From Jeffrey.Gosper@brunel.ac.uk Tue Nov 11 04:32:21 1997 Received: from eros.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.8.3/950822.1) id EAA00780; Tue, 11 Nov 1997 04:00:25 -0500 (EST) From: Received: from molnir.brunel.ac.uk by eros.brunel.ac.uk with SMTP-BRUNEL (PP); Tue, 11 Nov 1997 09:00:23 +0000 Message-Id: <9818.199711110900@molnir.brunel.ac.uk> Subject: Re: CCL:Visualization of ADF vib. modes To: Ole.Swang@chem.sintef.no (Ole.Swang) Date: Tue, 11 Nov 1997 09:00:22 +0000 (GMT) Cc: chemistry@www.ccl.net In-Reply-To: <2.2.32.19971110121659.009069b0@mail.oslo.sintef.no> from "Ole.Swang" at Nov 10, 97 01:16:59 pm X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit > > > Dear all, > > I need to visualize vibration modes computed with the ADF program. Is there > available any software that can (at least) read ADF output and write > cartesian coordinates of the molecules deformed along the modes? I am aware > of the MSI stuff, but it costs more than I am able to pay presently. > > Any hint is appreciated, > > Best regards, > Dear Ole, If your prepared to do a little editing or even better write a script (or given the right incentive I would write a converter program) then you can use Re_View2 to view the vibrational results from any calculation. We have interface d MOPAC6, MOPAc93, GAMESS, G94, Turbomol using this method. Cheers Dr Gosper From hinsen@lmspc1.ibs.fr Tue Nov 11 06:32:21 1997 Received: from ibs.ibs.fr for hinsen@lmspc1.ibs.fr by www.ccl.net (8.8.3/950822.1) id GAA01221; Tue, 11 Nov 1997 06:11:08 -0500 (EST) Received: from lmspc1.ibs.fr (hinsen@lmspc1.ibs.fr [192.134.36.141]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id MAA04086; Tue, 11 Nov 1997 12:10:00 +0100 Received: (from hinsen@localhost) by lmspc1.ibs.fr (8.8.5/8.8.5) id MAA03978; Tue, 11 Nov 1997 12:08:19 +0100 Date: Tue, 11 Nov 1997 12:08:19 +0100 Message-Id: <199711111108.MAA03978@lmspc1.ibs.fr> From: Konrad Hinsen To: lijnzaad@ebi.ac.uk CC: C.Dubreuil@hgu.mrc.ac.uk, biowidgets-consortium@fruitfly.BDGP.Berkeley.EDU, javachem@wag.caltech.edu, bioobjects@ebi.ac.uk, chemistry@www.ccl.net In-reply-to: <199711101715.RAA01063@o2-4.ebi.ac.uk> (message from Philip Lijnzaad on Mon, 10 Nov 1997 17:15:23 GMT) Subject: Re: CCL:Sequence Classes and CORBA Servers > The demand for 50 copies is imposed by the OMG. They lack the infrastructure > and logistics to run off the responses themselves for the distribution among > attendants at meetings, and therefore ask the submitters to do this. I think > this is not unreasonable, given the amount of work that is going on in the > OMG. But it does raise the question whether an OMG acitivity is the right way to arrive at useful standards for scientific computing. The OMG was founded by and for large companies; participation of small companies and academic groups, although not ruled out in principle, was not one of the design goals. Few small groups and companies can even afford to participate in OMG activities with their heavy administrative overhead. A look at the member list of the life sciences group confirms this - there are hardly any academics in it. On the other hand, much innovative work happens in academic groups and small companies. Given that there is still very little practical experience with OO techniques in scientific applications, it doesn't seem useful to me to start a standards committee at all at this time, much less one which excludes an important part of the people working in the field. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From FLOWER_DR@charnwood.gb.astra.com Tue Nov 11 06:39:17 1997 Received: from mail-gw-1.astra.com for FLOWER_DR@charnwood.gb.astra.com by www.ccl.net (8.8.3/950822.1) id GAA01250; Tue, 11 Nov 1997 06:24:52 -0500 (EST) Received: from gatekeeper.astra.com by mail-gw-1.astra.com (5.65v3.2/1.1.10.5/30Jun97-0418PM) id AA07565; Tue, 11 Nov 1997 12:29:05 +0100 Received: by gatekeeper.astra.com; (5.65v4.0/1.3/10May95) id AA27173; Tue, 11 Nov 1997 12:25:12 +0100 Message-Id: From: "Flower, Darren" To: "'chemistry@www.ccl.net'" Subject: Molecular Modelling for Industry: the training issues Date: Tue, 11 Nov 1997 12:22:53 +0100 Return-Receipt-To: X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.995.52 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Molecular Modelling Group Royal Society of Chemistry:=20 Industrial Affairs Disivion ONE DAY SYMPOSIUM Molecular Modelling for Industry:=20 The Training Issues Thursday, 4 December 1997 Scientific Societies Lecture Theatre New Burlington Place, Piccadilly, London Molecular modelling is now widely used in the pharmaceutical, chemical and electronic industries. Its success depends to a large extent on how well integrated the modelling is with an on going experimental programme. Are the experimentalists and modellers adequately trained to ask relevant questions to each other - for the benefit of both? Where and what type of training they can get? How to get access to molecular modelling when no facilities exist in-house? These are some of the questions to be debated at this meeting. We have speakers from industry to talk on what they expect from Molecular Modelling and the efforts that they have made. In the afternoon, the speakers will describe the kind of training that they have provided both within the industry and in the academia. In the Panel Discussion, the audience will have an opportunity to assess and suggest any improvements, if necessary. AGENDA 10.00 Coffee & Registration 10.25 Welcome & Introduction 10.30 Prof Graham Richards (U. of Oxford & Oxford Molecular) 11.00 Dr Joe Howard (Applied Extrusion Technologies Ltd.) 12.00 Dr Kevin Ray (Horsell) 12.30 Lunch & Posters 14.15 Prof Nick Quirke (U. of Wales, Bangor) 14.45 Prof Dominic Tildesley (U. of Southampton) 15.15 Prof Rod Hubbard (U. of York) 15.45 Dr Mike Stapleton (MSI) 16.15 PANEL DISCUSSION=09 17.00 CLOSE=09 Registration Fee:=20 RSC & Modelling Group Members =A330.00, Others =A340.00 Contact: Dr John Kendrick, ICI Wilton, Middlesborough TS90 8JE Phone: 01642-437994 Fax: 01642-432244=20 E-mail: john_kendrick@ici.com From jecop@ebi.ac.uk Tue Nov 11 07:32:23 1997 Received: from alpha1.ebi.ac.uk for jecop@ebi.ac.uk by www.ccl.net (8.8.3/950822.1) id HAA01518; Tue, 11 Nov 1997 07:05:19 -0500 (EST) Received: from sol19.ebi.ac.uk (sol19.ebi.ac.uk [193.62.196.173]) by alpha1.ebi.ac.uk (8.8.7/8.8.7) with SMTP id MAA02133; Tue, 11 Nov 1997 12:05:03 GMT Date: Tue, 11 Nov 1997 12:05:02 +0000 (GMT) From: Jeroen Coppieters To: Konrad Hinsen cc: biowidgets-consortium@fruitfly.BDGP.Berkeley.EDU, javachem@wag.caltech.edu, bioobjects@ebi.ac.uk, chemistry@www.ccl.net, mark@omg.org, lifesciences@omg.org Subject: Re: CCL:Sequence Classes and CORBA Servers In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I had a typo in my address list of the previous mail. I resent it seperately to lifesciences@omg.org (instead of lifeciences@omg.org) Above is the full list of adresses the message went to. If you reply, make sure you got the correct address: lifesciences@omg.org Jeroen From jecop@ebi.ac.uk Tue Nov 11 07:48:52 1997 Received: from alpha1.ebi.ac.uk for jecop@ebi.ac.uk by www.ccl.net (8.8.3/950822.1) id GAA01457; Tue, 11 Nov 1997 06:58:01 -0500 (EST) Received: from sol19.ebi.ac.uk (sol19.ebi.ac.uk [193.62.196.173]) by alpha1.ebi.ac.uk (8.8.7/8.8.7) with SMTP id LAA01914; Tue, 11 Nov 1997 11:57:17 GMT Date: Tue, 11 Nov 1997 11:57:16 +0000 (GMT) From: Jeroen Coppieters Reply-To: Jeroen Coppieters To: Konrad Hinsen cc: biowidgets-consortium@fruitfly.BDGP.Berkeley.EDU, javachem@wag.caltech.edu, bioobjects@ebi.ac.uk, chemistry@www.ccl.net, mark@omg.org, lifeciences@omg.org Subject: Re: CCL:Sequence Classes and CORBA Servers In-Reply-To: <199711111108.MAA03978@lmspc1.ibs.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 11 Nov 1997, Konrad Hinsen wrote: [ I added Mark Lowenstein from OMG and the lifesciences mailing list to the recipients. If the readers of any of the other lists above feel that this topic should not be discussed on their list, then please let us know Jeroen] > > The demand for 50 copies is imposed by the OMG. They lack the infrastructure > > and logistics to run off the responses themselves for the distribution among > > attendants at meetings, and therefore ask the submitters to do this. I think > > this is not unreasonable, given the amount of work that is going on in the > > OMG. > > But it does raise the question whether an OMG acitivity is the right > way to arrive at useful standards for scientific computing. > > The OMG was founded by and for large companies; participation of > small companies and academic groups, although not ruled out in > principle, was not one of the design goals. Few small groups > and companies can even afford to participate in OMG activities OMG was founded by and for large companies, but they have been (and are) trying hard to make it open to all, including academia. A look at the membership list of OMG shows that many universities are members. I do not see that academics from lifesciences departments would be poorer than their counterparts from other departments. You do not have to attend each meeting to be involved. Most decisions can be reached by email discussions. > with their heavy administrative overhead. A look at the member > list of the life sciences group confirms this - there are hardly > any academics in it. There is no 'membership' to the life sciences research group. It is open to anyone who wants to contribute (by attending or by submitting information). I guess you have been looking at the attendace list for last meeting. This was the first meeting of the LSR group, so I do not think you can call it representative. I would like to repeat that this is an open forum, so anyone who feels he/she has something to share, please come forward. > > On the other hand, much innovative work happens in academic groups and > small companies. Given that there is still very little practical > experience with OO techniques in scientific applications, it doesn't OO has been around for a long time (and has been thought to undergrads for ages). Many developers of scientific software (both academic and commercial) are well educated in OO. On the other hand many life science researchers have been thinking about objects, long before OO became fashionable. > seem useful to me to start a standards committee at all at this time, > much less one which excludes an important part of the people working > in the field. The whole point of the OMG approach is that it is possible to start modeling subdomains, without the need for an allencompassing model of the world. I agree that innovative work happens in academic groups and small companies. But that does not mean that a standard interface for common objects would restrain that research. There is a core of entities, that many researchers use and would like to be able to exchange without constant reformating overhead. Large companies are backing this proposal, which you seem to interprete negative. I think that it's this backing which gives us hope of achieving something. Previous (mostly academic) standarisation attempts failed, because of the lack of worldwide support. Large pharms do innovative work as well, and also rely on academic groups and small companies (via funding, contracting etc). So it's in their interest to see them involved. Jeroen > -- > ------------------------------------------------------------------------------- > Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr > Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 > Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 > 41, av. des Martyrs | Deutsch/Esperanto/English/ > 38027 Grenoble Cedex 1, France | Nederlands/Francais > ------------------------------------------------------------------------------- > EMBL Outstation EBI Jeroen Coppieters (European Bioinformatics Institute) Research and Development Wellcome Trust Genome Campus Jeroen.Coppieters@embl-ebi.ac.uk Hinxton (or jecop@ebi.ac.uk) Cambridge CB10 1SD UK ++44 1223 494422 http://www.ebi.ac.uk fax ++44 1223 494468 From lijnzaad@alpha1.ebi.ac.uk Tue Nov 11 08:32:24 1997 Received: from alpha1.ebi.ac.uk for lijnzaad@alpha1.ebi.ac.uk by www.ccl.net (8.8.3/950822.1) id HAA01644; Tue, 11 Nov 1997 07:38:32 -0500 (EST) Received: from o2-4.ebi.ac.uk (o2-4.ebi.ac.uk [193.62.196.202]) by alpha1.ebi.ac.uk (8.8.7/8.8.7) with ESMTP id MAA03235; Tue, 11 Nov 1997 12:37:34 GMT Received: (from lijnzaad@localhost) by o2-4.ebi.ac.uk (8.8.6/8.8.6) id MAA01187; Tue, 11 Nov 1997 12:37:34 GMT Date: Tue, 11 Nov 1997 12:37:34 GMT Message-Id: <199711111237.MAA01187@o2-4.ebi.ac.uk> From: Philip Lijnzaad To: hinsen@ibs.ibs.fr CC: biowidgets-consortium@fruitfly.BDGP.Berkeley.EDU, javachem@wag.caltech.edu, bioobjects@ebi.ac.uk, chemistry@www.ccl.net In-reply-to: <199711111108.MAA03978@lmspc1.ibs.fr> (message from Konrad Hinsen on Tue, 11 Nov 1997 12:08:19 +0100) Subject: Re: CCL:Sequence Classes and CORBA Servers Reply-to: lijnzaad@ebi.ac.uk Konrad, thanks for your response. > > The demand for 50 copies is imposed by the OMG. They lack the infrastructure > > and logistics to run off the responses themselves for the distribution among > > attendants at meetings, and therefore ask the submitters to do this. I think > > this is not unreasonable, given the amount of work that is going on in the > > OMG. > > But it does raise the question whether an OMG acitivity is the right > way to arrive at useful standards for scientific computing. Well, that depends, I suppose. A sizeable amount of scientific computing (even if it's not cutting edge) is being done in the corporate world. Why not join efforts here, and arrive at a standard that will benefit both corporate and academic users ? Once there are reasonable standards, people will probably use them, and I think this is much preferable to the ad hoc solutions that keep popping up. > Few small groups > and companies can even afford to participate in OMG activities > with their heavy administrative overhead. I cannot agree on this. Academics will go a very long way to make things easier for themselves and especially to make their work more widely known to others. E.g. the amount of work that goes into polishing an article, getting your web server up and running, tricking your java applet to display just what you want, getting your demo ANSI C compliant, etc. etc. are not neglible. Scientist are prepared to do all this because it makes their work more useful for others. Along similar lines, I think spending a bit of time standardizing some of the entities you work with, is time very well spent. Or, along a different line, look at the work that goes into standardization of nomenclature in medicin, taxonomy, chemistry, physics. It is very much an academic effort, a lot of work, and it is very much needed. I think compared to this, the OMG process is not all that heavy. > On the other hand, much innovative work happens in academic groups and > small companies. Yes, I agree, and I think that it makes little sense to spend effort standardizing the cutting edge. But a lot of work has been in long use, and could benefit from standardization. > Given that there is still very little practical experience with OO > techniques in scientific applications, I don't agree on this: there is a lot of OO analysis going on, especially in bioinformatics. The main reason is that the data is so complex that it becomes too difficult to manage without OO. Take a look at rhdb, gdb, acedb, anubis, srs, micado, and many others. > much less one which excludes an important part of the people working > in the field. 'Excluding' is not true. If you refer to the 50 copies: it is not uncommon for scientists in academia to copy 100-page chapters from a textbook, or 20 copies of a 10-page article for the journal club. If you refer to the membership fee, there are academic discounts, and you don't need to be an OMG member to respond to the RFI. Moreover, a large number of academic institutes is actually meber of the OMG. If you refer to the administrative overhead, see my point about other scientific standards. So, even if the process may seem a bit cumbersome, I think it is very well worth it. Yours, Philip -- Philip Lijnzaad, lijnzaad@ebi.ac.uk | European Bioinformatics Institute +44 (0)1223 49 4639 | Wellcome Trust Genome Campus, Hinxton +44 (0)1223 49 4468 (fax) | Cambridge CB10 1SD, GREAT BRITAIN PGP fingerprint: E1 03 BF 80 94 61 B6 FC 50 3D 1F 64 40 75 FB 53 From Ole.Swang@chem.sintef.no Tue Nov 11 08:41:09 1997 Received: from hate.oslo.sintef.no for Ole.Swang@chem.sintef.no by www.ccl.net (8.8.3/950822.1) id IAA01775; Tue, 11 Nov 1997 08:09:24 -0500 (EST) From: Received: from chpc660 (pc-214-250.si.sintef.no [128.39.214.250]) by hate.oslo.sintef.no (8.8.5/8.8.5) with SMTP id OAA26498 for ; Tue, 11 Nov 1997 14:09:16 +0100 (MET) Message-Id: <2.2.32.19971111130816.0177cab4@mail.oslo.sintef.no> X-Sender: ole@mail.oslo.sintef.no X-Mailer: Windows Eudora Pro Version 2.2 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 11 Nov 1997 14:08:16 +0100 To: chemistry@www.ccl.net Subject: Summary: ADF freq. vis. Dear all, I have had a lot of answers to my query about possibilities of visualizing vibrational modes from ADF calculations. The answers are listed below; Thank you very much, one and all! However, yesterday evening I fell victim of an uncontrollable urge to write FORTRAN, and, into the night, I wrote a small program to read ADF output and write input files to Xmol (from MSC), one file for each mode. It is not well tested (and probably not very well written, either), but it seems to work OK. If anyone wants a copy, just give me a mail. Best regards, Ole #########################################################################3 Return-Path: Date: Mon, 10 Nov 1997 08:17:18 -0600 (CST) From: "Bradley A. Smith" To: Ole.Swang@chem.sintef.no Subject: Re: CCL:Visualization of ADF vib. modes If you can provide me with example ADF output files, I should be able to extend the xvibs utility to include ADF. Currently xvibs only handles Gaussian92, Guassian94, Gamess, and AcesII. It reads the output file and creates an XYZ file containing a set of coordinates animating the selected vibration. The XYZ file can be visualized with various utilities such as XMol or Chime. If you could email me example files, I'd be happy to try extending xvibs. -- Bas ######################################################################### Return-Path: From: Dongchul Lim Subject: Re: CCL:Visualization of ADF vib. modes To: Ole.Swang@chem.sintef.no Date: Mon, 10 Nov 97 9:36:10 EST Ole.Swang@chem.sintef.no writes: > > > Dear all, > > I need to visualize vibration modes computed with the ADF program. Is there > available any software that can (at least) read ADF output and write > cartesian coordinates of the molecules deformed along the modes? I am aware > of the MSI stuff, but it costs more than I am able to pay presently. > > Any hint is appreciated, Hi, XMOL can visualize vibrational modes. All you need to do is to extract normal modes from ADF output and reformat them in XMOL format. -DL ############################################################################# Return-Path: X-Sender: bickel@mail.chemie.uni-marburg.de Date: Mon, 10 Nov 1997 17:19:51 +0200 To: ole.swang@chem.sintef.no From: bickel@chemie.uni-marburg.de (Matthias Bickelhaupt) Subject: visualization Dear Ole, >I need to visualize vibration modes computed with the ADF program. Is there >available any software that can (at least) read ADF output and write >cartesian coordinates of the molecules deformed along the modes? I am aware >of the MSI stuff, but it costs more than I am able to pay presently. > >Any hint is appreciated, I think the program Molecule is a good one to tackle your problem. But right now it cannot read the ADF output and you have to transfer the data by hand into Molecule. For more information, see the web site: http://www.ccc.uni-erlangen.de/info/Molecule/overview.html Best regards from Marburg, Matthias ########################################################################### Return-Path: From: "DR R J DEETH" Organization: University of Warwick To: ole.swang@chem.sintef.no Date: Mon, 10 Nov 1997 16:28:14 +0100 (BST) Subject: ADF vibrations Priority: normal Dear Ole, We use the ADF output to generate a series of xyz cartesian files by hand and then use xmol (free off the Internet) to visualize and analyse vibrations. It's not an automated procedure (yet) but it's simple enough to do. Rob Deeth ############################################################################# Return-Path: From: "Mu-Hyun Baik" Date: Mon, 10 Nov 1997 14:40:18 -0500 References: To: adf-list@scm.com Subject: Re: graphical software for ADF Dear Ole, here is how we do it: We use a PC to extract XYZ format files from the adf-log file and then let the PC create a HTML - CHIME movie. The whole procedure takes just few seconds and you do not even have to worry about writing your own vizualization-routines. And everything is FREE ! For abstraction we use a house-made PC program that we call C-3PO. You can have it of course. Just send me a email and I will send you a copy of C-3PO as an email attachment - it's about 4MB zipped and therefor I do not want to send it right away with this reply. Mucky Baik Univ. of North Carolina Dept. of Chemistry Chapel Hill USA ########################################################################## Return-Path: Resent-From: oles@kjemi.uio.no Resent-Message-Id: <199711111217.NAA01098@halvan.trd.sintef.no> Old-Return-Path: Delivery-Date: Tue, 11 Nov 1997 13:16:43 +0100 Old-Received: from tungsten.chem.vu.nl (actually tungsten.chem.vu.nl [130.37.144.65]) by pat.uio.no with SMTP (PP); Tue, 11 Nov 1997 13:16:23 +0100 Old-Received: from gatekeeper.itqb.unl.pt (gatekeeper.itqb.unl.pt [193.136.177.1]) by tungsten.chem.vu.nl (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id MAA08686 for ; Tue, 11 Nov 1997 12:11:04 +0100 Old-Received: (from uucp@localhost) by gatekeeper.itqb.unl.pt (8.8.6/8.8.6) id LAA25200 for ; Tue, 11 Nov 1997 11:11:49 GMT Old-Received: from brutus.itqb.unl.pt(193.136.176.2) by gatekeeper.itqb.unl.pt via smap (V1.3) id sma025181; Tue Nov 11 11:11:46 1997 Old-Received: from localhost by brutus.itqb.unl.pt; (5.65/1.1.8.2/08Nov96-0323PM) id AA10677; Tue, 11 Nov 1997 11:10:46 -0100 Date: Tue, 11 Nov 1997 11:10:45 -0100 (GMT-0100) From: pedro lopes To: ADF mailing list Subject: Visualisation tools Resent-Date: Tue, 11 Nov 1997 13:16:47 +0100 Resent-To: ole.swang@chem.sintef.no Dear Ole, I think you can try VIEWKEL from Greg Landrum. The homepage for this software is http://overlap.chem.cornell.edu:8080/~landrum/yaehmop.html I've been using it to plot MOs produced by ADF. The program compiled with little effort in my linux machine. There are two other codes to extract geometries and vibrational modes but I didn't try yet. I hope this helps!! Bye. Pedro. ######################################################################### Return-Path: Date: Tue, 11 Nov 1997 13:04:52 +0100 From: Alessandro Bencini Subject: ADF visualization X-Sender: sandro@blu.chim1.unifi.it To: adf-list@scm.com X-MIME-Autoconverted: from quoted-printable to 8bit by hate.oslo.sintef.no id NAA25374 Dear All, we in Firenze have been interfacing MOLDEN to ADF. Up to now the version 3.2 of molden has some routine to plot the orbitals. More will follow. A interface program is required to read the tape21 file which is available upon request from myself or mariotti@chim1.unifi.it. this is a preliminar release. Alessandro ######################################################################### ---------------------------------------------------------------- Ole Swang Research scientist, Dr. Scient. SINTEF Applied Chemistry, Dept. of Hydrocarbon Process Chemistry POB 124 Blindern, N-0314 Oslo, Norway. Phone: +47 2206 7429 Email: ole.swang@chem.sintef.no Fax: +47 2206 7350 URL: http://www.sintef.no/units/chem/6630/ole.html ------------------ ._.. ._ ..___ ._ __.. --------------------- From jmartine@udec.cl Tue Nov 11 09:32:25 1997 Received: from UDEC.CL for jmartine@udec.cl by www.ccl.net (8.8.3/950822.1) id IAA02093; Tue, 11 Nov 1997 08:51:36 -0500 (EST) Received: from localhost ([152.74.92.2]) by UDEC.CL (8.8.7/8.8.7) with SMTP id KAA29599 for ; Tue, 11 Nov 1997 10:50:55 -0600 Date: Tue, 11 Nov 1997 10:50:55 -0600 Message-Id: <199711111650.KAA29599@UDEC.CL> X-Sender: jmartine@buho.dpi.udec.cl X-Mailer: Windows Eudora Version 1.4.3 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: jmartine@UDEC.CL (José Antonio Martínez O.) Subject: request parameter Content-Transfer-Encoding: 8bit Dear Sirs: I begin to work with AMBER but I don find parameter to Borate, which I need include in a molecular modelling bounded to the active site of my enzyme. Thanks in advances, Sincerelly Dr. Jose Martinez-Oyanedel Laboratorio de Enzimologia Universidad de Concepcion CHILE From hinsen@lmspc1.ibs.fr Tue Nov 11 09:43:40 1997 Received: from ibs.ibs.fr for hinsen@lmspc1.ibs.fr by www.ccl.net (8.8.3/950822.1) id IAA02000; Tue, 11 Nov 1997 08:37:10 -0500 (EST) Received: from lmspc1.ibs.fr (hinsen@lmspc1.ibs.fr [192.134.36.141]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id OAA04535; Tue, 11 Nov 1997 14:36:05 +0100 Received: (from hinsen@localhost) by lmspc1.ibs.fr (8.8.5/8.8.5) id OAA04338; Tue, 11 Nov 1997 14:34:25 +0100 Date: Tue, 11 Nov 1997 14:34:25 +0100 Message-Id: <199711111334.OAA04338@lmspc1.ibs.fr> From: Konrad Hinsen To: jecop@ebi.ac.uk, lijnzaad@ebi.ac.uk CC: biowidgets-consortium@fruitfly.BDGP.Berkeley.EDU, javachem@wag.caltech.edu, bioobjects@ebi.ac.uk, chemistry@www.ccl.net, mark@omg.org, lifesciences@omg.org In-reply-to: (message from Jeroen Coppieters on Tue, 11 Nov 1997 12:05:02 +0000 (GMT)) Subject: Re: CCL:Sequence Classes and CORBA Servers Jeroen Coppieters writes: > OO has been around for a long time (and has been thought to undergrads for > ages). Many developers of scientific software (both academic and > commercial) are well educated in OO. On the other hand many life science > researchers have been thinking about objects, long before OO became > fashionable. Maybe other branches of life sciences are more up to date, but in the field I am familiar with (protein modelling), I couldn't name any widely used tool based on OO technology, much less any published OO interface used by more than one software supplier. Yes, there are OO libraries etc. for certain applications, but they are used only by a handful of people. > world. I agree that innovative work happens in academic groups and small > companies. But that does not mean that a standard interface for common > objects would restrain that research. There is a core of entities, that It might prove insufficient and would then not be used at all. > Large companies are backing this proposal, which you seem to interprete > negative. I think that it's this backing which gives us hope of achieving Not at all. I just wish there were an additional less formal channel to encourage participation of people who can't dedicate significant resources (most of all time) to this. Philip Lijnzaad writes: > Well, that depends, I suppose. A sizeable amount of scientific computing > (even if it's not cutting edge) is being done in the corporate world. Why not > join efforts here, and arrive at a standard that will benefit both corporate > and academic users ? Once there are reasonable standards, people will No objections. But it is very well conceivable that a better standard (for everyone) could be reached by encouraging participation from academic scientists. > I cannot agree on this. Academics will go a very long way to make things > easier for themselves and especially to make their work more widely known to > others. E.g. the amount of work that goes into polishing an article, getting Only to the extent that helps in getting jobs and funding. > neglible. Scientist are prepared to do all this because it makes their work > more useful for others. Along similar lines, I think spending a bit of time > standardizing some of the entities you work with, is time very well > spent. Or, along a different line, look at the work that goes into I agree, but unless people who decide about jobs and funding agree as well, such efforts are still difficult to justify for most of us. > 'Excluding' is not true. If you refer to the 50 copies: it is not uncommon > for scientists in academia to copy 100-page chapters from a textbook, or 20 > copies of a 10-page article for the journal club. If you refer to the That's not the point; it is not the cost of copying that is the problem. But most scientists I know hate bureaucracy and would not be willing to deal with an organization that imposes such rules, certainly not unless it provides clear and immediate benefits to them. My expectation is that most academic scientist will completely ignore the OMG effort and continue work as before. And that would be a lost opportunity for everyone in my opinion. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From FLOWER_DR@charnwood.gb.astra.com Tue Nov 11 11:32:38 1997 Received: from mail-gw-1.astra.com for FLOWER_DR@charnwood.gb.astra.com by www.ccl.net (8.8.3/950822.1) id LAA02937; Tue, 11 Nov 1997 11:10:01 -0500 (EST) Received: from gatekeeper.astra.com by mail-gw-1.astra.com (5.65v3.2/1.1.10.5/30Jun97-0418PM) id AA08453; Tue, 11 Nov 1997 17:13:53 +0100 Received: by gatekeeper.astra.com; (5.65v4.0/1.3/10May95) id AA13708; Tue, 11 Nov 1997 17:09:14 +0100 Message-Id: From: "Flower, Darren" To: "'chemistry@www.ccl.net'" Subject: 1-Day Molecular Modelling Meeting Date: Tue, 11 Nov 1997 16:23:03 +0100 Return-Receipt-To: X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.995.52 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Molecular Modelling Group Royal Society of Chemistry: Industrial Affairs Disivion ONE DAY SYMPOSIUM Molecular Modelling for Industry: The Training Issues Thursday, 4 December 1997 Scientific Societies Lecture Theatre New Burlington Place, Piccadilly, London Molecular modelling is now widely used in the pharmaceutical, chemical and electronic industries. Its success depends to a large extent on how well integrated the modelling is with an on going experimental programme. Are the experimentalists and modellers adequately trained to ask relevant questions to each other - for the benefit of both? Where and what type of training they can get? How to get access to molecular modelling when no facilities exist in-house? These are some of the questions to be debated at this meeting. We have speakers from industry to talk on what they expect from Molecular Modelling and the efforts that they have made. In the afternoon, the speakers will describe the kind of training that they have provided both within the industry and in the academia. In the Panel Discussion, the audience will have an opportunity to assess and suggest any improvements, if necessary. AGENDA 10.00 Coffee & Registration 10.25 Welcome & Introduction 10.30 Prof Graham Richards (U. of Oxford & Oxford Molecular) 11.00 Dr Joe Howard (Applied Extrusion Technologies Ltd.) 12.00 Dr Kevin Ray (Horsell) 12.30 Lunch & Posters 14.15 Prof Nick Quirke (U. of Wales, Bangor) 14.45 Prof Dominic Tildesley (U. of Southampton) 15.15 Prof Rod Hubbard (U. of York) 15.45 Dr Mike Stapleton (MSI) 16.15 PANEL DISCUSSION 17.00 CLOSE Registration Fee: RSC & Modelling Group Members GBP 30.00, Others GBP 40.00 Contact: Dr John Kendrick, ICI Wilton, Middlesborough TS90 8JE Phone: 01642-437994 Fax: 01642-432244 E-mail: john_kendrick@ici.com From shenkin@still3.chem.columbia.edu Tue Nov 11 12:32:26 1997 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id LAA03222; Tue, 11 Nov 1997 11:40:48 -0500 (EST) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id LAA29462 for <@smtp.columbia.edu:chemistry@www.ccl.net>; Tue, 11 Nov 1997 11:40:36 -0500 (EST) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) for chemistry@www.ccl.net id LAA03239; Tue, 11 Nov 1997 11:40:35 -0500 From: "Peter Shenkin" Message-Id: <9711111140.ZM3237@still3.chem.columbia.edu> Date: Tue, 11 Nov 1997 11:40:35 -0500 In-Reply-To: Konrad Hinsen "CCL:Sequence Classes and CORBA Servers" (Nov 11, 2:34pm) References: <199711111334.OAA04338@lmspc1.ibs.fr> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Re: CCL:Sequence Classes and CORBA Servers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii We have been thinking about CORBA. I know the big players in molecular modeling are serious about CORBA as well. Here, however, is a major problem that I see (aside from specification of classes, which I realize was the original topic). Most applications of CORBA are written in-house by large firms who have purchased CORBA technology, which is expensive. Even the run-time ORB is expensive to put on all platforms. We, on the other hand, as a (small) third-party vendor, cannot with impunity build our distributed applications around CORBA, because there's no guarantee that our customers will have the technology up and running in-house. They would have to license it, possibly from us -- but that would be a significant extra expense for them and bookkeeping of pass-through expenses for us. CORBA technology is now being integrated into WWW browsers, but not all jobs will be run from (or tied to) browsers; some will just be large distributed number-crunching applications launched from a shell or from some front end. How do those who are enthusiastic about the technology feel this issue can be addressed? -P. -- ****************** Sir Isaiah Berlin, 1909 - 1997, RIP ******************** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From elewars@alchemy.chem.utoronto.ca Tue Nov 11 12:39:49 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id LAA03335; Tue, 11 Nov 1997 11:58:39 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id LAA11497 for chemistry@www.ccl.net; Tue, 11 Nov 1997 11:58:38 -0500 (EST) Date: Tue, 11 Nov 1997 11:58:38 -0500 (EST) From: "E. Lewars" Message-Id: <199711111658.LAA11497@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: SLATER ORBITALS, EHM ON HHE+, SUMMARY 1997 Nov 11 To: chemistry@www.ccl.net >From: E. Lewars Re: Answers to my Q about Slater orbitals--summary Thanks very much to all who responded to my two questions about Slater orbitals. I now provide a summary of the answers. #1 wallenborn@phys.chem.ethz.ch Mon Nov 3 04:31 93/3072 CCL:G:OVERLAP INTEGRAL AN #2 aldert@chemde4.leidenuniv.nl Mon Nov 3 04:48 44/1863 Re: CCL:G:OVERLAP INTEGR #3 FREDVC@ESALP1.EMAIL.DUPONT.COM Mon Nov 3 09:31 111/5012 Re: CCL:G:OVERLAP INTEGRA #4 smithja@ucarb.com Mon Nov 3 09:41 111/4169 RE: G:OVERLAP INTEGRAL AN #5 herbert.homeier@chemie.uni-regensburg.de #6 ritschel@tc1.chem.uni-potsdam.de #7 satyam@indigo2.chem.pitt.edu #8 rene@mountain.chem.yorku.ca #9 chburger@aci.unizh.ch #10 davide@stinch10.csmtbo.mi.cnr.it ------------------- #1 >From wall@phys.chem.ethz.ch Mon Nov 3 04:31:11 EST 1997 Date: Mon, 3 Nov 1997 10:31:01 +0100 (CET) >From: Ernst-Udo Wallenborn To: "E. Lewars" Subject: CCL:G:OVERLAP INTEGRAL AND SLATER FUNNC E. Lewars writes: [snip] >that Mulliken et al published a long paper (J Chem Phys, 17 (1949) 1248-1267)) >with recipes for calculating overlap integrals you might also want to read Roothaan's article in J. Chem. Phys. _19_ (12) 1445 (1951) >(1) In the molecule H-He+ (yes, protonated helium) if the H nucleus has > Cartesians H1(x_1, y_1, z_1) and the He nucleus He2(x_2, y_2, z_2), > where the coordinates are in Angstroms (_not_ atomic units or Bohrs) > > and if we write > > for H: phi_1 = a_1 exp{b_1[(x-x_1)^2 + (y-y_1)^2 + (z-z_1)^2]^1/2} > and for He: phi_2 = a_2 exp{b_2[(x-x_2)^2 + (y-y_2)^2 + (z-z_2)^2]^1/2} > > (usually a is expressed in terms of zeta and pi, b = -zeta, and > the variable is a radius vector r) > QUESTION: what are a_1 and b_1, as numbers, not Greek letters? b_1 is arbitrarily chosen (well, not completely arbitrarily, but the rules they're chosen in accordance with are prescriptions rather than rules). For Hydrogen one usually has b_1=1.3, for Carbon b_1=1.625 and so on. a_1 then is the normalisation factor, given for 1s orbitals as a_1=Sqrt[b_1^3/Pi] (ok, on Greek letter left). >(2) If (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, 0.800), > (0.800 Angstroms) what is S_12 (as a number, e.g 0.4273 or whatever)? If i take b_1=b_2=1.3 then S_12 is 0.595868. But why did you want to know this number? >(3) For (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, d), > is there a simple function S_12 = f(d) ? (for H, He? for any two > 1s orbitals)? Of course f will depend parametrically on the a's and b's. For all 1s orbitals this is not too complicated, S_12 = -(1-k)*[(2(1+k)+ra)*exp(-ra)+(2(1-k)+rb)*exp(-rb)]*(Sqrt[(1-t^2)/(r*t)] with t = (b_1-b_2)/(b_1+b_2) ra = b_1*R rb = b_2*R r = 0.5*(b_1+b_2)*R R = [(x-x_1)^2 + (y-y_1)^2 + (z-z_1)^2]^1/2 k = 0.5*(t+1/t) if t != 0; but you'll find this in the Roothaan article i cited above (the formula was derived by him, if i'm not mistaken, of course all typos are mine.) ============ #2 >From aldert@chemde4.leidenuniv.nl Mon Nov 3 04:48:24 EST 1997 Date: Mon, 3 Nov 97 10:50:09 +0100 >From: aldert@chemde4.leidenuniv.nl (Aldert Westra Hoekzema) To: "E. Lewars" Subject: Re: CCL:G:OVERLAP INTEGRAL AND SLATER FUNNC Hi, Analytic expressions for all kinds of two-center integrals for Slater orbitals can be found in: C.C.J. Roothaan, J. Chem. Phys., 19(12), 1445-58 (1951). "A Study of Two-Center Integrals Useful in Calculations on Molecular Structure. I" The expresion for overlap of 2 Slater 1s orbitals with different screening constants and the function you are looking for, can be found under formula 25. As to the screening constants (your b), for H it is simply 1, for He I am not aware of a more recent value then 1.6875 taken from: E. Clementi & D.L. Raimondi, J. Chem. Phys. 38(11), 2686-9 (1963). line 1 [h for help] Hope this helps, Aldert ------------------------------------------- A.J.A. Westra Hoekzema Conformational Analysis (Organic Chemistry) Leiden Institute of Chemistry, Gorlaeus Laboraties, Leiden University P.O. Box 9502, 2300 RA Leiden The Netherlands Phone : +31 715274505 Fax : +31 715274488 E-mail: aldert@chemde4.LeidenUniv.nl ------------------------------------------- ============== #3 >From FREDVC@ESALP1.EMAIL.DUPONT.COM Mon Nov 3 09:31:11 EST 1997 >From: FREDVC@ESALP1.EMAIL.DUPONT.COM Date: Mon, 03 Nov 1997 09:21:06 -0500 (EST) Subject: Re: CCL:G:OVERLAP INTEGRAL AND SLATER FUNNC To: elewars@alchemy.chem.utoronto.ca The a's are normalization constants dependent on the b's; the b's are STO orbital exponents within a multiplicative factor, depending on whether Angstroms or Bohrs are being used. Search out "Slater's rules" on how to generate these exponents. >> >> S_12 = the triple integral from 0--> infinity of phi_1.phi_2 dxdydz >> must = the correct overlap, if the six Cartesian coordinates are in >> Angstroms. And of course integral of S_11 = S_22 = 1. >> The "Angstroms" restriction is a conceptual one on your part. As long as we are *consistent* in units-usage, the overlap is independent of this. >>(2) If (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, 0.800), >> (0.800 Angstroms) what is S_12 (as a number, e.g 0.4273 or whatever)? >> >>(3) For (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, d), >> is there a simple function S_12 = f(d) ? (for H, He? for any two >> 1s orbitals)? Of course f will depend parametrically on the a's and b's. You are thinking in the wrong coordinate system. STO Overlap integrals are carried out in confocal elliptical coordinates; see Eyring, Walter & Kimball, (e.g., EWK), "Quantum Chemistry", page 367. This transformation makes it convenient to express STO overlaps in terms of the A & B auxiliary functions; see Mulliken's paper, and pages 388-389 of EWK. There is lore that is almost lost on the best way(s) to generate the A & B functions. You should be aware of this before proceeding to doing actual calculations. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 or 529-2076 Central Research & Development Dept. || The DuPont Company || FAX: (302) 695-9658 P. O. Box 80320 || Wilmington DE 19880-0320 || Internet: fredvc@esvax.dnet.dupont.com -------------------------------------------------------------------------------- Opinions expressed in this electronic message should ***> NOT <*** be taken to represent the official position(s) of the DuPont Company. *****> ANY OPINIONS EXPRESSED ARE THE PERSONAL VIEWS OF THE AUTHOR ONLY. <***** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ============ #4 >From smithja@ucarb.com Mon Nov 3 09:41:40 EST 1997 >From: "Smith JA (Jack)" To: "'E. Lewars'" Subject: RE: G:OVERLAP INTEGRAL AND SLATER FUNNC Date: Mon, 3 Nov 1997 08:40:32 -0600 X-Priority: 3 > There is some info' about overlap integrals and Slater functions that > I am > finding it hard to dig out of the literature. I should state at the > outset > that _I know_: > > that there are programs for calculating overlap integrals > Why do you not want to use existing routines? > that in most molecular quantum chem Gaussian functions, not Slater > functions, > are used > > that Mulliken et al published a long paper (J Chem Phys, 17 (1949) > 1248-1267)) > with recipes for calculating overlap integrals > > that all kinds of tricks exist for "simplifying" the calculation of > overlap > integrals > So what didn't you understand or like? > --------- > OK, but what I want is simply this: > > (1) In the molecule H-He+ (yes, protonated helium) if the H nucleus > has > Cartesians H1(x_1, y_1, z_1) and the He nucleus He2(x_2, y_2, > z_2), > where the coordinates are in Angstroms (_not_ atomic units or > Bohrs) > > and if we write > > for H: phi_1 = a_1 exp{b_1[(x-x_1)^2 + (y-y_1)^2 + > (z-z_1)^2]^1/2} > and for He: phi_2 = a_2 exp{b_2[(x-x_2)^2 + (y-y_2)^2 + > (z-z_2)^2]^1/2} > > (usually a is expressed in terms of zeta and pi, b = -zeta, and > the variable is a radius vector r) > QUESTION: what are a_1 and b_1, as numbers, not Greek letters? > what are a_2,and b_2 as numbers, not Greek letters? > (i.e a_1 = 0.5647 or whatever, etc etc (4 decimals). > These are just standard normalization constants (in terms of zeta and pi, as you stated). You know the values of zeta and pi, so what's the problem? > S_12 = the triple integral from 0--> infinity of phi_1.phi_2 > dxdydz > must = the correct overlap, if the six Cartesian coordinates are > in > Angstroms. > If you do the integral right, the units shouldn't matter. > And of course integral of S_11 = S_22 = 1. > That's the normalization condition that gives the normalization constants. > (2) If (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, > 0.800), > (0.800 Angstroms) what is S_12 (as a number, e.g 0.4273 or > whatever)? > > (3) For (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, d), > is there a simple function S_12 = f(d) ? (for H, He? for any two > 1s orbitals)? Of course f will depend parametrically on the a's > and b's. > I recommend that you get a copy of Slater's book "Quantum Theory of Matter" (2nd Edition, McGraw-Hill, 1968) and look at chapter 20 (the H2+ problem). You should be able to solve your HHe+ problem by hand based on this alone (and perhaps some of the earlier chapters dealing with Slater functions - although Slater doesn't call them that, of course!). If you can't find a copy, I'll send you the actual formulas. I can't tell whether you're over-complicating a simple problem, or over-simplifying a complicated problem. - Jack P.S. I also have a complete STO package for all 1-center (1-and 2-electron) integrals and all 2-center overlap and nuclear attraction-type integrals for any arbitrary orientation (with no hard limit on quantum numbers). It's not a stand-alone package, but rather part of a larger molecular package that I wrote over 20 years ago, and it's in old ANSI-66 Fortran. (It uses most of the "tricks" with the A and B functions involving recursion formulas, etc., that you probably read about, and perhaps a few you haven't read about). ============= #5 >From herbert.homeier@chemie.uni-regensburg.de Mon Nov 3 11:08:00 EST 1997 Date: Mon, 3 Nov 97 17:59:30 +0100 >From: Herbert Homeier t4720 To: elewars@alchemy.chem.utoronto.ca Subject: Re: CCL:G:OVERLAP INTEGRAL AND SLATER FUNNC Cc: CHEMISTRY@ccl.net Reply-To: herbert.homeier@na-net.ornl.gov Hello, > Date: Sun, 2 Nov 1997 16:54:11 -0500 (EST) > From: "E. Lewars" > Message-Id: <199711022154.QAA26919@alchemy.chem.utoronto.ca> > To: chemistry@www.ccl.net > Subject: CCL:G:OVERLAP INTEGRAL AND SLATER FUNNC > > > There is some info' about overlap integrals and Slater functions that I am > finding it hard to dig out of the literature. I should state at the outset > that _I know_: > > that there are programs for calculating overlap integrals > > that in most molecular quantum chem Gaussian functions, not Slater > functions, > are used > > that Mulliken et al published a long paper (J Chem Phys, 17 (1949) > 1248-1267)) > with recipes for calculating overlap integrals that contains quite a few errors .... > > that all kinds of tricks exist for "simplifying" the calculation of overlap > integrals > --------- > OK, but what I want is simply this: > (1) In the molecule H-He+ (yes, protonated helium) if the H nucleus has > Cartesians H1(x_1, y_1, z_1) and the He nucleus He2(x_2, y_2, z_2), > where the coordinates are in Angstroms (_not_ atomic units or Bohrs) > > and if we write > > for H: phi_1 = a_1 exp{b_1[(x-x_1)^2 + (y-y_1)^2 + (z-z_1)^2]^1/2} > and for He: phi_2 = a_2 exp{b_2[(x-x_2)^2 + (y-y_2)^2 + (z-z_2)^2]^1/2} The best source of information on such questions is still the "classical" paper E. Clementi and C. Roetti, At. Data & Nucl. Data Tables 14 (1974) 177 [maybe in atomic units, though 8^)] > > (usually a is expressed in terms of zeta and pi, b = -zeta, and > the variable is a radius vector r) > QUESTION: what are a_1 and b_1, as numbers, not Greek letters? > what are a_2,and b_2 as numbers, not Greek letters? > (i.e a_1 = 0.5647 or whatever, etc etc (4 decimals). > > S_12 = the triple integral from 0--> infinity of phi_1.phi_2 dxdydz line 48 [h for help]> must = the correct overlap, if the six Cartesian coordinates are in > Angstroms. And of course integral of S_11 = S_22 = 1. > > (2) If (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, 0.800), > (0.800 Angstroms) what is S_12 (as a number, e.g 0.4273 or whatever)? > > (3) For (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, d), > is there a simple function S_12 = f(d) ? (for H, He? for any two > 1s orbitals)? Of course f will depend parametrically on the a's and b's. > ---------- The answer to your final question is given below, however, in somewhat different notation: alpha : -b_1 beta : -b_2 R : d my S : Overlap of exp(-alpha*r_1) and exp(-beta*r_2), ie., for a_1=a_2=1, where r_1=sqrt(x**2+y**2+z**2) and r_2=sqrt(x**2+y**2+(z-R)**2) The result of the fortran program listed below contains also the value where a_1 and a_2 are chosen so that the 1s orbitals are normalized. See the output. There is an WWW interface to this: http://www.chemie.uni-regensburg.de/~hoh05008/form-Soverlap.html For 1s functions, of course, the result for the overlap integral does only depends on a_1,a_2,b_1,b_2 and d, not on the particular geometry of the centers (only their distance d matters). As regards units: If you enter R in Angstroem, and alpha and beta in 1/Angstroem, everything should be fine in the case of the overlap integral of normalized 1s functions. You may be interested also in the following papers: @ARTICLE{HomeierSteinborn92ote, author={H. H. H. Homeier and E. O. Steinborn}, title={On the Evaluation of Overlap Integrals with Exponential--type Basis Functions}, journal="Int. J. Quantum Chem.", volume=42, pages="761--778", year="1992" } @ARTICLE{HomeierWenigerSteinborn92pft, author={H. H. H. Homeier and E. J. Weniger and E. O. Steinborn}, title={Programs for the Evaluation of Overlap Integrals with {$B$} Functions}, journal="Comput. Phys. Commun.", volume=72, pages="269--287", year="1992" The latter describes a fortran program package S_INT for more general orbitals. The output generated by the programs given below has been checked against the output of this package. One should be careful (!), however, with the closed form expression coded in the programs below in the case that alpha and beta are not equal, but very close, and in the case that R is small but not exactly zero. The reason is that in these cases, cancelling singularities turn up. For instance, one gets a result somewhat greater than one for the normalized functions for alpha=1.000 beta=1.001 R=0.01 and this, of course is wrong (overlaps of normalized functions have to be smaller than 1. The package S_INT generates accurate output even in the case described above. Best regards Herbert Homeier ----------[PROGRAMS AVAILABLE FROM HERBERT HOMEIER]- -------------------------------------------------------------- Priv.-Doz. Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg, D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX: +49-941-943 4719/+49-941-943 2305 email: herbert.homeier@na-net.ornl.gov WWW: http://www.chemie.uni-regensburg.de/~hoh05008 =============== #6 >From ritschel@tc1.chem.uni-potsdam.de Tue Nov 4 07:25:07 EST 1997 >From: ritschel@tc1.chem.uni-potsdam.de (Thomas Ritschel) Subject: Overlap Integrals over Slater Functions To: elewars@alchemy.chem.utoronto.ca Date: Tue, 4 Nov 1997 13:24:35 +0100 (MET) Dear Dr. Lewars, some months ago I wrote a small C program which computes overlap integrals over slater type functions. The program was originally written with Turbo C on a PC, but it runs also on an IBM RS/6000 and therefore it shold be runing at yours too. The code is not very fast and sometimes it makes some trouble. The calculation is done in elliptical coordinates and with the use of auxiliary integrals A and B. The theory about this I found in the (german) book "Quantenchemie - Ein Lehrgang. Band 5: Ausgewaehlte Mathematische Methoden der Chemie" by H.-J. Glaeske, J. Reinhold and P. Volkmer, but I think that there are a lot of english written books on this topic too. Some words to the use of the program: You have to specify the bond distance, e.g. the distance between the 2 nuclei. In your CCL mail you wrote that you use cartesian coordinates, so you have to calc r = sqrt(x*x + y*y + z*z). The program internally uses atomic units (bohr) - so you have to convert your angstrom values to a.u. by dividing them by 0.529177. This value is defined as a constant with the name "bohr" in my program. The function for computing the overlap integral is called in that way: s = overlap(s1s, 1.24, s1s, 2.0925, sigma, r/bohr); The six parameters are: s1s ... use a 1s orbital on first atom 1.24 ... the slater orbital exponent on first atom (= zeta) s1s ... use a 1s orbital on second atom 2.0925 ... the slater orbital exponent on second atom (= zeta) sigma ... we have a sigma type of bond r/bohr ... bond distance in a.u. (r is in angstrom) I've tested it on your H + He(+) and it seems to work well. The zeta value's may be different to them you use. For hydrogen normally a value of 1.30 is taken for extended huckel calculations. Be sure that you never call the overlap function with r = 0.0 otherwise you'll get some waste data. If you want to calc S12(0.0) then take r = 0.0001 or so. That's all to say about the program. I hope I could help you. Fell free to ask me if you have some trouble with the code. Thomas. ---------------------------------------- Thomas Ritschel Universitaet Potsdam Institut fuer Physikalische und Theoretische Chemie ritschel@tc1.chem.uni-potsdam.de ----------------------------------1997-- [PROGRAM AVAILABLE FROM THOMAS RITSCHEL] ========== #7 >From: IN%"satyam@indigo2.chem.pitt.edu" "satyam" To: IN%"elewars@alchemy.chem.utoronto.ca" "E. Lewars" CC: IN%"chemistry@www.ccl.net" Subj: CCL:SLATER ORBITALS-THANKS AND A REQUEST A quick calculation using HYPERCHEM5.01 version gives the following result : H-He+ R=0.8 Ang R=0.774 Ang HOMO -25.8147 eV -25.8767 eV LUMO - 2.3698 eV - 1.2903 eV The results with Weighted Diffusion option gives the following HOMO -26.1629 eV -26.2390 LUMO - 0.9855 eV + 0.2135 Satyam On Fri, 7 Nov 1997, E. Lewars wrote: > Friday 1997 Nov 7 > > Thanks to all those who responded to my question about Slater orbitals; I wi ll > post a summary and an explanation in a couple days. > > One more request: if anyone has an extended Hueckel program and a couple > minutes to spare, could he/she tell me what eigenvalues and eigenvectors it > gives for H-He+ at an internuclear distance of 0.800 A (1.512 a.u.); at 0.774 A > (1.463 a.u.) ? Unfortunately, most programs probably aren't parameterized > for helium, in the mistaken belief that it can't form strong bonds. > (I can do _ab initio_ calculations on this molecule; but I have a reason for > wanting the extended Hueckel result). > > Thanks > > E. Lewars ----------------------------------------------------- Dr. Satyam Priyadarshy 107D, Chevron, Department of Chemistry University of Pittsburgh, Pittsburgh, PA 15260, U.S.A Fon/Fax: +1-412-624-8200(Extn 1217or 8589) / 624-8552 email: satyam+@pitt.edu OR satyam@hathi.chem.pitt.edu ----------------------------------------------------- ============= #8 >From rene@mountain.chem.yorku.ca Fri Nov 7 14:54:52 EST 1997 Date: Fri, 7 Nov 1997 14:49:00 -0500 (EST) >From: Rene Fournier To: elewars@alchemy.chem.utoronto.ca Subject: STOs Dear Dr. Lewars: I am also interested in how to calculate overlap (and maybe other matrix elements, e.g., kinetic energy) from STOs. Please post (or send me) a summary. My *impression* is that calculating any integral involving STOs is so complicated that the best practical solution may simply be to use a multicenter numerical integration method, such as was described by Becke some years ago, and which is now in widespread use in DFT (where numerical integration CAN NOT be avoided). For a diatomic that would amount more or less to taking the product STO(r_i;A)*STO(r_i;B) for i=1,2000 (roughly 2000 quadrature points); it's rather time consuming, but a lot simpler than what I've seen of "analytical STO" integral algorithms, and maybe even more efficient?!?!? If efficiency is not an issue for your problem, and you can tolerate errors of, say, one part per million, than numerical integration would seem best. -- Rene Fournier. -------------------------------------------------------------------- | Rene Fournier | Bureau/Office 303 Petrie | | Chemistry, York University | (416) 736 2100 Ext. 30687 | | 4700 Keele Street, North York | FAX: (416) 736-5936 | | Ontario, CANADA M3J 1P3 | e-mail: renef@yorku.ca | -------------------------------------------------------------------- =========== #9 >From chburger@aci.unizh.ch Fri Nov 7 16:34:24 EST 1997 >From: "Dr. Peter Burger" Subject: Re: CCL:SLATER ORBITALS-THANKS AND A REQUEST To: elewars@alchemy.chem.utoronto.ca (E. Lewars) Date: Fri, 7 Nov 1997 22:34:19 +0100 (MET) Hi, here do come your EHT results on HHe+ Have fun! Peter --------------------- Peter Burger Anorg.-Chem. Institut Universitaet Zuerich chburger@aci.unizh.ch ********************************************************* * Carlo MEALLI and Davide M. PROSERPIO (1990) * * EHC (Extended Huckel Calculation program) * * A major revision of the original program SIMCON * * Roald Hoffmann, Cornell University * * Symmetry routines written by Klaus Linn (1991) * * New revisions by A. Sironi and J.A. Lopez (1992) * * Ref.: Journal of the Chemical Education (1990,67,399) * ********************************************************* hhe+ 77.4 pm ST. 1 ==== DISTANCE MATRIX. (values X 10**3)==== H 1 He 2 H 1 0 He 2 774 0 ======================================================================== ***************************************************************************** !!!!!!! Control+BREAK for interrupting the program !!!!!! $w2o2.in ST. 1 .00 .00 .00 .00 EXTENDED HUCKEL CALCULATION (WEIGHTED HIJ FORMULA) ATOM X Y Z N EXP-S COUL-S N EXP-P COUL-P N EXPD1 COUL-D C1 C2 EXPD2 H 1 .000 .000 .000 1 1.300 -13.600 He 2 .000 .000 .774 1 1.300 -10.600 CHARGE = 1 ELECTRONS = 2 HUCKEL CONSTANT = 1.750 **** POINTGROUP = Civ **** This run requires 124 bytes for the matrices Matrix Factorized according to symmetry Ci ENERGY LEVELS (EV). E( 1) = 2.784 .000 2a1 E( 2) = -15.816 2.000 1a1 SUM OF ONE-ELECTRON ENERGIES = -31.63190 EV. REDUCED OVERLAP POPUL. MATRIX, ATOM BY ATOM (10**3) H 1 He 2 H 1 899 He 2 718 381 TOTAL ELECTRONS= 2 SUM OF: OP(I,I)= 1.281 ( 64.055%) OP(I,J)= .719 ( 35.945%) ATOM NET CHG. ATOMIC ORBITAL OCCUPATION FOR GIVEN MO OCCUPATION S Px Py Pz x2-y2 z2 xy xz yz H 1 -.259 1.259 He 2 1.259 .741 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * EHMO execution time: .05 seconds. Stop - Program terminated. ********************************************************* * Carlo MEALLI and Davide M. PROSERPIO (1990) * * EHC (Extended Huckel Calculation program) * * A major revision of the original program SIMCON * * Roald Hoffmann, Cornell University * * Symmetry routines written by Klaus Linn (1991) * * New revisions by A. Sironi and J.A. Lopez (1992) * * Ref.: Journal of the Chemical Education (1990,67,399) * ********************************************************* hhe+ 80 pm ST. 1 ==== DISTANCE MATRIX. (values X 10**3)==== H 1 He 2 H 1 0 He 2 800 0 ======================================================================== ***************************************************************************** !!!!!!! Control+BREAK for interrupting the program !!!!!! $w2o2.in ST. 1 .00 .00 .00 .00 EXTENDED HUCKEL CALCULATION (WEIGHTED HIJ FORMULA) ATOM X Y Z N EXP-S COUL-S N EXP-P COUL-P N EXPD1 COUL-D C1 C2 EXPD2 H 1 .000 .000 .000 1 1.300 -13.600 He 2 .000 .000 .800 1 1.300 -10.600 CHARGE = 1 ELECTRONS = 2 HUCKEL CONSTANT = 1.750 **** POINTGROUP = Civ **** This run requires 124 bytes for the matrices Matrix Factorized according to symmetry Ci ENERGY LEVELS (EV). E( 1) = 1.754 .000 2a1 E( 2) = -15.759 2.000 1a1 SUM OF ONE-ELECTRON ENERGIES = -31.51737 EV. REDUCED OVERLAP POPUL. MATRIX, ATOM BY ATOM (10**3) H 1 He 2 H 1 913 He 2 704 382 TOTAL ELECTRONS= 2 SUM OF: OP(I,I)= 1.296 ( 64.788%) OP(I,J)= .704 ( 35.212%) ATOM NET CHG. ATOMIC ORBITAL OCCUPATION FOR GIVEN MO OCCUPATION S Px Py Pz x2-y2 z2 xy xz yz H 1 -.266 1.266 He 2 1.266 .734 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * EHMO execution time: .06 seconds. Stop - Program terminated. ============== #10 >From davide@stinch10.csmtbo.mi.cnr.it Sat Nov 8 04:30:39 EST 1997 Date: Sat, 8 Nov 1997 10:26:21 +0100 >From: davide@stinch10.csmtbo.mi.cnr.it (Davide Proserpio) To: "E. Lewars" Subject: Re: CCL:SLATER ORBITALS-THANKS AND A REQUEST Dear E. Lewars here I send you the results form a EHT calculation done with CACAO, using you will find all the parameters and WF and more for a set of internuclear dista nces. Obviously there is no minimum with a standard EHT calculation only with 1s orbit als. note : all the walues of Wavefunction, Charge Matrix, reduced Ov. Pop, Bond orde rs are multiplied *1000 regards Davide ********************************************************* * Carlo MEALLI and Davide M. PROSERPIO (1990) * * EHC (Extended Huckel Calculation program) * * A major revision of the original program SIMCON * * Roald Hoffmann, Cornell University * * Symmetry routines written by Klaus Linn (1991) * * New revisions by A. Sironi and J.A. Lopez (1992) * * Ref.: Journal of the Chemical Education (1990,67,399) * ********************************************************* RESULTS: EL's INTERPRETATION/SUMMARY OF OUTPUT OF ABOVE: #1---#6 ------------------ H 1 0 DIST #1 E = -49.8 HE 2 852 0 <------------------0.852 A psi_1 c's: 0.300, 0.822 DU -1 426 426 0 ======================================================================== $# molecular H-He+ with FMO ST. 2 0.413 ---------------------------- H 1 0 DIST #2 E = -50.0 HE 2 826 0 <-----------------0.826 A psi_1 c's 0.304, 0.814 DU -1 413 413 0 ======================================================================== H 1 0 DIST #3 E = -50.1 HE 2 800 0 <-----------------0.800 A psi_1 c's: 0.308, 0.807 DU -1 400 400 0 ======================================================================== H 1 0 HE 2 774 0 <---------------- DIST #4 E = -50.3 DU -1 387 387 0 0.774 A psi_1 c's: 0.311, 0.800 ======================================================================== H 1 0 HE 2 748 0 <----------------- DIST #5 E = -50.4 DU -1 374 374 0 0.748 A psi_1 c's: 0.314, 0.793 ======================================================================== H 1 0 HE 2 722 0 <------------------DIST #6 E = -50.6 DU -1 361 361 0 0.722 A psi_1 c's: 0.317, 0.786 ======================================================================== From Gerald.Loeffler@univie.ac.at Tue Nov 11 13:40:20 1997 Received: from mailbox.univie.ac.at for Gerald.Loeffler@univie.ac.at by www.ccl.net (8.8.3/950822.1) id NAA03904; Tue, 11 Nov 1997 13:05:49 -0500 (EST) Received: from univie.ac.at (gerilap.imp.univie.ac.at [131.130.80.125]) by mailbox.univie.ac.at (8.8.4/8.8.4) with ESMTP id TAA20332; Tue, 11 Nov 1997 19:05:09 +0100 Message-ID: <34689E04.34C4ECE9@univie.ac.at> Date: Tue, 11 Nov 1997 19:03:49 +0100 From: Gerald Loeffler Reply-To: Gerald.Loeffler@univie.ac.at Organization: I.M.P. X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: Jon Siegel CC: biowidgets-consortium@fruitfly.BDGP.Berkeley.EDU, javachem@wag.caltech.edu, bioobjects@ebi.ac.uk, chemistry@www.ccl.net, lifesciences@omg.org Subject: OMG Life Sciences Effort References: <3.0.1.32.19971111100632.00a2b6a0@192.67.184.65> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Two things: 1) Just a remark - without becoming political, which is honestly not what I want: What is striking to me is the apparent absence of any representative of the NCBI in the OMG Life Sciences Group (am I wrong?). Without judging the scientific influence of any of the organizations involved in the OMG effort, I wonder how a standard in bioinformatics can be developed without support and contribution from the NCBI?! 2) I started this thread by a question mainly about class libraries for sequences and homology searches. When can we expect an early specification or even implementation from the OMG Life Sciences Group? cheers, gerald -- Gerald Loeffler PostDoc in Theoretical Biophysics EMail: Gerald.Loeffler@univie.ac.at WWW: http://www.imp.univie.ac.at/Loeffler/ 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 siegel@omg.org Tue Nov 11 17:32:29 1997 Received: from emerald for siegel@omg.org by www.ccl.net (8.8.3/950822.1) id QAA05191; Tue, 11 Nov 1997 16:57:39 -0500 (EST) Received: from sauron.omg.org by emerald (SMI-8.6/SMI-SVR4) id QAA18411; Tue, 11 Nov 1997 16:59:29 -0500 Message-Id: <3.0.1.32.19971111160051.00a43a50@192.67.184.65> X-Sender: siegel@192.67.184.65 X-Mailer: Windows Eudora Pro Version 3.0.1 (32) Date: Tue, 11 Nov 1997 16:00:51 -0500 To: Gerald.Loeffler@univie.ac.at From: Jon Siegel Subject: Re: OMG Life Sciences Effort Cc: biowidgets-consortium@fruitfly.BDGP.Berkeley.EDU, javachem@wag.caltech.edu, bioobjects@ebi.ac.uk, chemistry@www.ccl.net, lifesciences@omg.org In-Reply-To: <34689E04.34C4ECE9@univie.ac.at> References: <3.0.1.32.19971111100632.00a2b6a0@192.67.184.65> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello, Gerald and all -- Good questions both, but properly addressed to the group since it is they (perhaps including you, Gerald?) who determine the direction and speed of your work. Could someone please help Gerald with these queries? Thanks and see you in New Brunswick -- Jon Siegel OMG DTC Chair At 07:03 PM 11/11/97 +0100, Gerald Loeffler wrote: >Two things: > >1) Just a remark - without becoming political, which is honestly not what I want: > >What is striking to me is the apparent absence of any representative of the NCBI in >the OMG Life Sciences Group (am I wrong?). Without judging the scientific influence of >any of the organizations involved in the OMG effort, I wonder how a standard in >bioinformatics can be developed without support and contribution from the NCBI?! > >2) I started this thread by a question mainly about class libraries for sequences and >homology searches. When can we expect an early specification or even implementation >from the OMG Life Sciences Group? > > cheers, > gerald > >-- >Gerald Loeffler >PostDoc in Theoretical Biophysics > >EMail: Gerald.Loeffler@univie.ac.at >WWW: http://www.imp.univie.ac.at/Loeffler/ >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 > > > > ================================================================== Jon Siegel Phone: 508-820-4300 X124 Director, Domain Technology Fax: 508-820-4303 Object Management Group 492 Old Connecticut Path email: siegel@omg.org Framingham, Massachusetts 01701 USA http://www.omg.org ================================================================== From herbert.homeier@chemie.uni-regensburg.de Wed Nov 5 07:35:18 1997 Received: from rrzs2.rz.uni-regensburg.de for herbert.homeier@chemie.uni-regensburg.de by www.ccl.net (8.8.3/950822.1) id GAA07390; Wed, 5 Nov 1997 06:59:41 -0500 (EST) Received: from rchs1.chemie.uni-regensburg.de (rchs1.chemie.uni-regensburg.de [132.199.48.1]) by rrzs2.rz.uni-regensburg.de (8.8.5/8.8.5) with SMTP id MAA16534; Wed, 5 Nov 1997 12:59:20 +0100 (MET) Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA10474; Wed, 5 Nov 97 13:51:13 +0100 Date: Wed, 5 Nov 97 13:51:13 +0100 From: Herbert Homeier t4720 Message-Id: <9711051251.AA10474@rchs1.chemie.uni-regensburg.de> To: elewars@alchemy.chem.utoronto.ca, chemistry@www.ccl.net Subject: Re: CCL:G:OVERLAP INTEGRAL AND SLATER FUNNC Reply-To: herbert.homeier@na-net.ornl.gov Hello, > Date: Sun, 2 Nov 1997 16:54:11 -0500 (EST) > From: "E. Lewars" > Message-Id: <199711022154.QAA26919@alchemy.chem.utoronto.ca> > To: chemistry@www.ccl.net > Subject: CCL:G:OVERLAP INTEGRAL AND SLATER FUNNC > > 1997 Nov 2 > > SLATER OVERLAP INTEGRALS > >From E. Lewars > To CCL > > Hello, > > There is some info' about overlap integrals and Slater functions that I am > finding it hard to dig out of the literature. I should state at the outset > that _I know_: > > that there are programs for calculating overlap integrals > > that in most molecular quantum chem Gaussian functions, not Slater > functions, > are used > > that Mulliken et al published a long paper (J Chem Phys, 17 (1949) > 1248-1267)) > with recipes for calculating overlap integrals it contains several errors, be careful. > > that all kinds of tricks exist for "simplifying" the calculation of overlap > integrals > --------- > OK, but what I want is simply this: > > (1) In the molecule H-He+ (yes, protonated helium) if the H nucleus has > Cartesians H1(x_1, y_1, z_1) and the He nucleus He2(x_2, y_2, z_2), > where the coordinates are in Angstroms (_not_ atomic units or Bohrs) > > and if we write > > for H: phi_1 = a_1 exp{b_1[(x-x_1)^2 + (y-y_1)^2 + (z-z_1)^2]^1/2} > and for He: phi_2 = a_2 exp{b_2[(x-x_2)^2 + (y-y_2)^2 + (z-z_2)^2]^1/2} Please check the "classical" paper E.Clementi and C. Roetti, At. Data & Nucl. Data Tables 14 (1974) 177 > > (usually a is expressed in terms of zeta and pi, b = -zeta, and > the variable is a radius vector r) > QUESTION: what are a_1 and b_1, as numbers, not Greek letters? > what are a_2,and b_2 as numbers, not Greek letters? > (i.e a_1 = 0.5647 or whatever, etc etc (4 decimals). > > S_12 = the triple integral from 0--> infinity of phi_1.phi_2 dxdydz > must = the correct overlap, if the six Cartesian coordinates are in > Angstroms. And of course integral of S_11 = S_22 = 1. > > (2) If (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, 0.800), > (0.800 Angstroms) what is S_12 (as a number, e.g 0.4273 or whatever)? > > (3) For (x_1, y_1, z_1) = (0, 0, 0) and (x_2, y_2, z_2) = (0, 0, d), > is there a simple function S_12 = f(d) ? (for H, He? for any two > 1s orbitals)? Of course f will depend parametrically on the a's and b's. The answer to your last question is given below in form of some programs for int( exp(-alpha*r) * exp(-beta*abs(\vec r -\vec R) d^3 r). But be careful for alpha approx beta, especially for small R>0. (cancelling singularities, alpha=1.000, beta=1.001, R=0.001 yield overlap integral >1 for normalized 1s functions (which is wrong!), The program in package S_INT (Comput Phys Commun 72 (1992) 269) is correct in this case.) Geometry should only enter as distance of the centers for s orbitals. There is a forms-based web interface to the fortran programs at http://www.chemie.uni-regensburg.de/~hoh05008/form-Soverlap.html Good luck for your investigations and best regards Herbert Homeier ---------------- C program ------------------------- double S(alpha,beta,R) double alpha; double beta; double R; { if (R == 0) return(8*0.3141592653589793E1/pow(alpha+beta,3)); else if (alpha != beta) return(8*0.3141592653589793E1*(-4*alpha*beta+4*exp(-(alpha-beta)*R)*alpha *beta-exp(-(alpha-beta)*R)*R*beta*beta*beta+R*alpha*alpha*alpha-R*alpha*beta* beta+exp(-(alpha-beta)*R)*R*alpha*alpha*beta)*exp(-R*beta)/R/pow(alpha+beta,3)/ pow(alpha-beta,3)); else return((R*R*alpha*alpha/3+1+R*alpha)*0.3141592653589793E1*exp(-R*alpha)/( alpha*alpha*alpha)); } -------------- maple procedure S:= proc(alpha, beta, R) if R = 0 then 8*Pi/(alpha + beta)^3 elif alpha <> beta then 8*Pi*(-4*alpha*beta + 4*exp(- (alpha - beta)*R)*alpha*beta - exp(- (alpha - beta)*R)*R*beta^3 + R*alpha^3 - R*alpha*beta^2 + exp(- (alpha - beta)*R)*R*alpha^2*beta)*exp(- R*beta)/(R*(alpha + beta)^3*(alpha - beta)^3) else (1/3*R^2*alpha^2 + 1 + R*alpha)*Pi*exp(- R*alpha)/alpha^3 fi end; --------------- f77 program doubleprecision function S(alpha,beta,R) C C Author and Copyright: Herbert H. H. Homeier, 1997 C C Purpose: computes the three-dimensional integral C C int( exp(-alpha*r) * exp(-beta*|\vec r - \vec R|) d^3 r) C C Parameters: alpha > 0 C beta > 0 C R=|vec R| >=0 C C The restrictions are not checked by the function. C doubleprecision alpha doubleprecision beta doubleprecision R if (R .eq. 0.D0) then S = 8.D0*0.3141592653589793D1/(alpha+beta)**3.D0 else if (alpha .ne. beta) then S = 8.D0*0.3141592653589793D1*(-4.D0*alpha*beta+4.D0*exp(-(a #lpha-beta)*R)*alpha*beta-exp(-(alpha-beta)*R)*R*beta**3+R*alpha**3 #-R*alpha*beta**2+exp(-(alpha-beta)*R)*R*alpha**2*beta)*exp(-R*beta #)/R/(alpha+beta)**3.D0/(alpha-beta)**3.D0 else S = (R**2*alpha**2/3.D0+1.D0+R*alpha)*0.3141592653589793D1*e #xp(-R*alpha)/alpha**3 endif endif return end C program mainS C C Author and Copyright: Herbert H. H. Homeier, 1997 C C Purpose: Simple driver program for function S C double precision a,b,r,S,SS,SSS external S C input section read(*,*,ERR=99999,END=99999) a,b,r if(a.le.0.d0) goto 99999 if(b.le.0.d0) goto 99999 if(R.lt.0.d0) goto 99999 C compute overlap C C without normalization SS=S(a,b,r) C with normalization SSS=SS/0.3141592653589793D1*DSQRT(a*b)**3 C output section write(*,*) 'int(exp(-',a,'*sqrt(x**2+y**2+z**2))' write(*,*) ' *exp(-',b,'*sqrt(x**2+y**2+(z-',r,')**2))' write(*,*) ' dx dy dz ) = ' write(*,*) ' = ',SS write(*,*) write(*,*) 'int(exp(-',a,'*sqrt(x**2+y**2+z**2))' write(*,*) ' *exp(-',b,'*sqrt(x**2+y**2+(z-',r,')**2))' write(*,*) ' dx dy dz ) /Pi *(',a,'*',b,')**(3/2) = ' write(*,*) ' = ',SSS stop 99999 write(*,*) 'Input ends or errs' stop end -------------------------------------------------------------- Priv.-Doz. Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg, D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX: +49-941-943 4719/+49-941-943 2305 email: herbert.homeier@na-net.ornl.gov WWW: http://www.chemie.uni-regensburg.de/~hoh05008 PS: I tried to send more or less this message already yesterday. But it did not turn up in the CCL, so far. So please apologize if this is a duplicate. From sis@dmc22.com Wed Nov 5 10:38:52 1997 Received: from dfw-ix5.ix.netcom.com for sis@dmc22.com by www.ccl.net (8.8.3/950822.1) id JAA08335; Wed, 5 Nov 1997 09:49:51 -0500 (EST) From: Received: (from smap@localhost) by dfw-ix5.ix.netcom.com (8.8.4/8.8.4) id IAA29236 for ; Wed, 5 Nov 1997 08:47:43 -0600 (CST) Date: Wed, 5 Nov 1997 08:47:43 -0600 (CST) Message-Id: <199711051447.IAA29236@dfw-ix5.ix.netcom.com> Received: from trn-nj1-07.ix.netcom.com(206.214.121.39) by dfw-ix5.ix.netcom.com via smap (V1.3) id rma029164; Wed Nov 5 08:47:07 1997 To: chemistry@www.ccl.net Subject: Toxicology Proj Dir Needed I am looking for a Scientist to serve as the MSE (Medicines Safety Evaluation) Project Coordinator for assigned compounds, and represent MSE on International Product Development Teams. This person will coordinate toxicology development activities for compounds, review protocols, final reports, study documentation and Standard Operating Procedures to support the conduct of non-clinical toxicity studies, write and review regulatory submissions (e.g., Investigational New Drug Application and New Drug Applications) and answers to written questions from the FDA and other international regulatory authorities. We require a wide understanding of toxicology and its customer supplier interfaces with R&D, the ability to foster networks within the organization and with national and international toxicology circles. This person should have the technical knowledge in conducting toxicity studies with laboratory animals, especially rodents and dogs. A BA/BS degree with 7 years experience as a Project Coordinator, or a MS degree with 6 years experience, or a Ph.D. and at least 3 years experience are ideal. We are a leading pharmaceutical company with research facilities in North Carolina and can provide excellent benefits (health insurance, dental, and vision plan, bonus program, paid vacation and more). Excellent compensation package. A high impact, high profile position with excellent opportunity for advancement. If you know anyone that may be interested please contact : Scott Shanes voice 609-584-8733 Ext. 218, fax: 609-584-9575 E-Mail sis@dmc22.com From gmercier@mail.med.upenn.edu Thu Nov 6 14:40:37 1997 Received: from mail.med.upenn.edu for gmercier@mail.med.upenn.edu by www.ccl.net (8.8.3/950822.1) id NAA07335; Thu, 6 Nov 1997 13:44:47 -0500 (EST) Received: (from gmercier@localhost) by mail.med.upenn.edu (8.8.6/8.8.6) id NAA09008 for chemistry@www.ccl.net; Thu, 6 Nov 1997 13:44:47 -0500 (EST) From: "Gustavo A. Mercier Jr" Message-Id: <199711061844.NAA09008@mail.med.upenn.edu> Subject: Dual PPro/PII, Linux, etc. To: chemistry@www.ccl.net Date: Thu, 6 Nov 1997 13:44:46 -0500 (EST) X-Mailer: ELM [version 2.4 PL23-upenn3.1] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi! A while back I asked about PPro/PII dual boxes running Linux for CC applications. I got several interesting replies that are very helpful. (See below!) There are two vendors that specialize in setting boxes like these: www.swt.com www.varesearch.com They will set up the system including activating SMP for parallel applications. Obviously you still need some message passing system, etc. and compilers. (See comments below.) The real twist to a dual system is the following: 1) My computer vendor indicated that Intel has an announcement recommending that PII chips not be used in dual systems due to some bug in running with dual mode. I did not get messages from people running dual PII, but dual PPro's only. Has anybody heard anything about the PIIx2 systems problems? Looks like for now PProx2 work. VA Research report impressive performance in PProx2 using the fx chip set and scsii disks. Their prices are also very reasonable. (I must thank the people in Advanced Computech, www.advancedcomputech.com, who warned me about this issue before I bought the board making me cancel the entire order!) 2) Also, proper cooling is important, particularly if you overclock! A very useful site is www.sysopt.com where you will find info on optimizing your box, and even a survey of the experience web users had in buy from several vendors. (AC received top honors here!) 3) SMP under Linux is still under development. You have to recompile Linux with the proper changes in the makefile. SWT and VAResearch will do this for you. I hope this helps! Bye! ----- Messages below ------ > I am in the market for a PC-Linux box to use with MD & DFT > applications, adf, amber, and moldy, primarily. I am using Turbomole & adf & gaussian94 under Linux. I do prefer Turbomole however, mostly, for execution speed due to its auxiliary base model for the calculation of Coulombic terms in its RIDFT (DFT) module. The gradient module runs also in parallel. By the way I have heard that Oxford Molecular's Unichem for WinNT 4.0 will also be out soon - this will also run in parallel. > I wonder if anybody has any experience trying to run > in parallel under (a measley) dual PPro/PII system using Linux. PII's are definitely faster (see below) Yipp, I just got the new parallelized ridft code for Linux from Ahlrichs group - I don't quite know whether that is an official version yet. My platforms include: Dual PPro 2x 200 MHz-256 KB cache, 128 MB RAM Dual PPro 2x 166 MHz-256 KB cache, 256 MB RAM (at home my own machine) PII 266 MHz-512K cache, 64 MB RAM 30% faster than single PPro 200 MHz PPro 1x 133 MHz (no typo), 64 MB The Turbomole program uses MPI and parallel speedup on the dual machine itself is ca. >= 80%. I have also tried running it on a network (10MB Ethernet) with 2 machines and have seen a speedup from 3min30 to 2min30 (just one bench I haven't done more so far but might try it over the next weekend on 4 CPUs i.e. three machines) > I understand that under Linux you may not gain much in execution > speed. Any other alternatives? 1) not right 2) see above > Any fortran compiler that would be best for parallel execution > under Linux, if any? Portland group Fortran Compiler => best code ever as good as Intel's specfp95 reference compiler - it exists as f77 and hpf Fortran (parallel) and also allows for autoparallelization. Code is fabulous and compiler fast: price great f77: $299 Turbomole speedup 2x compared to g77 !!! no typo !(pls don't quote that on the net - since it is still inofficial) f77 and hpf (High performance Fortran) $499. check www.pgroup.com for more info. This is also the compiler used in Sandia National Labs x1000 Intel PPro machine > I will summarize to the list if there is interest! Sure is. Hope this helps, let me know if you need more info. By the way LINUX/Turbomole was ca. $700 for academics. Peter P.S. By the way - what kind of sofware rns on the Beowulf? ----------------------------- Dr. Peter Burger Anorganisch-Chemisches Institut Universitaet Zuerich 8057 Zuerich Switzerland chburger@aci.unizh.ch ------------------------------------------------------------------------ Hi! You really DO want to talk to Michael Colvin at Sandia.. He'll give you executables for ab initio.... Tell him what you're interested in... He'll have the code...NT or LINUX Colvin@gutenburg.llnl.gov 510-423-9177 Regards, John -- ************************************ * John McKelvey * * Computational Science Laboratory * * Imaging Research and Development * * Building 83 * * Research Laboratories * * Eastman Kodak Company * * Rochester, NY 14650-2216 * * (V)716-477-3335 * * (F)716-722-2327 * * (E)McKelvey@Kodak.COM * ************************************ ---------------------------------------------------------------------- Hi, I'm intersted in seeing what responses you get to your question about dual Pentiums with Linux. I have ordered one from SWT (www.swt.com). They install Linux for you and have reasonable prices. Windows NT has support for SMP. Someone here at Northwestern runs Gaussian in the background while wordprocessing under NT. They said it was too painful to do that before they got the dual Pentium system. Gary Kedziora ---------------------------------------------------------------------- Hi, I noticed your post to the CCL about a Pentium/LINUX box for running DFT and MD. I don't have much to say about the dual motherboard other than I am very interested in your results. However, we at the Ziegler group just got a PPRO 200 at it runs very well. It is so far the best price/performance ratio machine for running ADF. Also, we found out that you get the theoretical performance without the need of an expensive SCSI drive. When you set up the machine for ADF, give me a shout. I just set it up with Redhat 4.2 linux and there is a bunch of issues that come up for getting ADF running on this. Tom ******************************************************************************** * Tom Woo voice:(403) 220-7176 * * The Ziegler Group fax: (403) 289-9488 * * Department of Chemistry email: tkwoo@zinc.chem.ucalgary.ca * * University of Calgary homepage: http://www.ucalgary.ca/~tkwoo * * 2500 University Drive, N.W. room: SB 427 * * CALGARY, Alberta, Canada, T2N 1N4 * ******************************************************************************** ------------------------------------------------------------------------------- Dear Dr. Mercier, > I wonder if anybody has any experience trying to run > in parallel under (a measley) dual PPro/PII system using Linux. I have a 2xPPro and a 1xPentium, so I have some experience. > My question is limited to systems with > two chips in a single motherboard using off the shelve LInux, say > Red Hat 4.2, and public domain software for message passing. You have to recompile the kernel. The SMP part is still considered to be experimental. You edit the Makefile in /usr/src/linux. Be aware that some kernels (2.0.30 if I remember correctly) might be a bit unstable. It is said that cheap S3 based graphics card is a ploblem, but I haven't experienced any problems. I have compiled and used PVM with no problem. Originally my MD program was written for a IBM SP computer, but I didn't have to do any porting! MPI should be working as well; I haven't tried, but I frequently talk with one who does. Best wishes and happy computing Kenneth Geisshirt +-------------------------------------------------------------+ | Kenneth Geisshirt Ph.D.-student | | Dept. of Life Sciences and Chemistry Roskilde University | +-------------------------------------------------------------+ | Viva la penguin | +-------------------------------------------------------------+ ------------------------------------------------------------------- Gustavo A. Mercier Jr wrote: > I wonder if anybody has any experience trying to run > in parallel under (a measley) dual PPro/PII system using Linux. We have build up a cluster of 16 Dual Pentium Pro machines running under RedHat 4.2. For more information about the programs we run on this platform take a look at our web site http://terra.chem.emory.edu. Hope this helps. Stefan +----------------------------------------------------------------------+ Dr. Stefan Dapprich Philipps-Universitaet Marburg, FB Chemie Hans-Meerwein-Str. D-35032 Marburg Phone +49-6421-28-5561 Fax +49-6421-28-2189 Email dapprich@mailer.uni-marburg.de URL http://euch4m.chem.emory.edu/~dapprich "to be or nut^H^H -- sh^Gt, how do I delete.^?^? Oh No Oh NO^D^D -- How do I get out of this thing anyway ^C^C^C Kill it ^Z^Z^Z (mumble mumble) Bus error (core dumped) +----------------------------------------------------------------------+ ----------------------------------------------------------------------- Hi Gustavo, I think an SMP Linux box won't help you unless those programs are multithreading... There is a code freeze for kernel 2.2 in the making. Among other things, 2.2 is supposed to have much better SMP support. There are commercial (and free) fortran compilers for Linux. Check out the GNU project's g77, NAG (http://www.nag.com), and the Portland Group (http://www.pgroup.com) which has auto-parallelization). good luck, Rich ------- End of Messages ---------------- -- ("`-/")_.-'"``-._ Gustavo A. Mercier,Jr.,MD,PhD (. . `) -._ )-;-,_() Division of Nuclear Medicine (v_,)' _ )`-.\ ``- Dept. of Radiology _;- _,-_/ / ((,' University of Pennsylvania ((,.-' ((,/ 3400 Spruce St. gmercier@mail.med.upenn.edu Philadelphia, PA 19104 215-662-3069/3091 fax: 215-349-5843 From duca@uic.edu Thu Nov 6 16:31:22 1997 Received: from tigger.cc.uic.edu for duca@uic.edu by www.ccl.net (8.8.3/950822.1) id QAA07849; Thu, 6 Nov 1997 16:04:17 -0500 (EST) Received: from localhost (duca@localhost) by tigger.cc.uic.edu (8.8.5/8.8.5) with SMTP id PAA59246 for ; Thu, 6 Nov 1997 15:04:19 -0600 X-Authentication-Warning: tigger.cc.uic.edu: duca owned process doing -bs Date: Thu, 6 Nov 1997 15:04:18 -0600 (CST) From: Jose Santiago Duca X-Sender: duca@tigger.cc.uic.edu To: chemistry@www.ccl.net Subject: average structures Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers, I'd like to know which is (are) the criteria to found an average structure once a molecular dynamics is run on a flexible system (for instance, a polyethylene chain with 50 ethylene units) starting the MD from different seed numbers. If the chain is flexible, a lot of different conformations of similar energies can be reached depending on their initial random velocities, after e.g. 50 ps. keeping the kinetic energy constant. Is there any "usual" convention about finding an average structure of this set of corformations? I know sometimes the standard deviation of the units' length is used. Do you have knowledge of any others? If you have any citation about it (or any comments or whatever), please let me know. Thanks a priori, Jose S. Duca From jmiller@sandcastle.cosc.brocku.ca Thu Nov 6 18:40:10 1997 Received: from spartan.ac.BrockU.CA for jmiller@sandcastle.cosc.brocku.ca by www.ccl.net (8.8.3/950822.1) id RAA08227; Thu, 6 Nov 1997 17:50:35 -0500 (EST) Received: from [139.57.81.109] (applepie.chem.BrockU.CA [139.57.81.109]) by spartan.ac.BrockU.CA (8.8.7/8.8.7) with ESMTP id RAA14807 for ; Thu, 6 Nov 1997 17:50:28 -0500 (EST) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 6 Nov 1997 17:50:52 -0500 To: chemistry@www.ccl.net From: Jack Martin Miller Subject: gears for old Mettler balances Please pass on to your experimental colleagues As a result of having perfectly good 30 year old Mettler analytical balances except for broken plastic gears our machine shop has developed a method for reparing them. Brock can thus now provide fixed gears for the old green and grey Mettler analytical balances. All we need is the broken gear, and the machine shop will provide a repaired one for about $100 Can.each. Jack Martin Miller Professor of Chemistry Adjunct Professor of Computer Science Brock University, St. Catharines, Ontario, Canada, L2S 3A1. Phone (905) 688 5550, ext 3402 FAX (905) 682 9020 e-mail jmiller@sandcastle.cosc.brocku.ca http://chemiris.labs.brocku.ca/~chemweb/faculty/miller/ From lavelle@mbi.ucla.edu Thu Nov 6 19:31:22 1997 Received: from rho.ben2.ucla.edu for lavelle@mbi.ucla.edu by www.ccl.net (8.8.3/950822.1) id TAA08742; Thu, 6 Nov 1997 19:30:03 -0500 (EST) 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 QAA82008; Thu, 6 Nov 1997 16:17:16 -0800 Received: from red5.mbi.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA17666; Thu, 6 Nov 1997 16:17:09 -0800 Message-Id: <3.0.32.19971106161943.00a1b930@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Thu, 06 Nov 1997 16:19:47 -0800 To: "C.F. Matta" , hyperchem@hyper.com, chemistry@www.ccl.net From: Laurence Lavelle Subject: Re: CCL:Hypechem Hardware Resources Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Hi C.F, Your question does not state which OS, and if you intend to use other software at the same time as HyperChem. I will assume (and recommend) that you are using NT Workstation and no other (large) software. HyperChem 5.02 is the fastest HyperCube offers for ab initio calculations. There are however, faster ab initio packages. HyperChem has options within ab initio that greatly reduce the RAM and virtual memory requirements. So 64MB of RAM and 200MB virtual memory would be fine for your calculations. To give you an example of what I mean by greatly reduced memory requirements with respect to the 2e-integrals: For a system with 731 (=m) basis functions. Not using direct SCF (more memory, less CPU time): # 2e- integrals = 3.5 x 10^10 and memory required = 571 GB But using direct SCF (less memory, more CPU time): The # 2e- integrals = m^2 log m = 1.5 MB So clearly you would use direct SCF. However I should also inform you that: The original required memory was 571 GB which on using the (much more) computationally intensive direct SCF was reduced to ~1.5 MB (depending on the 2e- integral cutoff point) and finally HC actually limits the total 2e- integral storage to 256KB of RAM, and if it is larger than 256KB it writes to HD. Although I have asked HyperCube why the 256KB RAM limitation, I have had no reply. So you don't need lots of RAM and virtual memory, what you need is fast RAM. In terms of HD's I recommend a fast (7200-10000RPM), large (~8GB, because you always need storage space) with 0.5 to 1MB buffer. Or start with one 4GB (similar specs) and add another HD when you need it. Here comes the bad news. If you want these jobs (70 atoms, using 6311++G** with ~650 basis functions) to converge in two days there is no PC (with HyperChem) available to do it. Which means you need a large capital expenditure to buy some non-Intel/AMD/Cyrix unix/NT machine (e.g. Digital Alpha 600MHz workstation, etc). However things would be different if HyperChem was a multi-threaded application. All the major vendors produce multi-CPU machines (NCR, HP, SGI, Digital, etc.) not to mention that one can order a multitude of inexpensive multi-CPU clones. In addition the strongest HyperChem user base is the PC or PC-workstation/server with MS-Windows as the OS. Windows NT (Workstation & Server) is one of the few OS's that utilizes multi-CPU hardware. Some of your options are: Spend 5 to 10 times more on a non-Intel unix/NT machine. Wait for HyperCube to release a multi-threaded version of HyperChem. **Buy a PC with a Pentium II, 300MHz processor with 512KB to 1MB L2 cache and wait twice as long for the results. **Best option. Laurence Lavelle At 09:49 AM 11/5/97 -0500, you wrote: > >Hi everybody, >I am planning to upgrade a machine with the intension to purchase >Hyperchem 05. I am interested to obtain highly accurate ab initio >wavefunctions medium-sized organic molecules (C,O,N,H) at a RHF >6-311++G**//6-31+G* level of theory). >Such molecules would have approx 70 atoms (including H), and using >6311++G** we are talking perhaps of 650 basis functions and perhaps some >1200 primitives. >What sort of CPU, RAM, virtual memory, and HD space should I aim at if I'd >like such a job to converge within a few days? >Thank you very much. >C.Matta >McMaster University, >Hamilton, Ontario, Canada.
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read.
From borghet@ipruniv.cce.unipr.it Thu Nov 6 23:31:24 1997 Received: from ipruniv.cce.unipr.it for borghet@ipruniv.cce.unipr.it by www.ccl.net (8.8.3/950822.1) id XAA09820; Thu, 6 Nov 1997 23:23:43 -0500 (EST) From: Received: by ipruniv.cce.unipr.it (AIX 3.2/UCB 5.64/4.03) id AA35094; Fri, 7 Nov 1997 05:23:40 +0100 Date: Fri, 7 Nov 1997 05:23:40 +0100 (NFT) Subject: Re: CCL:SCSI hard disk for DEC 3000-300 To: Trunec Cc: chemistry@www.ccl.net In-Reply-To: <199711061141.MAA13463@elanor.sci.muni.cz> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 6 Nov 1997, Trunec wrote: > Dear CCLers, > we have a workstation DEC 3000-300 with 32MB RAM and 1GB hard disk. > We would like to enlarge the RAM memory and buy second hard disk. > Unfortunately, the components from DEC are very expensive. So we would > like to buy SIMM modules for PC and a SCSI hard disk from IBM. > Has anybody experience with installation of non DEC RAM modules and > hard disks in DEC 3000-300 ? > Any help will be appreciated. > > David Trunec > Dep. of Physical Electronics > Masaryk University > Brno, Czech Republic > e-mail trunec@sci.muni.cz > Dear David Trunec, Last year I have the same problem with my Digital (Alphastation 255,32Mb of RAM and an hard disk of 1.05 Gb ); to solve my problem I've bought Kingstone RAM (128 MB) (this factory produce RAM for PC, laser printer and for almost all workstation) saving a lot of money. For the second hard disk I have bought a Quantum Fireball 4.3Gb. Hoping that this information could be useful for you and Best wishes Antonello Romani P.S. if you want to know something else mail me //\\______________________ \\// Antonello Romani Istituto di Patologia Generale Plesso Biotecnologico Integrato Facolta' di Medicina e Chirurgia Universita' degli Studi di Parma via Volturno,39 43100 - Parma ITALY E-Mail : A.Romani@leonardo.biomed.unipr.it _____________________________________//\\ \\// From ccl@www.ccl.net Fri Nov 7 16:31:37 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id QAA13374; Fri, 7 Nov 1997 16:10:23 -0500 (EST) Received: from europe.std.com for jle@world.std.com by bedrock.ccl.net (8.8.6/950822.1) id QAA28372; Fri, 7 Nov 1997 16:10:20 -0500 (EST) Received: from world.std.com by europe.std.com (8.7.6/BZS-8-1.0) id QAA03630; Fri, 7 Nov 1997 16:10:18 -0500 (EST) Received: by world.std.com (5.65c/Spike-2.0) id AA05897; Fri, 7 Nov 1997 16:10:17 -0500 Date: Fri, 7 Nov 1997 16:10:17 -0500 From: jle@world.std.com (Joe M Leonard) Message-Id: <199711072110.AA05897@world.std.com> To: chemistry@ccl.net Subject: PDB file format - residue sequence numbers in ATOM records... Folks, Does this particular integer field have to be included in all ATOM (and HETATM) records of a PDB file? Or, do things like end-groups have a blank for this field? Missing entries in data records strike me as odd, but that's probably the result of too much coding over the years... I would appreciate hearing from anybody expert in these matters. I've read the PDB documentation web page, and can't really see an obvious answer (and worry that holes are ok)... Thanks in advance, Joe Leonard jle@world.std.com From ccl@www.ccl.net Fri Nov 7 21:31:38 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id VAA14509; Fri, 7 Nov 1997 21:18:51 -0500 (EST) Received: from csb0.IPC.PKU.EDU.CN for mao@csb0.IPC.PKU.EDU.CN by bedrock.ccl.net (8.8.6/950822.1) id VAA03158; Fri, 7 Nov 1997 21:18:44 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@ccl.net id AA01839; Sat, 8 Nov 97 09:17:01 -0800 Date: Sat, 8 Nov 1997 09:17:01 -0800 (PST) From: Fenglou Mao To: herbert.homeier@na-net.ornl.gov Cc: CHEMISTRY@ccl.net, csc@imb-jena.de, noertema@theochem.tu-muenchen.de Subject: Re: CCL:Scientific Questions and Answers Database (#2) In-Reply-To: <9710301226.AA02422@rchs1.chemie.uni-regensburg.de> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 30 Oct 1997, Herbert Homeier t4720 wrote: > > Dear colleagues, > > I am sorry that there was an error in the announced URL for the > database. This has now been fixed. Sorry for any inconvenience > caused. And many thanks to all those who sent me the information > that the URL was faulty. > > Please try now > > http://www.chemie.uni-regensburg.de/pub/QA > I think what you have done will benefit all scientists. If you think I can help you, give me a mail! Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725 From lavelle@mbi.ucla.edu Sat Nov 8 22:31:50 1997 Received: from rho.ben2.ucla.edu for lavelle@mbi.ucla.edu by www.ccl.net (8.8.3/950822.1) id WAA18591; Sat, 8 Nov 1997 22:02:09 -0500 (EST) 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 TAA67758; Sat, 8 Nov 1997 19:02:10 -0800 Received: from red5.mbi.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA30874; Sat, 8 Nov 1997 19:02:10 -0800 Message-Id: <3.0.32.19971108190512.00a2a3d0@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Sat, 08 Nov 1997 19:05:12 -0800 To: hyperchem@hyper.com, chemistry@www.ccl.net From: Laurence Lavelle Subject: Improving ab initio computational speed Mime-Version: 1.0 Content-Type: text/enriched; charset="us-ascii" Two possible ways to speed up ab initio calculations are: 1) Use a bases set with fewer bases functions first. Then, after convergence, use a bases set with more bases functions. Repeat this process until convergence is obtained with the (largest) bases set that was originally intended. 2) Use the largest bases set with a higher 2e integral cuttoff point (e.g. 10^-7 Hartree) and after convergence decrease the 2e integral cuttoff point. Repeat until convergence is obtained with the originally intended 2e integral cuttoff point (e.g. 10^-11 Hartree). Do either of these approaches have potential downfalls. Is one approach better than the other? Thanks Laurence Lavelle
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read.
From toukie@zui.unizh.ch Sun Nov 9 07:31:57 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id HAA19711; Sun, 9 Nov 1997 07:24:14 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA04592; Sun, 9 Nov 1997 13:24:00 +0100 Message-Id: <3.0.3.32.19971109132643.00688474@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Sun, 09 Nov 1997 13:26:43 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: sec-butylphenols Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues; In connection with some calculations I am conducting on sec-butylphenols, I was able to find in the literature that (R)-o-sec-butylphenol is laevorotatory (sodium D-line) and that (S)-o-sec-butylphenol is dextrotatory. However, I could not find any information relating to the absolution configurations of m- or p-sec-butylphenols and their corresponding optical rotations. If anyone has access to such information, or would care to share their thoughts, ideas, or calculations on the possible correspondence between absolute configurations of the m- and p-sec-butylphenols and their optical rotations, I would be very glad to hear from you. Thanks in advance to all responders, S. Shapiro toukie@zui.unizh.ch From toukie@zui.unizh.ch Sun Nov 9 08:31:56 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id IAA19798; Sun, 9 Nov 1997 08:06:15 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA01639; Sun, 9 Nov 1997 14:05:58 +0100 Message-Id: <3.0.3.32.19971109140842.00687d00@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Sun, 09 Nov 1997 14:08:42 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Seeking GA regress. anal. software Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues; I am seeking software that will run on a PC fitted with Win95 (i.e., DOS, Win 3.x, Win95) that can perform a "best subsets" regression analysis using a genetic algorithm. The number of indepedent variables can range from 5 up to 100, depending upon the nature of the analysis. Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From toukie@zui.unizh.ch Sun Nov 9 08:32:00 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id HAA19765; Sun, 9 Nov 1997 07:52:21 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA05789; Sun, 9 Nov 1997 13:52:20 +0100 Message-Id: <3.0.3.32.19971109135504.00688474@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Sun, 09 Nov 1997 13:55:04 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Biomembrane orderliness/disorderliness Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues; I am seeking recent reviews and original articles dealing with the state of "orderliness" or "disorderliness" of biomembranes and how small moelcular weight compounds interact with the membrane per se (as opposed to, for example, ligand interactions with discrete receptors in or on the membrane) to either enhance or reduce that membrane's state of orderliness. I would especially value publications dealing with real biomembranes, particularly bacterial membranes; but reports covering artificial membranes are also very welcome. Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From turner@ocisgi28.unizh.ch Mon Nov 10 03:33:14 1997 Received: from ocisgi28.unizh.ch for turner@ocisgi28.unizh.ch by www.ccl.net (8.8.3/950822.1) id DAA22375; Mon, 10 Nov 1997 03:30:55 -0500 (EST) Received: from ocisgi28.unizh.ch (localhost [127.0.0.1]) by ocisgi28.unizh.ch (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id JAA12275 for ; Mon, 10 Nov 1997 09:30:42 +0100 Sender: turner@ocisgi28.unizh.ch Message-ID: <3466C631.510F5D1C@ocisgi28.unizh.ch> Date: Mon, 10 Nov 1997 09:30:41 +0100 From: Alexander J Turner Organization: OCI - University of Zurich X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: C++ summary Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! Thanks for all the info on C++. I enclose a summary covering several books. Best wishes Alex ############################################################################ Well, I can tell you what I used to learn C++ without any previous knowledge of C (but with experience with other programming languages): C++ Programming 101 by Greg Perry, published by SAMS Publishing. This is pretty much all I read, and I have been writing my own molecular dynamics code in C++ ever since then, so it must be pretty good. This book is at an introductory level, though, so depending on what you're looking for it may not be sufficient. Hope this helps. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Naoko Akiya nakiya@engin.umich.edu University of Michigan Dept. of Chemical Engineering phone (313) 764-7121 Ann Arbor, MI 48109-2136 fax (313) 763-0459 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= You might want to look at Scientific and Engineering C++ by J. Barton and L. Nachman. Addison-Wesley Publishing Co., ISBN # 0-201-53393-6 =================================================================== Enrico O. Purisima Biotechnology Research Institute e-mail: rico@bri.nrc.ca National Research Council of Canada phone : (514) 496-6343 6100 Royalmount Avenue fax : (514) 496-5143 Montreal, Quebec H4P 2R2 CANADA =================================================================== "cpluscplus.mal" 155 lines, 5453 characters > cat Suspended > jobs [1] - Suspended (tty input) rsh ocisgi15 /usr/programs/gv/gv [2] + Suspended cat > kill %2 > cat cpluscplus.mal Well, I can tell you what I used to learn C++ without any previous knowledge of C (but with experience with other programming languages): C++ Programming 101 by Greg Perry, published by SAMS Publishing. This is pretty much all I read, and I have been writing my own molecular dynamics code in C++ ever since then, so it must be pretty good. This book is at an introductory level, though, so depending on what you're looking for it may not be sufficient. Hope this helps. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Naoko Akiya nakiya@engin.umich.edu University of Michigan Dept. of Chemical Engineering phone (313) 764-7121 Ann Arbor, MI 48109-2136 fax (313) 763-0459 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= You might want to look at Scientific and Engineering C++ by J. Barton and L. Nachman. Addison-Wesley Publishing Co., ISBN # 0-201-53393-6 =================================================================== Enrico O. Purisima Biotechnology Research Institute e-mail: rico@bri.nrc.ca National Research Council of Canada phone : (514) 496-6343 6100 Royalmount Avenue fax : (514) 496-5143 Montreal, Quebec H4P 2R2 CANADA =================================================================== I used B.Stroustrup, "The C++ Programming Language", 2nd Ed., Addison-Wesley 1991 (it's the classic by the inventor of the language) and G.Buzzi-Ferraris, "From Fortran to C++: An Introduction to Oject-Oriented Programming Applied to Numerical Problems", Addison-Wesley 1991 or later Regards Guido Germano PhD student in Computational Chemistry Dipartimento di Chimica e Chimica Industriale e-mail germano@dcci.unipi.it Universita` di Pisa http://www.dcci.unipi.it/~germano Via Risorgimento 35 finger guido@hal.icqem.pi.cnr.it I-56126 Pisa phone +39-50-918.266, .295 or .239, fax .260 Professor Turner: There is an *excellent* book on C++ that I would recommend highly: "Practical C++ Programming" by Steve Oualline O'Reilly & Associates, Inc. 1995 (list price is 32.95 U.S. dollars) In general, computer books published by O'Reilly tend to be extremely well-written and user-friendly. Good luck! --Jack Hammer Graduate Student, Yale University Dear Dr.Turner, There is a lot of C++ tutorial on the net. You can find a list of them at http://www.yahoo.com/Computers_and_Internet/Programming_Languages/C_and_C__/ http://www.strangecreations.com/library/c/index.htm Hope this help. Yours, Somsak Tonmunphean. Hi I stumbled upon this WWW site which is quite a useful resource for C, C++, and Java. http://www.mit.edu:8001/afs/athena.mit.edu/user/t/h/thomasc/Public/ prog/index.html I still ended up buying a book though. (I'm not at my desk right now, so I can't remember which one.) Regards Rod ------------------------------------------------- R. M. Macrae Muon Science Laboratory Institute of Physical and Chemical Research (RIKEN) e-mail: macrae@rikaxp.riken.go.jp (normal) and : macrae@rikmtl.riken.go.jp (MIME-encoded) Tel : (81) 484 62 1111 ext 3336 Fax : (81) 484 62 4648 ------------------------------------------------- Stroutstrup's original book (the C++ programming language) is not bad for people who already know programmin in general - it teaches C++ without first teaching you what a variable is. There is a book called "Scientific and Engineering C++" (or a similar title), published by Addison-Wesley, which is of a more advanced nature (not necessarily a very good introduction, although it claims to be), but aims at the correct audience. It's probably easier to learn C++ with some well-written and meaningful code at hand. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- Hi Alex, the same question I asked half a year ago. I got the following answer : John J. Barton, Lee R. Nackman Scientific and Engineering C++ An Introduction with Advanced Techniques and Examples Addison Wesley Longman, Inc., 1994, Reprint March 1997 ISBN 0-201-53393-6 I think, it is really good. From the preface : "We expect the book to be useful to three (overlapping) groups : (1) Engineers and scientists who are experienced programmers in FORTRAN or C, (2) Professional programmers experienced in C or C++ lloking for a new systematic discussion of object-oriented programming in C++, and (3) C++ programmers interested in advanced examples useful as a basis for scientific and engineering programming." Hope this helps, Ciao Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst Research & Technology Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com ------------------------------------------------------------------- | Dr. Alexander J Turner | | | Universitaet Zuerich |Tel.: (41)-1-6354239 | | Organisch-Chemisches Institut|Fax: (41)-1-6356812 | | Winterthurerstrasse 190 | | | CH-8057 Zuerich |E-Mail: turner@ocisgi28.unizh.ch | | Switzerland | | ------------------------------------------------------------------- From rivelino@ufba.br Mon Nov 10 08:32:08 1997 Received: from lencois.ufba.br for rivelino@ufba.br by www.ccl.net (8.8.3/950822.1) id IAA23174; Mon, 10 Nov 1997 08:25:38 -0500 (EST) Received: from localhost by lencois.ufba.br (AIX 4.1/UCB 5.64/4.03) id AA26392; Mon, 10 Nov 1997 10:22:54 -0300 Date: Mon, 10 Nov 1997 10:22:53 -0300 (GRNLNDST) From: Roberto Rivelino de Melo Moreno To: chemistry@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Here are the answers about Li2 molecule data: ********************************************************************* I would look in Huber and Herzberg, "Constants of Diatomic Molecules". They have data. The book was published in 1979 so there may be newer references. The book contains data for 5 observed electronic states. Martin L. Sage Syracuse University ********************************************************************* Hello: In general, "K. P. Huber, and G. Herzberg, Molecular Spectra and Molecular Structure, Vol. IV., Constants of Diatomic Molecules, (Van Nostrand, Toronto, 1979)." is an extremely useful book. It is a compilation (and critical evaluation) of practically all known spectroscopic data for all diatomics UP TO 1979. For Li2, D_0=1.04(6) ; R_e=2.6729 Angstrom; and omega_e=351.4 cm-1. The latter is not from HH, it is from: D.D. Konalow and M. L. Olson, J. Chem. Phys. 71, 450 (1979). When I don't find the info on the diatomic I want, I try: M. D. Morse, Chem. Rev. 86, 1049-1109 (1986) [transition-metal dimers] or make an author search (mostly in J. Chem. Phys.) for articles having as co-author either: M. D. Morse or B. Simard or A. J. Merer or R. W. Field or C.W. Bauschlicher; I'm sure this is very incomplete list, but it's often a good starting point for the diatomics that I am interested in (transition metals). Cheers, Rene Fournier. *************************************************************************** Did you check Huber and Herzberg? The full title is something like "Constants of Diatomic Molecules" and it is volume 4 in the Herzberg set of classics. ************************************************************************** May be in : V. Bonacic-Koutecky, P. Fantucci and J. Koutecky, Chem. Rev. , 91, 1035 (1991). They deal wit Li clusters and possibly refer to experimental data. (I Cannot remember exactly) Hope it helps Pascal ***************************************************************************** If you do a web search on Li clusters, some references will come up. Irene Newhouse **************************************************************************** Sear Sir Probably, you can find some fererences in {Ab initio potential energy surface and vibrational energies of Li-over 3.} {Chemical Physics Letters, APR 25 1997 v 269 n1/2} Timothy G Shinkevich Postgraduate student of Laboratory of Spectrochemistry of Chemical dep. of St.Petersburg State University *************************************************************************** I think there are references for electron affinity and UV spectra of diatomic molecules in the CRC Handbook of Chemistry and Physics. *************************************************************************** Thanks all. From duca@tigger.cc.uic.edu Tue Nov 11 19:32:27 1997 Received: from tigger.cc.uic.edu for duca@tigger.cc.uic.edu by www.ccl.net (8.8.3/950822.1) id SAA07273; Tue, 11 Nov 1997 18:46:21 -0500 (EST) Received: from tigger.cc.uic.edu (SLIP5B-14.DIALIN.UIC.EDU [128.248.28.130]) by tigger.cc.uic.edu (8.8.5/8.8.5) with ESMTP id RAA395402 for ; Tue, 11 Nov 1997 17:46:18 -0600 Message-ID: <3468EE20.F9C42D58@tigger.cc.uic.edu> Date: Tue, 11 Nov 1997 17:45:36 -0600 From: "José Santiago Duca" X-Mailer: Mozilla 4.03 [en] (Win95; I) MIME-Version: 1.0 To: CCL Subject: average structures Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCLers, I'd like to know which is (are) the criteria to found an average structure once a molecular dynamics is run out on a flexible system (for instance, a polyethylene chain with 50 ethylene units) starting the MD from different seed numbers. If the chain is flexible, a lot of different conformations of similar energies can be reached depending on their initial random velocities, after e.g. 50 ps. and keeping the kinetic energy constant. Is there any "usual" convention about finding an average structure of this set of corformations? I know sometimes the standard deviation of the units' length is used. Do you have knowledge of any others? If you have any citation about it (or any comments or whatever), please let me know. Thanks a priori, Jose S. Duca From qiang@tammy.harvard.edu Tue Nov 11 19:39:40 1997 Received: from tammy.harvard.edu for qiang@tammy.harvard.edu by www.ccl.net (8.8.3/950822.1) id RAA05814; Tue, 11 Nov 1997 17:35:56 -0500 (EST) Received: from topanga.harvard.edu (topanga [128.103.92.179]) by tammy.harvard.edu (8.8.2/8.8.2) with ESMTP id RAA01548 for ; Tue, 11 Nov 1997 17:41:57 -0500 (EST) Received: from localhost (qiang@localhost) by topanga.harvard.edu (8.8.2/8.8.2) with SMTP id RAA03108 for ; Tue, 11 Nov 1997 17:30:36 -0500 (EST) Date: Tue, 11 Nov 1997 17:30:35 -0500 (EST) From: Qiang Cui To: chemistry@www.ccl.net Subject: cavity choice in SCRF for a reaction... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, folks. A simple question here concernining the choice of cavity in SCRF calculations for a chemical reaction in solution. Put it in concise words, should one choose different cavity radius for the intermediates and transition states involved in a reaction? One might argue that choosing a common radius is more consistent, especially if the solute is charged, 'cause otherwise the Born term is not even the same for structures with the same charge. On the other hand, since the molecule does change its conformation as the reaction proceeds, it might be reasonable to use different radius for structures of different size and all.... So what choice should I make? Any systematic studies? Suggestions? Thanks for ur time. ______________________________________________________________ Qiang Cui Dept. of Chem. Harvard Univ. 65 Dane Street 12 Oxford St. Cambridge, MA 02138 Somerville, MA 02143 (617)-495-1775 (617)-623-5123 (617)-495-8997 http://tswww.cc.emory.edu/~qcui ______________________________________________________________