From Krys.Radacki@ac.rwth-aachen.de Tue Oct 7 03:29:04 1997 Received: from mail.rwth-aachen.de for Krys.Radacki@ac.rwth-aachen.de by www.ccl.net (8.8.3/950822.1) id DAA23962; Tue, 7 Oct 1997 03:06:35 -0400 (EDT) Received: from 407L.ac.rwth-aachen.de (r304.ac.RWTH-Aachen.DE) by mail (PMDF V5.0-8 #23726) id <01IOIQ6XB16O8WVYJT@mail> for chemistry@www.ccl.net; Tue, 07 Oct 1997 09:06:37 +0200 Date: Tue, 07 Oct 1997 09:06:11 +0100 From: Krzysztof Radacki Subject: 3D probability X-Sender: kradacki@mail.rwth-aachen.de To: chemistry@www.ccl.net Message-id: <3.0.3.32.19971007090611.00794640@mail.rwth-aachen.de> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Dear Colleagues, sorry for my unknowledge and maybe basic question (but if I knew the answer, I wouldn't ask). Let me describe my question. I have 10 000 cartessian points (X,Y,Z - known) in space. 1. How can I calculate 3D function describing probability of finding point in this space? 2. How can I plot 3D shape closing space with probability bigger than f.e. 50%. 3. What disciplin describe this question (I know generaly it's probability caclulation, but something more preciss - where can I try to look for it)? 4. Is there free available algorithm to make one of this two steps? If someone could answer I would apreciate. Krzys Radacki _________________________---------------------------------------------------- ------------------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE --- ---------------------------------------------------------------------------- - From schiffer@h1tw0036.hoechst.com Tue Oct 7 03:55:37 1997 Received: from www.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id DAA23973; Tue, 7 Oct 1997 03:07:26 -0400 (EDT) Received: by www.hoechst.com id JAA10153; Tue, 7 Oct 1997 09:07:13 +0200 Received: from unknown(134.81.76.36) by www id sma010120; Tue Oct 7 09:06:36 1997 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id JAA10236; Tue, 7 Oct 1997 09:03:59 +0200 Message-ID: <3439DEDC.41C6@h1tw0036.hoechst.com> Date: Tue, 07 Oct 1997 09:03:56 +0200 From: "Dr. Heinz Schiffer" Organization: Hoechst Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Hu Hao CC: Computational Chemistry List Subject: DFT and H2O Dimer References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hu Hao wrote: > > Dear CCLers, > > Weeks ago I've posted a mail about the DeFT optimization of water > dimer. Thanks for replies from Dr. Frederic A. Van-Catledge and > Dr. Rudolf Herrmann. > > I have solved the problem now. There are two main reasons responsible > to the results. > > The first is the basis sets used. The problem could be partly solved > by using larger basis sets, e.g., using DZVP4 or TZVP basis as AO > basis, and A3 or A4 basis as auxiliary basis. > > The second is as what Dr. Rudolf Herrmann said : "The functionals > currently available for DF calculations are not meant to treat > long range interactions such as Van der Waals forces, which should > be highly important for your water dimer. DFT will be well suited > for, lets say, an ice crystal, but not for this case of a water > dimer." It seems that the system of water dimer needs careful > consideration when studied. > > Sincerely > > Hao Hu Hi CCL'ers, I am not d'accord with Rudolf Herrmann's statement, that DFT is not suitable for the water dimer, because "DFT methods are not meant to treat long range interactions such as van der Waals forces". The electrostatic part of the intermolecular interaction ist really the most long range part and is treated the same way in DFT as in conventional ab initio methods. What is really missing is Dispersion, which is important for the interaction of non-polar molecules like hydrocarbons and esp. for aromatic systems. Therefore the interactions in the water dimer, which are dominated by the electrostatic and polarization part of the interaction (i.e. H-bonds), are very well described by DFT methods, like BP, BLYP, B3LYP, etc. (not LDA !, but LDA is not DFT). On the other hand, the benzene dimer ( and of course all noble gas dimers ) is only poorly described by DFT methods. Best (!!!!) references : Michiel Sprik, Huerg Hutter, Michele Parrinello Ab initio molecular dynamics simulation of liquid water: Comparison of three gradient-corrected density functionals J. Chem. Phys. 105(3) (1996) 1142-1152 ( It is not only about liquid water, nearly half of the paper is about the water dimer ) Evert Jan Meijer and Michiel Sprik A density-functional study of the intermolecular interactions of benzene J. Chem. Phys. 105(19) (1996) 8684-8689 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 From Geoffrey@averell.umh.ac.be Tue Oct 7 06:29:04 1997 Received: from william.umh.ac.be for Geoffrey@averell.umh.ac.be by www.ccl.net (8.8.3/950822.1) id FAA24718; Tue, 7 Oct 1997 05:43:35 -0400 (EDT) Received: from localhost by william.umh.ac.be (AIX 4.1/UCB 5.64/4.03) id AA23132; Tue, 7 Oct 1997 11:44:19 +0200 Sender: Geoffrey@william.umh.ac.be Message-Id: <343A0473.41C6@averell.umh.ac.be> Date: Tue, 07 Oct 1997 11:44:19 +0200 From: Geoffrey Organization: Universite de Mons-Hainaut X-Mailer: Mozilla 3.0 (X11; I; AIX 1) Mime-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Convention for the d orbitals in G94 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, Is there anybody who could give me the matching between the labeling that Gaussian 94 uses to describe the LCAO coefficents of the d orbitals and the classical description of d orbitals (dZ2,dXY,DX2-Y2,...). I put below the labeling i got into the output of G94. D 0 -> D+1 -> D-1 -> D+2 -> D-2 -> I will sumarize the answers. Thank you very much. Geoffrey -- ================================================== Geoffrey Pourtois, PhD student - Assistant ------------------------------------------------ University of Mons-Hainaut Service de Chimie des Materiaux Nouveaux 20, Place du parc 7000 Mons Belgium ------------------------------------------------ e-mail : Geoffrey@averell.umh.ac.be tel : +32 65 37 3363 fax : +32 65 37 3366 http://morris.umh.ac.be/ ================================================== From Keith.Refson@earth.ox.ac.uk Tue Oct 7 07:29:06 1997 Received: from earth.ox.ac.uk for Keith.Refson@earth.ox.ac.uk by www.ccl.net (8.8.3/950822.1) id FAA24771; Tue, 7 Oct 1997 05:57:36 -0400 (EDT) Received: from metropolis.earth.ox.ac.uk (metropolis [163.1.22.59]) by earth.ox.ac.uk (8.8.5/8.8.5) with SMTP id KAA09202 for ; Tue, 7 Oct 1997 10:57:29 +0100 (BST) From: Keith Refson To: chemistry@www.ccl.net Subject: CCL:DFT and H2O Dimer In-Reply-To: <3439DEDC.41C6@h1tw0036.hoechst.com> References: <3439DEDC.41C6@h1tw0036.hoechst.com> X-Mailer: VM 6.30 under Emacs 19.34.1 Mime-Version: 1.0 (generated by tm-edit 7.92) Content-Type: text/plain; charset=US-ASCII Date: Tue, 07 Oct 1997 10:57:28 +0100 (BST) Message-Id: <19971007105728.541233.FMU22343@metropolis> Dr. Heinz Schiffer writes: > Therefore the interactions > in the water dimer, which are dominated by the electrostatic and > polarization part of the interaction (i.e. H-bonds), are very well > described by DFT methods, like BP, BLYP, B3LYP, etc. (not LDA !, but > LDA is not DFT). Perhaps I am being picky here but BP, BLYP, B3LYP etc are no more or no less DFT than LDA is. *All* are approximations to the "true" DFT exchange-correlation functional, which no-one knows -- it's just that some are better approximations than others. For the water dimer, and "nonbonded" fragments in general, the various GGAs are much closer to experiment than the LDA, and I agree with Heinz Schiffer that they are pretty reasonable. >On the other hand, the benzene dimer ( and of > course all noble gas dimers ) is only poorly described by DFT methods. Interesting. But the LDA makes a very good job of graphite, including the interlayer bonding, which goes to show that not every force that appears weak is really Van der Waals. Keith Refson -- ------------------------------------------------------------------------------ Email: Keith.Refson@ | Tel: +44 1865 272026 | Dr Keith Refson, | earth.ox.ac.uk | Fax: +44 1865 272072 | Dept of Earth Sciences | | Parks Road, Oxford OX1 3PR, UK| ------------------------------------------------------------------------------ From mbdtsnm@hpf.ch.man.ac.uk Tue Oct 7 08:16:40 1997 Received: from nessie.mcc.ac.uk for mbdtsnm@hpf.ch.man.ac.uk by www.ccl.net (8.8.3/950822.1) id HAA24997; Tue, 7 Oct 1997 07:10:02 -0400 (EDT) Received: from yama.mcc.ac.uk by nessie.mcc.ac.uk with SMTP (PP); Tue, 7 Oct 1997 12:09:31 +0100 Received: from serenity.mcc.ac.uk by yama.mcc.ac.uk with SMTP (PP); Tue, 7 Oct 1997 12:06:36 +0100 Received: from hpf.ch.man.ac.uk [130.88.12.28] by serenity.mcc.ac.uk with smtp (Exim 1.651 #21) id 0xIXTF-0005Zk-00; Tue, 7 Oct 1997 12:06:33 +0100 Date: Tue, 7 Oct 1997 12:05:20 +0100 Message-Id: <28762.9710071105@hpf.ch.man.ac.uk> From: "Nathaniel (noj) Malcolm" To: chemistry@www.ccl.net In-Reply-To: <3439DEDC.41C6@h1tw0036.hoechst.com> (schiffer@h1tw0036.hoechst.com) Subject: Re: CCL:DFT and H2O Dimer Reply-To: Noj.Malcolm@man.ac.uk >Hi CCL'ers, >I am not d'accord with Rudolf Herrmann's statement, that DFT is >not suitable for the water dimer, because "DFT methods are not meant >to treat long range interactions such as van der Waals forces". The >electrostatic part of the intermolecular interaction ist really the >most long range part and is treated the same way in DFT as in >conventional ab initio methods. What is really missing is Dispersion, >which is important for the interaction of non-polar molecules like >hydrocarbons and esp. for aromatic systems. Therefore the interactions >in the water dimer, which are dominated by the electrostatic and >polarization part of the interaction (i.e. H-bonds), are very well >described by DFT methods, like BP, BLYP, B3LYP, etc. (not LDA !, but >LDA is not DFT). On the other hand, the benzene dimer ( and of >course all noble gas dimers ) is only poorly described by DFT methods. >Best (!!!!) references : just a brief comment - on this comment to an earlier statement - i guess that one would generally be keen to use DFT (rather than HF say) due to its inclusion of correlation effects. As has also been discussed on the CCL recently the 'dispersion' effects are mainly driven by correlation effects therefore it seems to me that to say that DFT methods are 'good' for the water dimer problem because it gets most of the effects correct (except maybe dispersion, which should not be the main force) is placing too much faith in DFT - as it should really be able to deal with dispersion as well (if it got the correlation right). I guess my point is why not just use HF rather than DFT if its inclusion of correlation is not good enough to give a reasonable physical description of dispersion forces? noj p.s. i'm sure that DFT does in practice offer improvement over HF its just that i don't feel that Dr. Schiffer's argument explained why one should consider it a 'good' method for these interactions. (and i'm sure you could find the odd physicist out there who would be able to argue that LDA IS DFT - maybe just not 'good' DFT for chemists) -- Dr. Noj Malcolm Theory Group, Dept. of Chemistry, University of Manchester, Oxford Road, Manchester. M13 9PL e-mail noj.malcolm@man.ac.uk From seabra@NPD.UFPE.BR Tue Oct 7 08:29:12 1997 Received: from NPD1.NPD.UFPE.BR for seabra@NPD.UFPE.BR by www.ccl.net (8.8.3/950822.1) id IAA25298; Tue, 7 Oct 1997 08:12:32 -0400 (EDT) Received: from danon (danon.dqf.ufpe.br) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with ESMTP id <01IOIQCXFGG0000EHJ@NPD.UFPE.BR> for chemistry@www.ccl.net; Tue, 7 Oct 1997 09:11:27 GMT-3 Date: Tue, 07 Oct 1997 09:20:56 -0300 From: Gustavo de Miranda Seabra Subject: Langmuir films To: Computational Chemistry Letters Message-id: <343A2928.14807781@npd.ufpe.br> MIME-version: 1.0 X-Mailer: Mozilla 4.0 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Priority: 3 (Normal) Dear CCLers, Does anyone have info about calculations on Langmuir films? Thanks in advence, -- ----------------------------------------------------------------------------------- Gustavo de Miranda Seabra MSc Student in Chemistry E-Mail: seabra@npd.ufpe.br Universidade Federal de Pernambuco - Recife - Pernambuco - Brazil ----------------------------------------------------------------------------------- From jim.henshaw@aeat.co.uk Tue Oct 7 09:29:07 1997 Received: from aeat.co.uk for jim.henshaw@aeat.co.uk by www.ccl.net (8.8.3/950822.1) id JAA25698; Tue, 7 Oct 1997 09:22:19 -0400 (EDT) Received: from ccgate.aeat.co.uk by aeat.co.uk with SMTP (8.8.6/AEAT-GW-1.11) id OAA16472; Tue, 7 Oct 1997 14:22:17 +0100 (BST) sender jim.henshaw for Received: from ccMail by ccgate.aeat.co.uk (IMA Internet Exchange 2.02 Enterprise) id 43A378B0; Tue, 7 Oct 97 14:22:19 +0100 Mime-Version: 1.0 Date: Tue, 7 Oct 1997 14:18:40 +0100 Message-ID: <43A378B0.1268@ccgate.aeat.co.uk> From: jim.henshaw@aeat.co.uk (Jim Henshaw) Subject: Chem3D To: chemistry@www.ccl.net Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part Hi, I am a Chem3D user and I'm having problems running it on a Compaq Pentium II machine, under NT v4.0. My problem has to do with saving files after making a modification to a bond length. When I try to save the file I get an application error. I have contacted Cambridge Software who have suggested some fix's none of which have worked: switching off all other applications, running in VGA mode etc. Has anybody else had any problems similar to those I described ? Jim From balcells@quimica.UdL.es Tue Oct 7 10:29:13 1997 Received: from marraco.udl.es for balcells@quimica.UdL.es by www.ccl.net (8.8.3/950822.1) id JAA25901; Tue, 7 Oct 1997 09:54:53 -0400 (EDT) From: Received: from caragol.udl.es (caragol.udl.net [10.69.1.2]) by marraco.udl.es (8.8.5/8.8.5) with ESMTP id MAA20643 for ; Tue, 7 Oct 1997 12:40:12 -0100 (GMT) Received: from merce.etsea.udl.es (merce.etsea.udl.es [193.144.9.87]) by caragol.udl.es (8.7.5/8.7.3) with SMTP id MAA24233 for ; Tue, 7 Oct 1997 12:36:44 +0100 (WET DST) Message-Id: <199710071136.MAA24233@caragol.udl.es> Comments: Authenticated sender is To: CHEMISTRY@www.ccl.net Date: Tue, 7 Oct 1997 11:42:03 +0000 MIME-Version: 1.0 Content-type: Multipart/Mixed; boundary=Message-Boundary-24076 Subject: Conformational search with ChemPlus Priority: normal X-mailer: Pegasus Mail for Win32 (v2.53/R1) --Message-Boundary-24076 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body Merce Balcells Departament de Quimica, ETSEA Universitat de Lleida e-mail: balcells@quimica.udl.es --Message-Boundary-24076 Content-type: text/plain; charset=US-ASCII Content-disposition: inline Content-description: Attachment information. The following section of this message contains a file attachment prepared for transmission using the Internet MIME message format. If you are using Pegasus Mail, or any another MIME-compliant system, you should be able to save it or view it from within your mailer. If you cannot, please ask your system administrator for assistance. ---- File information ----------- File: CCLers1.doc Date: 7 Oct 1997, 11:28 Size: 2365 bytes. Type: MS-Richtext --Message-Boundary-24076 Content-type: Application/RTF; name=CCLers1.doc Content-disposition: attachment; filename="CCLers1.doc" Content-transfer-encoding: BASE64 e1xydGYxXGFuc2lcYW5zaWNwZzEyNTJcdWMxIFxkZWZmMFxkZWZsYW5nMTAzM1xkZWZsYW5n ZmUzMDgye1xmb250dGJse1xmMFxmcm9tYW5cZmNoYXJzZXQwXGZwcnEye1wqXHBhbm9zZSAw MjAyMDYwMzA1MDQwNTAyMDMwNH1UaW1lcyBOZXcgUm9tYW47fX17XGNvbG9ydGJsO1xyZWQw XGdyZWVuMFxibHVlMDtccmVkMFxncmVlbjBcYmx1ZTI1NTtccmVkMFxncmVlbjI1NVxibHVl MjU1O1xyZWQwXGdyZWVuMjU1XGJsdWUwO1xyZWQyNTVcZ3JlZW4wXGJsdWUyNTU7XHJlZDI1 NVxncmVlbjBcYmx1ZTA7XHJlZDI1NVxncmVlbjI1NVxibHVlMDtccmVkMjU1XGdyZWVuMjU1 XGJsdWUyNTU7XHJlZDBcZ3JlZW4wXGJsdWUxMjg7XHJlZDBcZ3JlZW4xMjhcYmx1ZTEyODtc cmVkMFxncmVlbjEyOFxibHVlMDtccmVkMTI4XGdyZWVuMFxibHVlMTI4O1xyZWQxMjhcZ3Jl ZW4wXGJsdWUwO1xyZWQxMjhcZ3JlZW4xMjhcYmx1ZTA7XHJlZDEyOFxncmVlbjEyOFxibHVl MTI4O1xyZWQxOTJcZ3JlZW4xOTJcYmx1ZTE5Mjt9e1xzdHlsZXNoZWV0e1xub3dpZGN0bHBh clx3aWRjdGxwYXJcYWRqdXN0cmlnaHQgXGxhbmcxMDI3XGNncmlkIFxzbmV4dDAgTm9ybWFs O317XCpcY3MxMCBcYWRkaXRpdmUgRGVmYXVsdCBQYXJhZ3JhcGggRm9udDt9fXtcaW5mb3tc dGl0bGUgRGVhciAgQ0NMZXJzLH17XGF1dGhvciBhfXtcb3BlcmF0b3IgYX17XGNyZWF0aW1c eXIxOTk3XG1vMTBcZHk3XGhyMTFcbWluMTR9e1xyZXZ0aW1ceXIxOTk3XG1vMTBcZHk3XGhy MTFcbWluMjh9e1x2ZXJzaW9uMX17XGVkbWluczEzfXtcbm9mcGFnZXMxfXtcbm9md29yZHMw fXtcbm9mY2hhcnMwfXtcKlxjb21wYW55IFVuaXZlcnNpdGF0IGRlIExsZWlkYX17XG5vZmNo YXJzd3MwfXtcdmVybjczfX1ccGFwZXJ3MTE5MDdccGFwZXJoMTY4NDBcbWFyZ2wyMTI2XG1h cmdyMTEzNFxtYXJndDE0MThcbWFyZ2IxMDIxIFxkZWZ0YWI3MDhcd2lkb3djdHJsXGZ0bmJq XGFlbmRkb2NcaHlwaGhvdHo0MjVcZm9ybXNoYWRlXHZpZXdraW5kNFx2aWV3c2NhbGU3NVxw Z2JyZHJoZWFkXHBnYnJkcmZvb3QgXGZldDBcc2VjdGQgXHBzejlcbGluZXgwXGhlYWRlcnkx NDQwXGZvb3RlcnkxNDQwXHNlY3RkZWZhdWx0Y2wge1wqXHBuc2VjbHZsMVxwbnVjcm1ccG5z dGFydDFccG5pbmRlbnQ3MjBccG5oYW5ne1xwbnR4dGEgLn19e1wqXHBuc2VjbHZsMlxwbnVj bHRyXHBuc3RhcnQxXHBuaW5kZW50NzIwXHBuaGFuZ3tccG50eHRhIC59fXtcKlxwbnNlY2x2 bDNccG5kZWNccG5zdGFydDFccG5pbmRlbnQ3MjBccG5oYW5ne1xwbnR4dGEgLn19e1wqXHBu c2VjbHZsNFxwbmxjbHRyXHBuc3RhcnQxXHBuaW5kZW50NzIwXHBuaGFuZ3tccG50eHRhICl9 fXtcKlxwbnNlY2x2bDVccG5kZWNccG5zdGFydDFccG5pbmRlbnQ3MjBccG5oYW5ne1xwbnR4 dGIgKH17XHBudHh0YSApfX17XCpccG5zZWNsdmw2XHBubGNsdHJccG5zdGFydDFccG5pbmRl bnQ3MjBccG5oYW5ne1xwbnR4dGIgKH17XHBudHh0YSApfX17XCpccG5zZWNsdmw3XHBubGNy bVxwbnN0YXJ0MVxwbmluZGVudDcyMFxwbmhhbmd7XHBudHh0YiAofXtccG50eHRhICl9fXtc KlxwbnNlY2x2bDhccG5sY2x0clxwbnN0YXJ0MVxwbmluZGVudDcyMFxwbmhhbmd7XHBudHh0 YiAofXtccG50eHRhICl9fXtcKlxwbnNlY2x2bDlccG5sY3JtXHBuc3RhcnQxXHBuaW5kZW50 NzIwXHBuaGFuZ3tccG50eHRiICh9e1xwbnR4dGEgKX19XHBhcmRccGxhaW4gXG5vd2lkY3Rs cGFyXHdpZGN0bHBhclxhZGp1c3RyaWdodCBcbGFuZzEwMjdcY2dyaWQge1xsYW5nMTAzMyBE ZWFyICBDQ0xlcnMsDQpccGFyICANClxwYXIgV2UgaGF2ZSByZWNlbnRseSBib3VnaHQgSHlw ZXJjaGVtIGFuZCBDaGVtUGx1cyBhbmQgSSBoYXZlIHNvbWUgcHJvYmxlbXMgd2l0aCBjb25m b3JtYXRpb25hbCBzZWFyY2guIFRoZXJlIGFyZSBtYW55IHBhcmFtZXRlcnMgdG8gc2V0IGlu IHRoZSBvcHRpb25zIG1lbnUgYW5kIElccnF1b3RlIG0gbm90IHN1cmUgaWYgSSBjaG9vc2Ug dGhlIGNvcnJlY3QgdmFsdWVzLiBJcyB0aGVyZSBhbnkgdHV0b3JpYWwgSSBjYW4gaGF2ZSB3 aGVyZSBJIGNhbiBzZWUgaG93IHRvIGRvIHRoYXQga2luZCBvZiBjYWxjdWxhdGlvbiB3aXRo IGEgc2ltcGxlIG1vbGVjdWxlIHdpdGggdGhlIGRpZmZlcmVudCBvcHRpb25zIGFuZCBhIGV4 cGxhbmF0aW9uIG9mIHRoZSBkaWZmZXJlbnQgY2hvaWNlcy4gKFRoZSBvbmUgaW4gdGhlIG1h bnVhbCBkb2VzblxycXVvdGUgdCByZXN1bHQgZW5vdWdoKS4NClxwYXIgU29ycnksIGp1c3Qg YSBiZWdpbm5lclxycXVvdGUgcyBwcm9ibGVtIHBlcmhhcHMgc28gZWFzeS4NClxwYXIgVGhh bmtzIGluIGFkdmFuY2UuDQpccGFyIE1lcmPoDQpccGFyIA0KXHBhciB9fQ== --Message-Boundary-24076-- From awittko@gwdg.de Tue Oct 7 11:29:09 1997 Received: from fw.gwdg.de for awittko@gwdg.de by www.ccl.net (8.8.3/950822.1) id KAA26105; Tue, 7 Oct 1997 10:30:24 -0400 (EDT) Received: from gwdu20.gwdg.de (actually gwdu20-eth.gwdg.de) by fw.gwdg.de with SMTP (PP); Tue, 7 Oct 1997 16:30:13 +0200 Received: from localhost by gwdu20.gwdg.de; (5.65v3.2/1.1.8.2/15Jan96-0158PM) id AA21425; Tue, 7 Oct 1997 16:29:56 +0200 Date: Tue, 7 Oct 1997 16:29:56 +0200 (MET DST) From: Alexander Wittkopp Reply-To: Alexander Wittkopp To: Computational Chemistry List Subject: DNMR5 (Dynamic NMR) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hey everybody, I am searching for the instructions of Binschs and Stephensons DNMR5-Program for the evaluation of Dynamic NMR-Studies. Maybe these instructions are somewhere in the net. Or: If you know another program which does the same job and which is a little bit more comfortable it would be great to hear about it. I will be grateful for any help. Thanks ******************************************************************************* Alexander Wittkopp Email: awittko@gwdg.de Institut fuer Organische Chemie URL : http://www.gwdg.de/~awittko Georg-August Universitaet Goettingen Tammannstrasse 2 D-37077 Goettingen Phone: +49-(0)551-393290 Germany FAX : +49-(0)551-399475 ****************************************************************************** From shenkin@still3.chem.columbia.edu Tue Oct 7 12:29:10 1997 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id LAA26749; Tue, 7 Oct 1997 11:37:09 -0400 (EDT) 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 LAA26809; Tue, 7 Oct 1997 11:36:58 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id LAA25603; Tue, 7 Oct 1997 11:36:49 -0400 From: "Peter Shenkin" Message-Id: <9710071136.ZM25601@still3.chem.columbia.edu> Date: Tue, 7 Oct 1997 11:36:48 -0400 In-Reply-To: Krzysztof Radacki "CCL:3D probability" (Oct 7, 9:06am) References: <3.0.3.32.19971007090611.00794640@mail.rwth-aachen.de> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Krzysztof Radacki , chemistry@www.ccl.net Subject: Re: CCL:3D probability Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Oct 7, 9:06am, Krzysztof Radacki wrote: > Subject: CCL:3D probability > I have 10 000 cartessian points (X,Y,Z - known) in space. > 1. How can I calculate 3D function describing probability > of finding point in this space? You want to convert a point sampling to a density distribution. One way to do this is to construct the Voronoi polyhedron about each point and ascribe a density of 1/its_volume to each polyhedral region. I think there are programs available the net that can determine the polyhedrons given a PDB file (others might be able to respond with detail). This doesn't work for the outermost points, which will have infinite volume (and give zero density). Anyway, if you normalize the density, you can view it as a probability distribution. Note that this density distribution is discrete: some region of space is tiled with these polhedra, and each polyhedron has a uniform density. You can ascribe each density to the location of the "central" point, and if you want a continuous distribution, use some method to interpolate density. This sort of thing is done by finite-element methods. You use different interpolation methods depending on whether the subsequent use of the distribution requires continuous function values only, or continuous function plus first derivative, etc. > 2. How can I plot 3D shape closing space with probability > bigger than f.e. 50%. This problem is not well defined. For instance, you can draw a plane parallel to the X axis and position it so that 50% of the points are on either side of it, then select either side of the plane as your solution. Or you can use the Y or Z axis. This is probably not what you have in mind. You probably have in mind a picture in which the density is highest in the middle and tails of gradually in all directions, and you want to draw your boundary along an isodensity countour so as to enclose the densest region. But your data may not look like this. Of course, if your data look *approximately* like this, you can fit them to some function that *does* look like this (for instance, a 3D gaussian), then do what I described. But you had better be sure this is a reasonable model for your data. > 3. What disciplin describe this question (I know generaly > it's probability caclulation, but something more > preciss - where can I try to look for it)? Finite element analysis; statistical pattern recognition. Hope this helps, -P. -- * ... and those who can remember the past are also condemned to repeat it.* * 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 postmaster@dera.gov.uk Sun Oct 5 19:28:46 1997 Received: from relay.mod.uk for postmaster@dera.gov.uk by www.ccl.net (8.8.3/950822.1) id TAA19408; Sun, 5 Oct 1997 19:23:09 -0400 (EDT) Received: from hermes.dra.hmg.gb by relay.mod.uk with local SMTP id ; Sun, 5 Oct 1997 23:35:10 +0100 Received: by hermes.dra.hmg.gb (MX V4.2 VAX) with SITE; Sun, 05 Oct 1997 23:34:54 GMT Received: from relay.mod.uk by hermes.dra.hmg.gb (MX V4.2 VAX) with SMTP; Tue, 30 Sep 1997 21:53:43 GMT Received: from www.ccl.net by relay.mod.uk with Internet SMTP id ; Tue, 30 Sep 1997 20:52:53 +0100 Received: for chemistry-request@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA10762; Tue, 30 Sep 1997 15:37:24 -0400 (EDT) Received: from DELTA.IS.TCU.EDU for MMENDEZ@DELTA.IS.TCU.EDU by www.ccl.net (8.8.3/950822.1) id PAA10645; Tue, 30 Sep 1997 15:19:03 -0400 (EDT) Received: from DELTA.IS.TCU.EDU by DELTA.IS.TCU.EDU (PMDF V5.1-7 #20456) id <01IO972MGV7S007NST@DELTA.IS.TCU.EDU> for chemistry@www.ccl.net; Tue, 30 Sep 1997 13:22:23 CDT Date: Tue, 30 Sep 1997 13:22:23 -0500 (CDT) From: "Miguel A. Mendez Rojas" Subject: CCL:New Issue of NetSci To: Network Science CC: chemistry@www.ccl.net Message-ID: The current issue of ALEPHZERO, Journal of Science Divulgation and Education is available in: http://rico.pue.udlap.mx/~aleph/index.html /////////////////////////////////////////////////////////////////////////// Miguel Angel Mendez Rojas, Editor & Director of the Chemistry Ph.D. Journal ALEPHZERO, of Sciences Texas Christian University Divulgation. Fort Worth, TX 76120 http://rico.pue.udlap.mx/~aleph http://delta.is.tcu.edu/~mmendez/ aleph@udlapvms.pue.udlap.mx e-mail: mmendez@delta.is.tcu.edu \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: MMENDEZ@DELTA.IS.TCU.EDU -- Original Sender From: Address: mmendez@DELTA.IS.TCU.EDU CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html From watts@gwinn.medc.umn.edu Sun Oct 5 20:28:47 1997 Received: from chet.medc.umn.edu for watts@gwinn.medc.umn.edu by www.ccl.net (8.8.3/950822.1) id UAA19608; Sun, 5 Oct 1997 20:09:59 -0400 (EDT) Received: from gwinn.medc.umn.edu (watts@gwinn.medc.umn.edu [160.94.158.215]) by chet.medc.umn.edu (8.8.5/8.8.5) with ESMTP id TAA07155 for ; Sun, 5 Oct 1997 19:09:57 -0500 (CDT) Received: from localhost (watts@localhost) by gwinn.medc.umn.edu (8.8.5/8.8.5) with SMTP id TAA08759 for ; Sun, 5 Oct 1997 19:09:54 -0500 (CDT) X-Authentication-Warning: gwinn.medc.umn.edu: watts owned process doing -bs Date: Sun, 5 Oct 1997 19:09:53 -0500 (CDT) From: Chuck Watts To: The Computational Chemistry List Subject: AMBER 4.1 Makefile Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL Members: Would anyone have a Makefile for AMBER v 4.1 on a Microway Alpha Station with Red Hat Linux and the Microway fortan compiler? Thanks, Charles R. Watts ************************************ Department of Medicinal Chemistry * * College of Pharmacy * An appeaser is one who feeds * University of Minnesota * a crocodile, hoping it will eat * 8-101 HSUF * him last. * 308 Harvard St. SE. * * Minneapolis, MN 55455 * -Winston Churchill * Phone: (612) 624-5486 * * Fax: (612) 626-4429 * * E-Mail: watts004@128.101.118.21 ************************************ From IJZERMAN@rulgca.LeidenUniv.nl Mon Oct 6 10:51:21 1997 Received: from rulgca.LEIDENUNIV.NL for IJZERMAN@rulgca.LeidenUniv.nl by www.ccl.net (8.8.3/950822.1) id KAA11719; Mon, 6 Oct 1997 10:09:54 -0400 (EDT) From: Received: from rulgca.leidenuniv.nl by rulgca.leidenuniv.nl (PMDF V5.1-5 #20174) id <01IOHQRUJPAO0003L7@rulgca.leidenuniv.nl> for chemistry@www.ccl.net; Mon, 6 Oct 1997 16:12:54 MET Date: Mon, 06 Oct 1997 16:12:54 +0100 (MET) Subject: software for elemental analysis To: chemistry@www.ccl.net Message-id: <01IOHQRUJT2A0003L7@rulgca.leidenuniv.nl> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII SEA: Sophisticated Elemental Analysis the fastest, easiest way to analyze elemental analyses SEA (Sophisticated Elemental Analysis) for Windows is an invaluable tool in dealing with all calculations concerning combustion or elemental analyses. 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Ad IJzerman (ijzerman@lacdr.leidenuniv.nl) From smb@smb.chem.niu.edu Tue Oct 7 18:38:03 1997 Received: from cz2.chem.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.8.3/950822.1) id RAA29893; Tue, 7 Oct 1997 17:52:40 -0400 (EDT) Received: from cz.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/920502.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA08917; Tue, 7 Oct 97 16:35:07 -0500 Received: from smb.chem.niu.edu by cz.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA18243; Tue, 7 Oct 97 16:51:17 -0500 Received: from smb by smb.chem.niu.edu via SMTP (940816.SGI.8.6.9/940406.SGI) for id QAA17501; Tue, 7 Oct 1997 16:49:01 -0500 Sender: smb@smb.chem.niu.edu Message-Id: <343AAE4D.7DE1@smb.chem.niu.edu> Date: Tue, 07 Oct 1997 16:49:01 -0500 From: Steven Bachrach X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP12) Mime-Version: 1.0 To: computational chemistry list Subject: ECCC4 Registration open and abstracts available Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit The Fourth Electronic Computational Chemistry Conference (ECCC-4) will be held during the month of November 1997. Registration is free and you can register now. Registration will allow you to participate in the discussions of the articles during the conference, and also to save any customizations you make. You can register now at http://hackberry.chem.niu.edu/ECCC4/ The abstracts of the 65 articles in the conference are also now available at the same address. We encourage all computational chemists to participate! Steve Bachrach on behalf of the Scientific Organizing Committee of ECCC4 -- Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802