Jun 1997 07:52:02 -0400 (EDT) Received: (from news@localhost) by franck.pc.Uni-Koeln.DE (8.8.5/8.8.5) id NAA01826 for CHEMISTRY@www.ccl.net; Wed, 18 Jun 1997 13:51:58 +0200 To: CHEMISTRY@www.ccl.net From: Rupert Rebentisch Newsgroups: local.CCL Subject: Re: iso MATRIX MANIPULATION libs Date: 18 Jun 1997 13:51:49 +0200 Organization: Physikalische Chemie Universitaet Koeln Lines: 27 Message-ID: References: <9706112042.AA16376@chasma.harvard.edu> NNTP-Posting-Host: hilbert.pc.uni-koeln.de Mime-Version: 1.0 (generated by tm-edit 7.105) Content-Type: text/plain; charset=US-ASCII X-Newsreader: Gnus v5.2.25/XEmacs 19.14 Xref: franck.pc.Uni-Koeln.DE local.CCL:123 berriz@chasma.harvard.edu (Gabriel Berriz) writes: > I'm writing some C code that must perform many multiplications of > small, non-square matrices of various shapes and sizes. Can anyone > recommend a good, convenient, freely available matrix manipulation C > library? Try www.nist.gov you will find a "decision tree" there, to find out which routines from which libraries might help you. Try blas1, blas2, blas3 may be lapack. You should be able to find these packages on elib. www.zib-berlin.de is the german mirror, but the original server is in the states. Most routines come in different forms: fortran, C, C++ and different kinds: double precision, real, complex. cu RR -- ---------------------------------------------------------------------- | Rupert Rebentisch | R.Rebentisch@uni-koeln.de | | Institut fuer Physikalische Chemie | fax: 0049-(0)221-470-5144 | | Lehrstuhl Prof. Dr. G. Hohlneicher | tel: 0049-(0)221-470-4816 | | Universitaet zu Koeln | www.rrz.uni-koeln.de/~acp50 | ---------------------------------------------------------------------- From nauss@beryllium.crs.uc.edu Wed Jun 18 09:49:44 1997 Received: from beryllium.crs.uc.edu for nauss@beryllium.crs.uc.edu by www.ccl.net (8.8.3/950822.1) id JAA24827; Wed, 18 Jun 1997 09:09:47 -0400 (EDT) Received: (from nauss@localhost) by beryllium.crs.uc.edu (8.8.5/8.8.5) id JAA17218 for chemistry@www.ccl.net; Wed, 18 Jun 1997 09:09:49 -0400 (EDT) From: nauss@beryllium.crs.uc.edu (Jeffrey L. Nauss) Message-Id: <9706180909.ZM17216@beryllium.crs.uc.edu> Date: Wed, 18 Jun 1997 09:09:48 -0400 In-Reply-To: Kenneth Geisshirt "CCL:semantics: molecular modelling" (Jun 18, 1:22pm) References: Organization: Dept. Chemistry, University of Cincinnati Reply-to: Jeffrey.Nauss@UC.Edu X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Re: CCL:semantics: molecular modelling Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Jun 18, 1:22pm, Kenneth Geisshirt wrote: > On Wed, 18 Jun 1997, Jens Spanget-Larsen wrote: > > Just one remark. On Tue, 17 Jun 1997, Jeffrey L. Nauss stated - > > > > > I have resolved the issue in my own mind as follows. Computational > > > chemistry would be the application of numerical calculations to the > > > study of molecular structure. > > > > But this is too limited a definition. > > > Computational chemistry might be defined as the application of > > numerical calculations in the study of chemical problems. > > Jens, your definition of computational chemistry is also too limited. Kenneth, I see your limited definition and raise you another. :-) > Computational chemistry is the application of any computational method > in chemistry. Computational method is understood to be any algorithm > implemented on a computer. Why does it have to be limited to "any algorithm implemented on a computer?" Valid computations can be done on a napkin with a pencil. Granted the computer allows more sophisticated calculations but they are nevertheless calculations. It seems from this discussion that some folks feel computational chemistry and molecular modeling are separate sets but that have an intersecting or overlapping region. Does anyone disagree with that? -- Jeffrey L. Nauss, PhD Telephone: 513-556-0148 Dir. Molec. Model. Serv. Fax: 513-556-9239 Department of Chemistry e-mail: Jeffrey.Nauss@UC.Edu University of Cincinnati URL http://www.che.uc.edu/~nauss From topper@cooper.edu Wed Jun 18 10:49:45 1997 Received: from magnum.cooper.edu for topper@cooper.edu by www.ccl.net (8.8.3/950822.1) id KAA00045; Wed, 18 Jun 1997 10:31:31 -0400 (EDT) Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA10318 (5.65c/IDA-1.4.4 for ); Wed, 18 Jun 1997 10:28:09 -0400 Received: by zeus.cooper.edu id AA07778 (5.67b/IDA-1.5 for CHEMISTRY@www.ccl.net); Wed, 18 Jun 1997 10:27:26 -0400 From: TOPPER ROBERT Message-Id: <199706181427.AA07778@zeus.cooper.edu> Subject: CCL:semantics: molecular modelling To: CHEMISTRY@www.ccl.net Date: Wed, 18 Jun 1997 10:27:26 -0400 (EDT) Cc: topper@cooper.edu (TOPPER ROBERT) X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi, I like Kenneth's definition but would like to expand on it a little; > Computational chemistry is the application of any computational method > in chemistry. Computational method is understood to be any algorithm > implemented on a computer. > I personally like to prefer to the use of computers to predict things by using atomistic descriptions as "computational molecular modeling (CMM)." This is a subdiscipline of computational chemistry and includes ab initio, molecular mechanics, MD, Monte Carlo, stochastic dynamics and any application of computational methods which involves an attempt to describe a system in terms of its atomic/molecular properties. It is also a particular kind of "molecular modeling." The traditional (but also effective in their own right) kind of molecular modeling might be coined "sculptural molecular modeling" (like Pauling and Watson / Crick). However, I'm not as set on this as I am on CMM. best to all, robert ******************************************************************************** Prof. Robert Q. Topper, Chemistry email: topper@cooper.edu The Cooper Union phone: (212) 353-4378 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 USA or the N/R to 8th St/NYU http://www.cooper.edu/engineering/chemechem/depts_info/topper.html Molecular Monte Carlo = http://www.cooper.edu/engineering/chemechem/monte.html ******************************************************************************** The Cooper Union, established by Peter Cooper in 1859, is a private engineering/ architecture/art college where all students receive full scholarships. ******************************************************************************** From smb@smb.chem.niu.edu Wed Jun 18 11:50:00 1997 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.8.3/950822.1) id LAA00625; Wed, 18 Jun 1997 11:28:39 -0400 (EDT) Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA19619 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:chemistry@www.ccl.net>); Wed, 18 Jun 1997 10:28:39 -0500 Received: from cz.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:chemistry@www.ccl.net) id AA03926; Wed, 18 Jun 97 10:22:27 -0500 Received: from smb.chem.niu.edu by cz.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:chemistry@www.ccl.net) id AA15047; Wed, 18 Jun 97 10:28:55 -0500 Received: from smb by smb.chem.niu.edu via SMTP (940816.SGI.8.6.9/940406.SGI) for id KAA13031; Wed, 18 Jun 1997 10:24:49 -0500 Sender: smb@smb.chem.niu.edu Message-Id: <33A7FDC0.41C6@smb.chem.niu.edu> Date: Wed, 18 Jun 1997 10:24:48 -0500 From: Steven Bachrach X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP12) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: ECCC-4 Preannouncement Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The Fourth Electronic Computational Chemistry Conference (ECCC-4) will be held on the Internet in November 1997. This is just a pre-announcement so that you can mark your calendars. Final deadlines have not yet been set, but abstracts will be due sometime in late September, with final versions of the articles due in late October. ECCC-4 will feature enhancements on last year's interface along with a new customizable interface to the articles. As always, ECCC-4 will have no registration fee and will be open to all who have www connections. More information and details will follow in mid-July. Steve -- Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From wtwinter@syr.edu Wed Jun 18 11:52:46 1997 Received: from mailbox.syr.edu for wtwinter@syr.edu by www.ccl.net (8.8.3/950822.1) id LAA00513; Wed, 18 Jun 1997 11:18:28 -0400 (EDT) Received: from xanthan.esf.edu (xanthan.esf.edu [149.119.4.13]) by mailbox.syr.edu (8.8.5/8.8.5) with ESMTP id LAA02243; Wed, 18 Jun 1997 11:18:01 -0400 (EDT) Message-ID: <33A7FC09.5365D36D@syr.edu> Date: Wed, 18 Jun 1997 11:17:29 -0400 From: "William T. Winter" Reply-To: wtwinter@syr.edu Organization: SUNY ESF X-Mailer: Mozilla 4.0b5 [en] (Win95; I) MIME-Version: 1.0 To: Jens Spanget-Larsen CC: chemistry@www.ccl.net, nauss@beryllium.crs.uc.edu Subject: Re: CCL:semantics: molecular modelling X-Priority: 3 (Normal) References: <256FB925A95@virgil.ruc.dk> Content-Type: text/plain; charset=iso-8859-1 Just one remark. On Tue, 17 Jun 1997, Jeffrey L. Nauss stated - > > I have resolved the issue in my own mind as follows. Computational > > chemistry would be the application of numerical calculations to the > > study of molecular structure. I do not usually get involved in these kinds of discussions but I must disagree with this definition which really refers to one aspect of computational chemistry, i.e. molecular modeling. In my mind, computational chemistry encompasses all aspects of applying computers to chemical problems. This certainly includes the prediction of molecular structure, but it also includes crystal structures, interactions of molecules, surface chemistry simulations, and other structural problems. It should include both "pure" calculations and those more clearly restrained by experiment- diffraction or spectroscopic data in particular. In addition to purely structural chemistry, computational chemistry includes, in my mind, those areas where computers are used to predict experimental data - spectroscopic simulations, etc. The design of synthetic pathways by computer, certain aspects of kinetics, and even the development of chemical/ chemistry databases can have computational chemistry aspects. I guess i have never outgrown my appreciation for the definition, which can be traced back at least to Gibbs, of physical chemistry as the study of everything which is interesting. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Prof. William T. Winter email:wtwinter@syr.edu SUNY-ESF FAX:315-470-6856 315 Baker Laboratory Phone: 315-470-6853 Syracuse, NY 13210 From lutz@ri.ac.uk Wed Jun 18 11:55:35 1997 Received: from mail-d.bcc.ac.uk for lutz@ri.ac.uk by www.ccl.net (8.8.3/950822.1) id LAA00443; Wed, 18 Jun 1997 11:05:20 -0400 (EDT) Received: from ri.ac.uk (actually davy.ri.ac.uk) by mail-d.bcc.ac.uk with SMTP (PP); Wed, 18 Jun 1997 15:56:21 +0100 Received: from faraday.ri.ac.uk by ri.ac.uk (5.x/SMI-SVR4) id AA00838; Wed, 18 Jun 1997 15:56:18 +0100 From: lutz@ri.ac.uk (Dr Lutz Ackermann) Received: by faraday.ri.ac.uk (950413.SGI.8.6.12) id PAA25505; Wed, 18 Jun 1997 15:56:17 +0100 Date: Wed, 18 Jun 1997 15:56:17 +0100 Message-Id: <199706181456.PAA25505@faraday.ri.ac.uk> To: CHEMISTRY@www.ccl.net Subject: CCL:Re:semantics : molecular modelling Jeffrey L. Nauss wrote: > Molecular modelling would be the application of some form of a model to > studying molecular structure. I agree with Jeffrey that although the term MM is normally used to indicate a certain type of method (i.e. empirical methods etc). one could well use it in a wider sense, comprising almost anything that has to do with the theory of molecules. If one follows this thought a bit further, it seems, however, that "MM" becomes a doubling of terms and that expressions like > Watson and Crick constructed a model of a molecule ... are tautological, because "molecule" itself, in the framework of the theory of matter, is a model (so what's a 'model of model'?) Jeffrey also mentions > hand-held CPK models and simple drawings on paper For the reason just given it would then be semanically corret to say "this molecule ..." while pointing at a picture on a computer screen (well, one could introduce another category, the "representation" of a model/molecule to refere to the actual drawing, input file etc). Of course 'model of a molecule' could refere to 'a simplified version of a molecular model', where the simplification could either be of chemical nature (e.g. replace CH3 by H group) or could point to the principal fact that different models describe physical reality with a variing degree of crudeness (or approximation) and no model covers all aspects of a theory. For example: if A' is a molecular model that includes vibrational aspects, and A" is a rigid version of A', one could say, that (1) A" is a model of the molecule A'. ----- -------- I do, however prefere to say: (2) both A' and A" are (different) models of the same physical reality ------ But what, then, is THE MOLECULE? Well take all the models A', A", A''' etc. i.e. all that is known about a compound and call it A. So A would be a model that includes every known fact about a given substance. Therefore A is the molecule. Maybe these semantic differences could be depicted in a little plot: physical reality | | | --------------------- | -------------------- | ------- | ------- V V V Theory A' A' A" | or V A" --------------------------------------------------------------------- representation: a drawing, a set of coordinates ... (1) (2) Very well so far, but where does A go? I think the semantic problem arises, because some people (mostly subconcsiously) introduce another 'layer' between theory and reality to accomodate A, THE MOLECULE. Some would even forget about the fact, that molecules are models of reality and place A in the upper section of the diagram above. The reason for this probably being, that "molecule" is a very succesfull and extremely usefull concept to which we have got used very much. Ok, that's been it, folks. I am afraid, I didn't have much time to explain these philosophical aspects in to much detail, but you shold be able to get the gist of what I am trying to say. Comments? <^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^> < Dr. Lutz Ackermann > < Research Assistent > < The Royal Institution of Great Britain > < Davy-Faraday Research Laboratory > < 21 Albemarle Street > < London W1X 4BS > < UK > < > < phone: +44-171-409 2992 ext 424 > < FAX: +44-171-629 3569 > < e-mail: lutz@ri.ac.uk > < http://www.ri.ac.uk/DFRL/L.Ackermann > vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv From yschickel@beilstein.com Mon Jun 9 02:47:47 1997 Received: from mail.beilstein.com for yschickel@beilstein.com by www.ccl.net (8.8.3/950822.1) id BAA28238; Mon, 9 Jun 1997 01:55:18 -0400 (EDT) Received: by mail.beilstein.com from localhost (router,SLMAILNT V2.2); Sun, 08 Jun 1997 23:58:53 Mountain Daylight Time Received: by mail.beilstein.com from pc-ysk.beilstein.de (194.152.36.150::mail daemon; unverified,SLMAILNT V2.2); Sun, 08 Jun 1997 23:58:52 Mountain Daylight Time Message-Id: <3.0.32.19970609075443.0069b320@mail.beilstein.com> X-Sender: "yschickel" X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Mon, 09 Jun 1997 07:55:06 +0200 To: chemistry@www.ccl.net From: "Yvonne Schickel" Subject: Beilstein Information Announces CrossFire for Microsoft Excel Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable PRESS RELEASE (09 June, 1997) Beilstein Informationssysteme GmbH Yvonne Schickel (phone: +49-69-7917 410; internet: yschickel@beilstein.com) Beilstein Information Systems Inc. Kirk Hanes (phone: +1-303-397 2296; internet: khanes@beilstein.com) Beilstein Informationsysteme Announces CrossFire for Microsoft Excel=99 Frankfurt, Germany =97 Today, at the opening of the Achema conference, Beilstein Informationssysteme GmbH announced the commercial availability of CrossFire for Excel, the new client application for the CrossFire System. For further information, please consult our Web Site at http://www.beilstein.com. ********************************************** Yvonne Schickel Beilstein Informationssysteme GmbH http://www.beilstein.com ********************************************** From gostowskir@apsu01.apsu.edu Wed Jun 18 12:49:47 1997 Received: from apsu02.apsu.edu for gostowskir@apsu01.apsu.edu by www.ccl.net (8.8.3/950822.1) id MAA01283; Wed, 18 Jun 1997 12:33:52 -0400 (EDT) Received: from gostowskir.apsu.edu by APSU02.APSU.EDU (PMDF V5.1-4 #16785) with ESMTP id <01IK7SXISEPS00039B@APSU02.APSU.EDU> for chemistry@www.ccl.net; Wed, 18 Jun 1997 11:32:32 CST Date: Wed, 18 Jun 1997 11:33:50 -0500 From: Rudy Gostowski Subject: spin contamination To: CCL group Message-id: <01IK7SXITAV600039B@APSU02.APSU.EDU> MIME-version: 1.0 X-Mailer: Microsoft Internet Mail 4.70.1155 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal Would someone please expand on the concept of spin contamination as applies to AM1/PM3 modeling of free radicals. thanks, Rudy Gostowski Department of Chemistry Austin Peay State University Box 4547 Clarksville, TN 37044 615-648-7624 FAX 615-648-5996 From peter@cherwell.com Mon Jun 9 12:47:51 1997 Received: from cherwell.com for peter@cherwell.com by www.ccl.net (8.8.3/950822.1) id MAA01043; Mon, 9 Jun 1997 12:16:38 -0400 (EDT) Received: from mersey.cherwell.com by cherwell.com (4.1/SMI-4.1) id AA08174; Mon, 9 Jun 97 17:16:56 BST Message-Id: <3.0.1.32.19970609171638.007da4a0@cherwell.com> X-Sender: peter@cherwell.com X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Mon, 09 Jun 1997 17:16:38 +0100 To: charwel@chrs1.chem.lsu.edu From: Peter Tebbutt Subject: animation Cc: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Chris & CCLers, Animation is one of the features of ChemSymphony (URL below) which is a publishing tool for including structures in HTML documents. This essentially works by creating a series of frames which are rendered in series. It recognises most file formats (XYZ, XMOL, PDB and so on) and allows the net user to change orientation and manipulate the structure whilst the animation is going on. A free demo is available from the Cherwell web site. Peter Tebbutt ----------------------------------------------------------- Peter Tebbutt | e-mail: peter@cherwell.com Development Support | Tel: +44 (0)1865 784812 Cherwell Scientific Publishing| Fax: +44(0)1865 784801 Oxford OX4 4GA, UK | http://www.cherwell.com ----------------------------------------------------------- Check Out ChemSymphony - rated top 1% Java applet by JARS http://www.cherwell.com/chemsymphony ----------------------------------------------------------- From Gerald.Loeffler@univie.ac.at Thu Jun 12 07:04:38 1997 Received: from mailbox.univie.ac.at for Gerald.Loeffler@univie.ac.at by www.ccl.net (8.8.3/950822.1) id GAA20171; Thu, 12 Jun 1997 06:36:56 -0400 (EDT) Received: from gerilap.imp.univie.ac.at (gerilap.imp.univie.ac.at [131.130.80.125]) by mailbox.univie.ac.at (8.8.4/8.8.4) with SMTP id MAA11650 for ; Thu, 12 Jun 1997 12:36:55 +0200 Message-ID: <339FD0DC.4043@univie.ac.at> Date: Thu, 12 Jun 1997 12:35:08 +0200 From: Gerald Loeffler Reply-To: Gerald.Loeffler@univie.ac.at Organization: I.M.P. X-Mailer: Mozilla 3.01 (Win95; I) MIME-Version: 1.0 To: Computational Chemistry List Subject: Removing Translation and Rotation after MD Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greetings! I would very much appreciate your comments to the following problem: I need to remove the translational and rotational motion of a protein after a Molecular Dynamics simulation. I know, this is a seemingly trivial problem. A) Up to now I didn't care much about the details and just fitted all protein structures along the MD trajectory to the start structure such that the C-alpha atoms are optimally (i.e., minimal root-mean-square deviation) superimposed (e.g. using the excellent profit program). B) However, it may be that for my current problem the other alternative that came to my mind would be better suited, namely 1) removing translation by superimposing the centers of gravity of all structures and subsequently 2) removing rotation by superimposing the "principal axes of inertia" of all structures. Firstly, I'm not sure if the terminology of B)2) is correct. Secondly, I'm missing the formulas to do B)1) and B)2). Thridly, I'd like to know if there are cases where either method A) or method B) are definitely prefered. Fourthly, it may be that there are other methods of removing translation and rotation?! Fifthly, which free program implements method B) or other intersting methods? As always, I thank you very much in advance for your help, and I will summarize to the list if there is some interest in that. Cheers, gerald -- Gerald Loeffler PostDoc in Theoretical Biochemistry EMail: Gerald.Loeffler@univie.ac.at Phone: +43 1 79730 554 Fax: +43 1 7987153 SMail: I.M.P. - Research Institute of Molecular Pathology Dr. Bohr-Gasse 7 A-1030 Vienna AUSTRIA From ccl@www.ccl.net Thu Jun 12 10:48:28 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA21524; Thu, 12 Jun 1997 10:35:30 -0400 (EDT) Received: from theory.tc.cornell.edu for richard@tc.cornell.edu by bedrock.ccl.net (8.8.3/950822.1) id KAA02080; Thu, 12 Jun 1997 10:35:31 -0400 (EDT) Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.244.22]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id KAA38881 for ; Thu, 12 Jun 1997 10:35:31 -0400 Sender: richard@TC.Cornell.EDU Message-ID: <33A00933.5E65@tc.cornell.edu> Date: Thu, 12 Jun 1997 10:35:31 -0400 From: Richard Gillilan X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL:more on animation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Since there has been recent interest in animation, I thought I'd throw in my 2c. We do quite a lot of general scientific animation here at the Cornell Theory Center. Our main tool is IBM Visualization Data Explorer (DX). I've written a few molecular graphics modules which create most of the constructs I need for biomolecular systems. Because DX is so general, it's not as easy to work with as a dedicated application program like VMD. Generality can be an advantage when you need to do unusual things like have a point moving on a colored potential energy surface while a corresponding molecular model changes its conformation. A video Paul Bash and I are about to finish has a ball-and-stick model, ribbon, electron density surfaces and a point on P.E. curve all moving while a photon excites the works to a higher state. DX, AVS and similar packages are good for this kind of thing. We use RenderMan to do high-quality rendering and special effects when needed. Anyone who already has DX can download these modules (no cost). http://www.tc.cornell.edu/Visualization/Staff/richard/CM/CM.html Art Olson's group at Scripps may also have some tools like this for AVS http://www.scripps.edu/pub/olson-web/ Also, I should mention VPLA, the Visual Programming Language for Animation. This was written by Wayne Lytle, a former staff member here and is also available at no cost: http://www.tc.cornell.edu/Visualization/Software/VPLA/ It is a VERY nice alternative to SoftImage, Alias and other unaffordable professional animation programs. I use it whenever I need nice choreography and special effects in a scene: like swimming bacteria with bumps and moving cilia and flagella or fly-though scenes with fancy camera angles and special lighting (like underwater). Richard Gillilan Cornell Theory Center http://www.tc.cornell.edu/~richard/ From ccl@www.ccl.net Thu Jun 12 14:48:29 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id OAA23605; Thu, 12 Jun 1997 14:46:36 -0400 (EDT) Received: from po6.andrew.cmu.edu for hpaik+@andrew.cmu.edu by bedrock.ccl.net (8.8.3/950822.1) id OAA09221; Thu, 12 Jun 1997 14:46:35 -0400 (EDT) Received: (from postman@localhost) by po6.andrew.cmu.edu (8.8.2/8.8.2) id OAA04441 for CHEMISTRY@ccl.net; Thu, 12 Jun 1997 14:46:31 -0400 Received: via switchmail; Thu, 12 Jun 1997 14:46:29 -0400 (EDT) Received: from pcs35.andrew.cmu.edu via qmail ID ; Thu, 12 Jun 1997 14:45:50 -0400 (EDT) Received: from pcs35.andrew.cmu.edu via qmail ID ; Thu, 12 Jun 1997 14:45:49 -0400 (EDT) Received: from mms.4.170.Jun.27.1996.16.34.50.sun4.51.MacMail.5.2.CUILIB.3.45.SNAP.NOT.LINKED.pcs35.andrew.cmu.edu.sun4m.54 via MS.5.6.pcs35.andrew.cmu.edu.sun4_51; Thu, 12 Jun 1997 14:45:49 -0400 (EDT) Message-ID: <4nc4DRW00iWU058l40@andrew.cmu.edu> Date: Thu, 12 Jun 1997 14:45:49 -0400 (EDT) From: Hyun-Jong Paik To: CHEMISTRY@ccl.net Subject: Thermal Radical Initiator Hi, I need your help. I need spcecil thermal initiator for my research. I don't have exact sturcture in mind. I'd like to take a look at the catalogues of companies which provide special initiator. Could you recommend the companies? Thanks in advance. From polymer@rmit.EDU.AU Thu Jun 12 18:48:30 1997 Received: from rmit.EDU.AU for polymer@rmit.EDU.AU by www.ccl.net (8.8.3/950822.1) id SAA25116; Thu, 12 Jun 1997 18:34:01 -0400 (EDT) Received: from bunyip.ph.rmit.edu.au (bunyip.ph.rmit.EDU.AU [131.170.94.250]) by rmit.EDU.AU (8.8.5/8.7.3/voga/ram2) with ESMTP id IAA29797 for ; Fri, 13 Jun 1997 08:33:23 +1000 (EST) Received: from BUNYIP/SpoolDir by bunyip.ph.rmit.edu.au (Mercury 1.21); 13 Jun 97 08:34:12 +1000 Received: from SpoolDir by BUNYIP (Mercury 1.21); 13 Jun 97 08:33:46 +1000 From: "Prof. Robert Shanks" Organization: RMIT Applied Physics To: chemistry@www.ccl.net Date: Fri, 13 Jun 1997 8:34:01 EST-10ESUT Subject: CCL:Molecular modeling software for non-theorists? Reply-to: ShanksRA@rmit.EDU.AU Priority: normal X-mailer: Pegasus Mail/Mac (v2.2.0, wide beta 6) Message-ID: <14F7D709BE@bunyip.ph.rmit.edu.au> To: Julius Su Molecular modeling software for non-theorists? We use: Chem3D (Macintosh) Hyperchem (MS Windows) CAChe (Macintosh) MSI Insight II Polymer (Silicon Graphics) Unichem (Silicon Graphics interface, Cray computations) I can reiterate your experience with Chem3D, in fact the Chem Office programs are well integrated and offer full scripting and web interaction. Hyperchem is similar, but a stand alone modelling program. It has more display facility than Chem3D in that it can display orbitals. It can also compute vibrational modes. It has similar ease of use to Chem3D. CAChe has more extensive computations than either of the above and it is property based. On the Macintosh it has an automatic spreadsheet type entry system (Project Leader) for molecules and properties - once this has been setup the program will automatically move through all the properties desired for each molecule and place the values in the cells. It has some QSPR type computations in addition to the quantum mechanical and molecular mechanics methods. MSI Insight we use onlt for polymers. It is a research tool which is not in the same category as the above programs. Unichem is a quantum mechanics program. It is only difficult to use in that it requires links with a Cray Supercomputer. Sincerely Robert Shanks From: jsu@ugcs.caltech.edu (Julius Su) Subject: CCL:Molecular modeling software for non-theorists? To: chemistry@www.ccl.net Date: Mon, 9 Jun 1997 21:40:42 -0700 (PDT) Hello, I work for a research group that uses laser spectroscopy to investigate the basic dynamics of chemical systems on a short time scale. Some members of our group have done fairly high level ab initio and molecular dynamics simulations in the past; however, the main focus of the group has definitely been experimental. Because of this, there has been no standard way to model chemical systems in our group. Individuals in the group have either written their own molecular dynamics routines or have had access to facilities where programs like Gaussian 92 could be run, but no convenient in-group facility to do simple molecular modeling has existed. We are currently seeking to change this. We would like to have some standard way of finding the geometries of small to medium molecules at a reasonable level of theory (semiemperical would be fine) and for doing molecular dynamics of photoexcited systems. This system would have to be accessible and easy enough to use that any experimentalist that wished to carry out an experiment would be able to quickly throw together a rough simulation of the system in question. Our group plans to purchase two fairly high end PCs to run the software that would be needed to do this. I have recently purchased a copy of Chem3D Pro with MOPAC for my personal use, and have found the interface for molecule building and geometry optimization to be intuitive and easy to use. We also have some simple code that was written within the group to do molecular dynamics on small clusters of rigid molecules. This code can be easily interfaced with Chem3D. Alternatively, we have found information on the Web about HyperChem, which appears to have the ability to do model building, geometry optimization, and a feature that would be especially useful to us, reactive molecular dynamics. It also appears to have facilities built in to visualize vibrational modes and molecular oribtals (althought the latter feature would not be nearly as important.) Since our group already has a copy of Gaussian 94, the added ab initio capabilities of the program are nice but not essential. The main concern at this point, however, is how easy HyperChem would be to use. Chem3D has impressed us with its intuitive interface and its tight integration with ChemDraw. We have not been able to find a demo of version of HyperChem with enabled building facilities to compare. Since 90% of the time will probably be spent doing simple model building and geometry optimization, this is particularly important to us. So, has anyone on this list had experience with HyperChem and Chem3D? How easy is it to build molecules in HyperChem? Does it have a reasonably useable interface? Can it generate publication quality graphics? Can experimentalists who don't want to spend too much time learning the nitty-gritty of semiemperical theory do simple calculations using it? Thank you very much for your help. Later, Julius Su jsu@cco.caltech.edu --- Administrivia: This message is automatically appended by the mail exploder: 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 --- __________________________________ Prof. Robert A. Shanks Professor of Polymer Science Department of Applied Chemistry Royal Melbourne Institute of Technology Box 2476V GPO Melbourne Victoria 3001 Australia Telephone and Fax +61 3 6602122 Mobile Telephone +61 041 935 8001 WWW RMIT Polymer Science Page: http://www.rmit.edu.au/departments/cm/polymer/index.html __________________________________ From trout@central.co.nz Fri Jun 13 01:48:34 1997 Received: from iconz.co.nz for trout@central.co.nz by www.ccl.net (8.8.3/950822.1) id BAA26186; Fri, 13 Jun 1997 01:46:12 -0400 (EDT) Received: from trout.iconz.co.nz (trout.central.co.nz [202.36.36.33]) by iconz.co.nz (8.6.12/8.6.10) with ESMTP id RAA18983 for ; Fri, 13 Jun 1997 17:45:56 +1200 Message-Id: <199706130545.RAA18983@iconz.co.nz> From: "Bruce Levett" To: Subject: Chemistry Software for Teachers and Students Date: Fri, 13 Jun 1997 17:44:40 +1200 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_01BC7821.77E85520" Content-Transfer-Encoding: 7bit This is a multi-part message in MIME format. ------=_NextPart_000_01BC7821.77E85520 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear List, I teach at Napier Boys' High School, New Zealand, and have developed some Windows software for my students which is for sale. It has been well received here in NZ and in other countries (USA, Canada, Finland, Belgium, Denmark, Hong Kong, Israel, Germany, Italy, UK so far) The software is sold separately or as a suite of 4 programs -"The Chemware Suite". These can be found on The Chemware Home Page at: http://www.iconz.co.nz/~trout/ The Suite programs are: ======================= 1. Organic Chemistry - version 2.2 http://www.iconz.co.nz/~trout/org.htm The functional groups can be set and student users are drilled. Also includes a hypertext set of notes in the help file. There is a downloadable SHAREWARE VERSION of version 2.0 (which you can download from my page or a number of other shareware sites). It only includes alkenes. ==================== 2. Volumetric Analysis - ver 1.1 http://www.iconz.co.nz/~trout/va.htm Acid-Base and Redox Titration questions/problems and solutions as student drills, or perhaps as a utility to check concentration calculations (you can enter you own data and set the standard solution). Very useful for some students who really struggle with these sort of problems. =================== 3. pH and Titration Curves - ver 2.1 http://www.iconz.co.nz/~trout/ph.htm pH, pOH, concentrations of hydrogen ions, hydroxide ions and degrees of dissociation for strong and weak acids and bases and buffers. Good for student drills or as a utility for the teacher! since concentrations pKa values etc are able to be set by the user. Worked solutions and titration curves can be shown. Also whether the standard assumptions are made or not can be set by the user. You can show any titration curve you like and even use any acid or base you want to. =================== 4. Electrochemical Cells - ver 1.0 http://www.iconz.co.nz/~trout/ecells.htm Students construct a virtual electrochemical cell, then check out their own: balanced equations for each half cell, or overall, electron flow, cell voltage, which electrodes is positive / negative, which electrodes is the anode /cathode, which electrodes oxidation or reduction occurs at. ................................... Bruce Levett e-mail: trout@central.co.nz WWW: http://iconz.co.nz/~trout ------=_NextPart_000_01BC7821.77E85520 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear List,

I teach at Napier = Boys' High School, New Zealand, and have developed some Windows software = for my students which is for sale.
It has been well received here in = NZ and in other countries (USA, Canada, Finland, Belgium, Denmark, Hong = Kong, Israel, Germany, Italy, UK so far)

The software is sold = separately or as a suite of 4 programs -"The Chemware = Suite".
These can be found on The Chemware Home Page = at:

http://www.iconz.co.nz/~trout/

The Suite programs = are:
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D
1. Organic Chemistry - version 2.2
http://www.iconz.co.nz/~trout/org.htm

The functional groups can be set and student = users are drilled. Also includes a hypertext set of notes in the help = file.
There is a downloadable SHAREWARE VERSION of version 2.0 (which = you can download from my page or a number of other shareware sites). It = only includes = alkenes.
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<= br>2.  Volumetric Analysis - ver 1.1
http://www.iconz.co.nz/~trout/va.htm

Acid-Base and Redox Titration = questions/problems and solutions as student drills, or perhaps as a = utility to check concentration calculations (you can enter you own data = and set the standard solution). Very useful for some students who really = struggle with these sort of = problems.
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D3.  pH and Titration Curves - ver 2.1
http://www.iconz.co.nz/~trout/ph.htm

pH, pOH, concentrations of hydrogen ions, = hydroxide ions and degrees of dissociation for strong and weak acids and = bases and buffers. Good for student drills or as a utility for the = teacher! since concentrations pKa values etc are able to be set by the = user. Worked solutions and titration curves can be shown. Also whether = the standard assumptions are made or not can be set by the user. You can = show any titration curve you like and even use any acid or base you want = to.
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
4. =  Electrochemical Cells - ver 1.0
http://www.iconz.co.nz/~trout/ecells.htm

Students construct a virtual electrochemical = cell, then check out their own:
balanced equations for each = half cell, or overall,
electron flow,
cell = voltage,
which electrodes is positive / = negative,
which electrodes is the anode = /cathode,
which electrodes oxidation or reduction occurs = at.
...................................
Bruce Levett
e-mail: =   trout@central.co.nz
WWW:      http://iconz.co.nz/~trout

------=_NextPart_000_01BC7821.77E85520-- From ooms@scf.fundp.ac.be Sat Jun 14 05:48:50 1997 Received: from spsrv.scf.fundp.ac.be for ooms@scf.fundp.ac.be by www.ccl.net (8.8.3/950822.1) id FAA02389; Sat, 14 Jun 1997 05:25:03 -0400 (EDT) Received: from [138.48.16.161] (cms-mac5.scf.fundp.ac.be [138.48.16.161]) by spsrv.scf.fundp.ac.be (AIX4.2/UCB 8.7/8.7) with SMTP id LAA37006 for ; Sat, 14 Jun 1997 11:24:20 +0200 (DFT) X-Sender: fooms@spsrv.scf.fundp.ac.be (Unverified) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sat, 14 Jun 1997 11:34:47 +0100 To: CHEMISTRY@www.ccl.net From: ooms@scf.fundp.ac.be (ooms fred) Subject: MEP similarity Dear netters I would like to compare similarities between MEP of different molecules and also to compare the MEP obtained by different methods for the same compound. Which are the similarity index to be used to do this kind of job. Any assistance would be appreciated. Thanks Fred --------------------------------------- Ooms Frederic Faculte Universitaire Notre-Dame de la Paix Laboratoire de Chimie Moleculaire Structurale Rue de Bruxelles 61 B-5000 Namur (BELGIUM) Tel : 32(81) 724569 - Fax : 32(81) 724530 e-mail :ooms@scf.fundp.ac.be From ccl@www.ccl.net Mon Jun 16 17:49:22 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id QAA13762; Mon, 16 Jun 1997 16:52:17 -0400 (EDT) Received: from destille.chemie.de for claessen@chemie.de by bedrock.ccl.net (8.8.3/950822.1) id QAA01920; Mon, 16 Jun 1997 16:52:15 -0400 (EDT) Received: by destille.chemie.de (Smail3.2.0.90) from claessen (132.187.248.124) with smtp id ; Mon, 16 Jun 1997 22:50:56 +0200 (MET DST) Message-Id: Comments: Authenticated sender is From: "Rolf Claessen" Organization: University of Wuerzburg, Dept. of Chemistry To: chemistry@ccl.net Date: Mon, 16 Jun 1997 21:09:39 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: ChemStarter - Online Discussion Forum Reply-to: s101264@stud-mail.uni-wuerzburg.de Priority: normal X-mailer: Pegasus Mail for Win32 (v2.52) ChemStarter - Online Discussion Forum I added an online discussion forum to the ChemStarter at http://destille.chemie.de/HyperNews/get/forums/chemstarter.html It is possible to use html. So you can include images, vrml, chime, ... into your messages to illustrate the discussion about chemistry problems. Yours Rolf Claessen claessen@chemie.de From qojskd@uscmail.usc.es Tue Jun 17 07:49:30 1997 Received: from uscmail.usc.es for qojskd@uscmail.usc.es by www.ccl.net (8.8.3/950822.1) id HAA16668; Tue, 17 Jun 1997 07:07:19 -0400 (EDT) Received: from [193.144.74.64] (qojskd.usc.es) by uscmail.usc.es (5.67b/1.34) id AA00144; Tue, 17 Jun 1997 13:05:02 +0200 Date: Tue, 17 Jun 1997 13:05:02 +0200 Message-Id: <199706171105.AA00144@uscmail.usc.es> From: "F. Javier Sardina" To: CHEMISTRY@www.ccl.net Subject: Freeware for NMR data processing Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Mailer: POPmail 2.3b5 Dear colleagues: The latest version of the freeware NMR data processing program MestRe-C (1.3 for Windows 95 and Windows NT) has just been released. It can be retrieved from any of the following anonymous ftp repositories: ftp://qobrue.usc.es/nmr/mestrec ftp.uniovi.es/pub/win95/nmr ftp.rediris.es/software/incoming/science/nmr/mestrec ftp://www.ccl.net/pub/chemistry/software/MS-WINDOWS95/MestRe-C *What's new in MestRe-C 1.3* ========================= - MestRe-C now runs under Windows NT (tested under version 4.0). - Processing of Bruker files from DnX spectrometers is now possible. - Expanded regions (up to 5 of them) can be displayed (and printed) with the spectrum. - Capability to add/substract two FID's/spectra has been added - FID's/spectra can be exported as metafiles (or bitmaps) to the clipboard (at last!). - Text comments can be included (and printed) in the spectra. - Improvements have been made in the following routines: INTEGRATION (use of a baseline-correction function). SET LIMITS (input limits through the keyboard). PHASE CORRECTION (the pivot point can be set by the user). PRINTING (portrait or lanscape modes, colour or B&W) MEASURE J (increased accuracy) - All routines have been optimized and are now considerably faster. For more information check MestRe-C WWW home page: http://qobrue.usc.es/jsgroup/MestRe-C/MestRe-C.html Happy NMR data processing F. Javier Sardina F. Javier Sardina Phone: 34-81-591085 Departamento de Quimica Organica 34-81-563100. Ext 14234 Universidad de Santiago de Compostela Fax: 34-81-595012 or 34-81-591091 15706 Santiago de Compostela e-mail: qojskd@usc.es SPAIN http://qobrue.usc.es/jsgroup/Js-eng.html From lestaw.k.bieniasz@uni-tuebingen.de Tue Jun 17 14:55:10 1997 Received: from outmail.zdv.uni-tuebingen.de for lestaw.k.bieniasz@uni-tuebingen.de by www.ccl.net (8.8.3/950822.1) id OAA20383; Tue, 17 Jun 1997 14:06:24 -0400 (EDT) Received: from echem5.orgchemie.chemie (echem5.orgchemie.chemie.uni-tuebingen.de) by outmail.zdv.uni-tuebingen.de (4.1/ZDV-Uni-Tuebingen-1.0) id AA16734; Tue, 17 Jun 97 20:06:17 MES Date: Tue, 17 Jun 1997 20:05:44 +0200 (W. Europe Daylight Time) From: "Lestaw K. Bieniasz" To: "Jeffrey L. Nauss" Cc: chemistry@www.ccl.net Subject: Re: CCL:semantics : molecular modelling In-Reply-To: <9706170920.ZM14533@beryllium.crs.uc.edu> Message-Id: X-X-Sender: coibi01@mailserv.uni-tuebingen.de Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Tuebingen, 17.06.97 On Tue, 17 Jun 1997, Jeffrey L. Nauss wrote: > The immediate question that comes into my mind with Alexandre's > statement is: what is "computational chemistry?" Why is there a > distinction between computational chemistry and molecular modelling? > > I have resolved the issue in my own mind as follows. Computational > chemistry would be the application of numerical calculations to the > study of molecular structure. Thus I would include in that definition > Thus I consider computational chemistry to be a subset of the more > general field of molecular modelling. Molecular modelling in itself may > not involve any computations. But computational chemistry must. I would suggest that you have a look at the introductions to "Reviews of Computational Chemistry". A definition of computational chemistry is provided in one of the volumes (I do not remember now which one, sorry, but you will easily find it). According to this definition, everything that requires the use of computers in chemical research, is computational chemistry. Application of numerical calculations to the study of molecular structures would be one of such areas of investigations. However, there are also other, like for example "classical" chemical kinetic computations, which assume a "continuum" approximation to the matter, and hence no molecular structure considerations are involved. Such computations are often very sophisticated and computationally demanding, and there is no reason to consider them less important or less difficult than quantum mechanical calculations. Similar examples occur let's say in electrochemical kinetic modelling which is my area of interest. Yet another examples are provided by the paper of Larter and Showalter in volume 10 of the above reviews. In my opinion the above definition of computational chemistry is the only one that should be used, and it removes a certain pathology from the contemporary practice in computational chemistry, which has been dominated by quantum chemical calculations. Such calculations are certainly important, but there are other areas which should also find their right place in the computational chemistry. If you are not convinced, look at computational physics. Physicists do not put an equality sign between quantum physics and computational physics. Sincerely, L.Bieniasz *-------------------------------------------------------------------* | Dr. Leslaw Bieniasz | | temporary address: (3rd April 1997 - 31st August 1997) | | Institut fuer Organische Chemie, Universitaet Tuebingen | | Auf der Morgenstelle 18, 72076 Tuebingen, Germany. | | E-mail: lestaw.k.bieniasz@uni-tuebingen.de | *-------------------------------------------------------------------* | permanent address: | | Institute of Physical Chemistry of the Polish Academy of Sciences,| | Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland. | | E-mail: nbbienia@cyf-kr.edu.pl | *-------------------------------------------------------------------* From lavelle@mbi.ucla.edu Wed Jun 18 15:49:52 1997 Received: from rho.ben2.ucla.edu for lavelle@mbi.ucla.edu by www.ccl.net (8.8.3/950822.1) id PAA03301; Wed, 18 Jun 1997 15:11:31 -0400 (EDT) Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by rho.ben2.ucla.edu (8.8.5/8.8.5) with SMTP id MAA40338; Wed, 18 Jun 1997 12:11:31 -0700 Received: from red5.mbi.ucla.edu by ewald.mbi.ucla.edu; (5.65/1.1.8.2/15May97-0203PM) id AA16704; Wed, 18 Jun 1997 12:11:31 -0700 Message-Id: <3.0.32.19970618121312.007070ec@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Wed, 18 Jun 1997 12:13:13 -0700 To: hyperchem@hyper.com, chemistry@www.ccl.net From: Laurence Lavelle Subject: Packing in the unit cell. Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi, I have spent some time tracking down MOLPAK only to find out that it does not do what I want. Apparently Chem3D is what I need. I'd appreciate any clarification on which program I should be looking for and where to find it. Currently I am in search of a program that will generate the contents of a unit cell (and possibly n+1 adjacent cells) given the coordinates of the asymmetric unit and cell parameters as input (CCD format). After obtaining the unit cell contents I intend to import the file into HyperChem Ver 5.01. I know ChemPlus 1.6 has the feature I need but it costs $400-$500 which is currently not feasible. Thanks Laurence """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Laboratory of Structural Biology & Molecular Medicine Molecular Biology Institute Los Angeles, CA90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone:(310)206-8270 Fax:(310)825-0982 http://www.mbi.ucla.edu/people/lavelle/lavelle.html """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" From woods@draco.pmmp.uic.edu Wed Jun 18 19:49:53 1997 Received: from draco.pmmp.uic.edu for woods@draco.pmmp.uic.edu by www.ccl.net (8.8.3/950822.1) id TAA05996; Wed, 18 Jun 1997 19:05:56 -0400 (EDT) From: Received: from draco by draco.pmmp.uic.edu via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id SAA04602; Wed, 18 Jun 1997 18:10:01 -0500 Sender: woods@draco.pmmp.uic.edu Message-ID: <33A86AC9.15FB@mmad1.pmmp.uic.edu> Date: Wed, 18 Jun 1997 18:10:01 -0500 X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Computaional Chemistry List Subject: Re: CCL:Packing in the unit cell. References: <3.0.32.19970618121312.007070ec@mbi.ucla.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Along these same lines, I am seeking a program that will allow one to build a lattice of molecules by inputting one or several different molecular files as well as the unit cell dimensions. I currently have a routine called bcell that will make a lattice of multiple copies of the SAME molecule file, but I need a routine that will allow a lattice to be built which will contain multiple copies of one molecule in the lattice, as well as ONE that is different. Anyone have any suggestions? Richard From yubofan@guomai.sh.cn Wed Jun 18 22:49:54 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id WAA06943; Wed, 18 Jun 1997 22:49:09 -0400 (EDT) Received: from ------ ([210.0.0.16]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id LAA05069 for ; Thu, 19 Jun 1997 11:44:57 +0800 Message-Id: <199706190344.LAA05069@gm-email.guomai.sh.cn> From: "·ΆΣύ²¨" To: Subject: What is the meaning of grid in G94W? Date: Thu, 19 Jun 1997 10:30:46 +0800 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1161 MIME-Version: 1.0 Content-Type: text/plain; charset=CN-GB Content-Transfer-Encoding: base64 SGksIEFsbCwNCg0KDQpXaGVuIEkgcmVhZCB0aGUgaGVscCBmaWxlIGFuZCBtYW51YWwgb2YgRzk0 VywgSSBmb3VuZCBhIGtleXdvcmQtLWdyaWQuIEkgZG9uJ3QgdW5kZXJzdGFuZCBpdCBkZWVwbHkg YW5kIHVzYWdlLiANCg0KSSBoYXZlIHRvIHNheSBJIGFtIGEgYmVnaW5ubmVyIG9mIHF1YW50dW0g Y2hlbWlzdHJ5LiBDYW4geW91IGdpdmUgc29tZSBoZWxwIGFuZCBleHBsYW5hdGlvbj8NCg0KVGhh bmsgeW91IHZlcnkgbXVjaCENCg0KDQpZLiBGQU4=