From borghet@ipruniv.cce.unipr.it Thu Oct 2 01:27:59 1997 Received: from ipruniv.cce.unipr.it for borghet@ipruniv.cce.unipr.it by www.ccl.net (8.8.3/950822.1) id BAA22736; Thu, 2 Oct 1997 01:10:46 -0400 (EDT) From: Received: by ipruniv.cce.unipr.it (AIX 3.2/UCB 5.64/4.03) id AA20553; Thu, 2 Oct 1997 07:10:46 +0100 Date: Thu, 2 Oct 1997 07:10:45 +0100 (NFT) Subject: Molecular dynamics software To: Computational Chemistry Mailing List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi netters, I'm looking for a scalar (or parallel) free molecular dynamics software, running on DEC or Silicon,user friendly and able to manage easily thousand atoms (proteins). If someone knows some programs with these features, please mail me. Thanking in advance, all the people who answer me Your faithfully Antonello Romani //\\______________________________________________________________ \\// Antonello Romani Istituto di Patologia Generale Plesso Biotecnologico Integrato Universita' degli Studi di Parma via Volturno, 39 43100 - Parma Italia E-Mail : borghet@ipruniv.cce.unipr.it ---------------------------------------------------------------//\\ \\// From schiffer@h1tw0036.hoechst.com Thu Oct 2 04:27:59 1997 Received: from www.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id EAA24392; Thu, 2 Oct 1997 04:05:42 -0400 (EDT) Received: by www.hoechst.com id KAA17167; Thu, 2 Oct 1997 10:05:44 +0200 Received: from unknown(134.81.76.36) by www id sma017164; Thu Oct 2 10:05:29 1997 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id KAA04007; Thu, 2 Oct 1997 10:03:28 +0200 Message-ID: <34335550.167E@h1tw0036.hoechst.com> Date: Thu, 02 Oct 1997 10:03:28 +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: Computational Chemistry List Subject: software for transition state searches Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear netters. I am looking for a free software package to perform transition state searches on molecular potential energy surfaces (computed on the fly !). If someone know such a program, please mail me. I would greatly appreciate any help. 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 schiffer@h1tw0036.hoechst.com Thu Oct 2 04:34:46 1997 Received: from www.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id EAA24344; Thu, 2 Oct 1997 04:02:18 -0400 (EDT) Received: by www.hoechst.com id KAA17020; Thu, 2 Oct 1997 10:02:11 +0200 Received: from unknown(134.81.76.36) by www id sma016989; Thu Oct 2 10:01:14 1997 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id JAA03940; Thu, 2 Oct 1997 09:58:40 +0200 Message-ID: <3433542F.41C6@h1tw0036.hoechst.com> Date: Thu, 02 Oct 1997 09:58:39 +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: Gustavo de Miranda Seabra CC: Computational Chemistry List Subject: Re: CCL:Ab-Initio potentials References: <3432CFEE.3911FE7C@npd.ufpe.br> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Gustavo de Miranda Seabra wrote: > > Dear All, > > I would appreciate very much if someone could indicate me any > references about > using ab-inito calculations to parametrize interatomic pair potentials. > Thanks in advance. Hi Gustavo, for a very recent paper see : Kritsana Sagarik, Prapasri Asawakun Intermolecular potential for phenol based on the test particle model Chem. Phys. Lett. 219 (1997) 173-191 and a somehow older paper about the test particle modell : H. J. Boehm, R. Ahlrichs, P. Scharf, and H. Schiffer Intermolecular potentials for CH4, CH3F, CHF3, CH3Cl, CH2CL2, CH3CN and CO2 J. Chem. Phys. 81(3) (1984) 1389-1395 see also : Daxu Yin and Alexander D. MacKerell, Jr. Ab Initio Calculations on the Use of Helium and Neon as Probes of the van der Waals Surfaces of Molecules J. Phys. Chem. 100 (1996) 2588-2596 Joerg-R. Hill Use of Test Particle Calculations for the Derivation of van der Waals Parameters Used in Force Fields J. Comput. Chem. 18(2) (1997) 211-220 For a somewhat different approach see A. Wallqvist and G. Karlstroem A New Non-Empirical Force Field for Computer Simulations Chemica Scripta 29A (1989) 131-137 Ola Engkvist, Per-Olof Astrand, and Gunnar Karlstroem Intermolecular Potential for the 1,2-Dimethoxyethane-Water Complex J. Phys. Chem. 100 (1996) 6950-6957 Concerning the electrostatic part of the interaction, see a recent review by Sarah Price : Sarah L. Price Applications of realistic electrostatic modelling to molecules in complexes, solids and proteins J. Chem. Soc., Faraday Trans. 92(17) (1996) 2997-3008 An extensive discussion and review of vdW Parameters can be found in: Thomas A. Halgren Representation of van der Waals (vdW) Interactions in Molecular Mechanics Force Fields : Potential Form, Combination Rules, and vdW Parameters J. Am. Chem. Soc. 114 (1992) 7827-7843 A warning and a proposal concerning the use of DFT methods to compute interaction energies : Evert Jan Meier and Michiel Sprik A density-functional study of the intermolecular interactions of benzene J. Chem. Phys. 105(19) (1996) 8684-8689 And last but not least the SAPT method (good, but expensive): Bogumil Jeziorski, Robert Moszynski, and Krzysztof Szalewicz Perturbation Theory Approach to Internolecular Potential Energy Surfaces of van der Waals Complexes Chem. Rev. 94 (1994) 1887-1930 Eric M. Mas, Krzysztof Szalewicz, Robert Bukowski, Bogumil Jeziorski Pair potential for water from symmetry-adapted perturbation theory J. Chem. Phys. 107(11) (1997) 4207-4218 ( Hi Eric, are you on the list ? ) I hope, these references may be of help for you. 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 awindemu@guarneri.curagen.com Thu Oct 2 10:28:01 1997 Received: from guarneri.curagen.com for awindemu@guarneri.curagen.com by www.ccl.net (8.8.3/950822.1) id KAA00941; Thu, 2 Oct 1997 10:13:51 -0400 (EDT) Received: from pc27.curagen.com by guarneri.curagen.com via SMTP (931110.SGI/930416.SGI.AUTO) for chemistry@www.ccl.net id AA28251; Thu, 2 Oct 97 10:09:53 -0400 Message-Id: <3433AA10.4A7FD394@curagen.com> Date: Thu, 02 Oct 1997 10:05:04 -0400 From: Andreas Windemuth X-Mailer: Mozilla 4.03 [en] (WinNT; U) Mime-Version: 1.0 To: borghet@ipruniv.cce.unipr.it Cc: Computational Chemistry Mailing List Subject: Re: CCL:Molecular dynamics software References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Antonello, You may want to look at PMD (http://tincan.bioc.columbia.edu/pmd/). Although the Web page is old, the program is still good. And, I still answer questions, too. PMD is scalar, scalable, parallel and free, and it can easily manage hundreds of thousands of atoms. User friendly may be a little bit of a stretch, but the included demos do work. Andreas borghet@ipruniv.cce.unipr.it wrote: > > Hi netters, > > I'm looking for a scalar (or parallel) free molecular dynamics software, > running on DEC or Silicon,user friendly and able to manage easily thousand > atoms (proteins). > > If someone knows some programs with these features, please mail me. > > Thanking in advance, all the people who answer me > > Your faithfully > > Antonello Romani > > //\\______________________________________________________________ > \\// > Antonello Romani > Istituto di Patologia Generale > Plesso Biotecnologico Integrato > Universita' degli Studi di Parma > via Volturno, 39 > 43100 - Parma > Italia > E-Mail : borghet@ipruniv.cce.unipr.it > ---------------------------------------------------------------//\\ > \\// > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: borghet@ipruniv.cce.unipr.it > -- Original Sender From: Address: borghet@ipruniv.cce.unipr.it > 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 ilya@icp.ac.ru Thu Oct 2 11:28:03 1997 Received: from netserv1.chg.ru for ilya@icp.ac.ru by www.ccl.net (8.8.3/950822.1) id KAA01088; Thu, 2 Oct 1997 10:34:32 -0400 (EDT) Received: from icp.ac.ru (icp.ac.ru [193.233.43.3]) by netserv1.chg.ru (8.8.5/8.8.3) with SMTP id SAA08515 for ; Thu, 2 Oct 1997 18:34:29 +0400 (MSD) Received: from lira.icp.ac.ru (conv.icp.ac.ru [193.233.43.4]) by icp.ac.ru (8.6.11/8.6.5) with ESMTP id SAA11714 for ; Thu, 2 Oct 1997 18:35:10 +0400 Posted-Date: Thu, 2 Oct 1997 18:35:10 +0400 Message-ID: <3433BEC6.70A7CE4C@icp.ac.ru> Date: Thu, 02 Oct 1997 18:33:27 +0300 From: ilya Goldschleger Reply-To: ilya@icp.ac.ru Organization: Institute of Chemical Physics in Chernogolovka X-Mailer: Mozilla 4.01 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: ab initio calculation of g-tensor X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Collegues, I wish to calculate theoretically g-tensor (eigen values and principal axes) on the basis of ab initio calculation resuts done for radical species. Can Gaussian-94 do this or how can it be done? Thank you. Sincerely Yours I. Goldschleger my e-mail: ilya@icp.ac.ru ------------------------------------- Ilya U. Goldschleger Institute of Chemical Physics in Chernogolovka, Russian Academy of Science. 142432, Chenogolovka, Russia e-mail: ilya@icp.ac.ru ------------------------------------- From s0rama02@homer.louisville.edu Thu Oct 2 11:31:59 1997 Received: from unix1.it-datacntr.louisville.edu for s0rama02@homer.louisville.edu by www.ccl.net (8.8.3/950822.1) id LAA01340; Thu, 2 Oct 1997 11:08:57 -0400 (EDT) Received: from homer.louisville.edu (homer.it-datacntr.louisville.edu [136.165.1.20]) by unix1.it-datacntr.louisville.edu (8.8.7/8.8.7) with ESMTP id LAA22448; Thu, 2 Oct 1997 11:07:49 -0400 Received: from localhost (s0rama02@localhost) by homer.louisville.edu (8.8.7/8.8.7) with SMTP id KAA19945; Thu, 2 Oct 1997 10:41:16 -0400 (EDT) Date: Thu, 2 Oct 1997 10:41:15 -0400 (EDT) From: Sriram Ramani Reply-To: Sriram Ramani To: CHEMISTRY@www.ccl.net cc: g@CCMSD.chem.uga.edu Subject: G94: Output notation... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL & G-list members, Sorry if you get this posting twice. During a routine optimization in G94, I got the following output of the optimized variables: (edited) ..... ! A18 A(11,1,14) 116.276 -DE/DX = 0.! ! A19 L(1,14,15) 152.0256 -DE/DX = 0.! ! A20 L(1,14,15) 105.7391 -DE/DX = 0.! ! A21 A(14,15,16) 106.4477 -DE/DX = 0.! .... I wonder if these two angle values for the same atoms (1,14,15) point to two local minima with equal energies, and what the L(1,14,15) refers to. Any suggestions? (This is a simple silica-alumina cluster HF/3-21G* OPT run). Thanks. Sincerely, Sriram ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ SRIRAM RAMANI Chemical Engineering Department TEL: (502)852-1557 (W);(502)636-5293 (H) University of Louisville WWW: http://www.louisville.edu/~s0rama02 Louisville, KY 40292 FAX: (502)852-6355 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From schiffer@h1tw0036.hoechst.com Thu Oct 2 11:34:37 1997 Received: from www.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id LAA01405; Thu, 2 Oct 1997 11:22:54 -0400 (EDT) Received: by www.hoechst.com id RAA03190; Thu, 2 Oct 1997 17:22:51 +0200 Received: from unknown(134.81.76.36) by www id sma003181; Thu Oct 2 17:22:36 1997 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id RAA04724; Thu, 2 Oct 1997 17:20:38 +0200 Message-ID: <3433BBC6.794B@h1tw0036.hoechst.com> Date: Thu, 02 Oct 1997 17:20:38 +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: Computational Chemistry List Subject: transition state search Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi netters, from the answers I got to my previous question concerning a program to perform transition state searches I learned, that it was not very precise. The original question was : > I am looking for a free software package to perform transition > state searches on molecular potential energy surfaces (computed > on the fly !). But I am really looking for such a program independent of an ab initio or semi-empirical package. I.e. I am looking for a stand-alone program which just reads energies, gradients, and (hopefully not) hessians, computed by any semi-empirical, force-field, or ab initio program, and then perform the search. And even better would be, if such a program would have implemented several different methods, like the one by Schlegel, Bofill, Quapp, Zerner, Baker, Ruedenberg, Carter, and many, many others. If anyone know such a program (for free), please mail me. I would greatly appreciate any help. 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 nauss@beryllium.crs.uc.edu Thu Oct 2 14:28:05 1997 Received: from beryllium.crs.uc.edu for nauss@beryllium.crs.uc.edu by www.ccl.net (8.8.3/950822.1) id NAA02778; Thu, 2 Oct 1997 13:29:15 -0400 (EDT) Received: (from nauss@localhost) by beryllium.crs.uc.edu (8.8.6/8.8.6) id NAA22757 for chemistry@www.ccl.net; Thu, 2 Oct 1997 13:29:13 -0400 (EDT) From: nauss@beryllium.crs.uc.edu (Jeffrey L. Nauss) Message-Id: <9710021329.ZM22755@beryllium.crs.uc.edu> Date: Thu, 2 Oct 1997 13:29:13 -0400 Organization: Dept. Chemistry, University of Cincinnati Reply-to: Jeffrey.Nauss@UC.Edu X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Parallel Pentium Computers Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii We are interested in any references, WWW links, and/or personal experiences about using Pentium II or Pentium Pro chips parallel with Linux as the OS. We are aware of the Beowulf project at URL http://cesdis.gsfc.nasa.gov/linux-web/beowulf/beowulf.html but are curious as to other experiences people have had. In particular is there any molecular dynamics code (such as AMBER and Tinker) and/or ab initio/semi-empirical code (such as GAMESS) for parallel Pentium hardware configurations. A summary will be made if enough responses are gathered. Thank you... -- Jeffrey L. Nauss, PhD Telephone: 513-556-0148 Dir. Molec. Model. Serv. Fax: 513-556-9239 Department of Chemistry e-mail: Jeffrey.Nauss@UC.Edu University of Cincinnati URL http://www.che.uc.edu/~nauss From dorina@ks.uiuc.edu Thu Oct 2 15:28:07 1997 Received: from london.ks.uiuc.edu for dorina@ks.uiuc.edu by www.ccl.net (8.8.3/950822.1) id OAA03379; Thu, 2 Oct 1997 14:49:15 -0400 (EDT) Received: from luxembourg.ks.uiuc.edu by london.ks.uiuc.edu with SMTP (1.37.109.20/16.2 [TBG Mods]) id AA025818157; Thu, 2 Oct 1997 13:49:17 -0500 Message-Id: <199710021849.AA025818157@london.ks.uiuc.edu> Received: by luxembourg.ks.uiuc.edu (NX5.67e/NX3.0X) id AA06850; Thu, 2 Oct 97 13:49:16 -0500 Content-Type: text/plain Mime-Version: 1.0 (NeXT Mail 3.3risc v118.3) X-Nextstep-Mailer: Mail 3.3 (Enhance 1.2) Received: by NeXT.Mailer (1.118.3) From: Dorina Kosztin Date: Thu, 2 Oct 97 13:49:16 -0500 To: chemistry@www.ccl.net Subject: hydration patterns Reply-To: Dorina Kosztin Hi, I'm looking for a program (free or not free software - it doesn't matter) that would allow one to calculate hydration patterns for molecules using data from a simulation trajectory. Thank you in advance for your replies. I'm willing to summarize all the answers I get. Dorina Kosztin --------------------------------------------------------- Theoretical Biophysics Group Email: dorina@ks.uiuc.edu Beckman Institute, UIUC Phone: (217) 244-8946 405 North Mathews Ave. Fax: (217) 244-6078 Urbana, IL 61801, USA http://www.ks.uiuc.edu/ --------------------------------------------------------- From urquhart@miranda.chemistry.McMaster.CA Thu Oct 2 16:28:20 1997 Received: from blackadder.cis.mcmaster.ca for urquhart@miranda.chemistry.McMaster.CA by www.ccl.net (8.8.3/950822.1) id PAA03692; Thu, 2 Oct 1997 15:34:35 -0400 (EDT) Received: from miranda.mcmaster.ca (miranda.chemistry.McMaster.CA) by blackadder.cis.mcmaster.ca with SMTP id AA01889 (5.65c/IDA-1.4.4 for ); Thu, 2 Oct 1997 15:34:18 -0400 Received: by miranda.mcmaster.ca (AIX 3.2/UCB 5.64/4.03) id AA17897; Thu, 2 Oct 1997 15:32:09 -0400 Date: Thu, 2 Oct 1997 15:32:09 -0400 (EDT) From: Stephen Urquhart To: chemistry@www.ccl.net Subject: CACAO, windows NT In-Reply-To: <3431B0C8.31DF@helix.nih.gov> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I used to use the program CACAO (neat EHMO program with excellent visualization tools) quite frequently. I have now moved to Windows NT OS, and I have not been able to get CACAO to run. Has anyone solved this problem? Thank you, Stephen Urquhart From s0rama02@homer.louisville.edu Thu Oct 2 16:34:19 1997 Received: from unix1.it-datacntr.louisville.edu for s0rama02@homer.louisville.edu by www.ccl.net (8.8.3/950822.1) id PAA03783; Thu, 2 Oct 1997 15:48:46 -0400 (EDT) Received: from homer.louisville.edu (homer.it-datacntr.louisville.edu [136.165.1.20]) by unix1.it-datacntr.louisville.edu (8.8.7/8.8.7) with ESMTP id PAA39196; Thu, 2 Oct 1997 15:48:29 -0400 Received: from localhost (s0rama02@localhost) by homer.louisville.edu (8.8.7/8.8.7) with SMTP id PAA00960; Thu, 2 Oct 1997 15:47:17 -0400 (EDT) Date: Thu, 2 Oct 1997 15:47:16 -0400 (EDT) From: Sriram Ramani To: CCList cc: Gaussian List Subject: G94: Output notations - Thanks. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL and G-List members, I had earlier posted a query about the L(*,*,*) notation in the G94 output of an optimization job. Thanks to Richard Hall, Eric V. Patterson and Doug Fox, I got the answer: The L-notation is used by Gaussian to indicate the linear angle, when encountered near the input structure. In my case too, an angle had approached 180 degrees, but then had moved away from the linearity during optimization. Thanks again for the help. Sincerely, Sriram ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ SRIRAM RAMANI Chemical Engineering Department TEL: (502)852-1557 (W);(502)636-5293 (H) University of Louisville WWW: http://www.louisville.edu/~s0rama02 Louisville, KY 40292 FAX: (502)852-6355 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From ccl@www.ccl.net Wed Oct 1 04:27:46 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id EAA14086; Wed, 1 Oct 1997 04:06:13 -0400 (EDT) Received: from cleo.univ-reims.fr for jean.brion@univ-reims.fr by bedrock.ccl.net (8.8.6/950822.1) id EAA23743; Wed, 1 Oct 1997 04:06:06 -0400 (EDT) Message-Id: <199710010806.EAA23743@bedrock.ccl.net> Received: from centre01.univ-reims.fr by cleo.univ-reims.fr with SMTP (1.37.109.4/16.2) id AA08612; Wed, 1 Oct 97 09:12:23 +0100 Received: by centre01.univ-reims.fr (1.38.193.4/16.2) id AA10755; Wed, 1 Oct 1997 08:45:00 +0100 From: BRION Jean Subject: High Pressure equilibrium data To: CHEMISTRY@ccl.net Date: Wed, 1 Oct 97 8:45:00 WETDST Mailer: Elm [revision: 70.85] Hello, I am modelling non-ideal behaviour for gazes equilibrium at high pressure and so I would need some experimental data at high pressure. For example, I am searching for Kp values, or equilibrium compositions ... particularly for ammonia synthesis. (other data on other compounds would be welcome also) I feel that there are few data at high pressure for such data... therefore thanks in advance ! E. Henon ************************************************** * E. Henon * * Laboratoire de Chimie Physique * * GSMA, UPRES-A 6089 * * Universite de Reims, Faculte des Sciences * * Moulin de la Housse * * B.P. 1039 * * 51687 Reims Cedex 2 * * FRANCE * * Tel: (33) (0)3-26-05-32-33 * * Fax: (33) (0)3-26-05-31-47 * * E-mail: jean.brion@univ-reims.fr * ************************************************** From toukie@zui.unizh.ch Wed Oct 1 05:27:47 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id EAA14319; Wed, 1 Oct 1997 04:58:32 -0400 (EDT) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA28554; Wed, 1 Oct 1997 09:58:31 +0100 Message-Id: <3.0.3.32.19971001100058.006881ec@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Wed, 01 Oct 1997 10:00:58 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: ? re ovality Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleagues; In JACS 111: 3783 ('89), Bodor et al. define ovality, O, the ratio of actual to minimum surface as O = (S/4*pi)[(3V/4*pi)^2/3] where S is the surface area and V is the volume. I should like to know if Bodor's reference is the _very first_ definition of ovality as given above, or if a comparable equation been published before. If so, please send me the exact citation. Thanks in advance to all responders. Sincerely, S. Shapiro toukie@zui.unizh.ch From peter@cherwell.com Wed Oct 1 07:27:48 1997 Received: from congo.cherwell.com for peter@cherwell.com by www.ccl.net (8.8.3/950822.1) id GAA14675; Wed, 1 Oct 1997 06:48:24 -0400 (EDT) Received: from mersey.cherwell.com ([193.82.249.217]) by congo.cherwell.com (Post.Office MTA v3.1.2 release (PO205-101c) ID# 0-0U10L2S100) with SMTP id AAA88 for ; Wed, 1 Oct 1997 11:48:23 +0100 Message-Id: <3.0.1.32.19971001114816.008347b0@cherwell.com> X-Sender: peter@cherwell.com X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Wed, 01 Oct 1997 11:48:16 +0100 To: chemistry@www.ccl.net From: Peter Tebbutt Subject: ChemSymphony Lite- new release Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Cherwell Scientific Publishing are pleased to announce the release of ChemSymphony Lite - a new evaluation version of the popular web structure rendering tool. ChemSymphony Lite is free for use on the WWW (subject to a license agreement) and can be used to include molecular structures in HTML documents. The features of ChemSymphony Lite are: * from small molecules to proteins rendered in a variety of styles - wireframe, ball and stick, ribbons strands etc * rendering using a variety of color schemes (including user defined) * manipulation using mouse for rotation, translation, zoom * structures can be renderered in floating frames with drop down menus for changing rendering styles * appearance fully configurable using applet parameters * Additional control applet allows users to manipulate the structure rendering options * most common file types recognized - XYZ, MDL MOL, PDB, ZMAT etc * compatible with all java enabled browsers and platforms. Unlike previous evaluation versions this is not time limited and may be used free of charge on the WWW and for evaluation purposes. You can download your copy from the chemSymphony web site now. http://www.chemsymphony.com Peter Tebbutt ----------------------------------------------------------- Peter Tebbutt | e-mail: peter@cherwell.com Development Support | Tel: +44 (0)1865 784812 Cherwell Scientific Publishing| Fax: +44(0)1865 784801 Oxford OX4 4GA, UK | http://www.cherwell.com ----------------------------------------------------------- Check Out ChemSymphony - rated top 1% Java applet by JARS http://www.cherwell.com/chemsymphony ----------------------------------------------------------- From Keith.Refson@earth.ox.ac.uk Wed Oct 1 07:27:56 1997 Received: from earth.ox.ac.uk for Keith.Refson@earth.ox.ac.uk by www.ccl.net (8.8.3/950822.1) id HAA14769; Wed, 1 Oct 1997 07:16:29 -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 MAA26317 for ; Wed, 1 Oct 1997 12:16:28 +0100 (BST) From: Keith Refson To: CCL Subject: CCL:summary: solid state/band structures In-Reply-To: References: 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: Wed, 01 Oct 1997 12:16:20 +0100 (BST) Message-Id: <19971001121620.113369.FMU15116@metropolis> Ulrike Salzner writes: > There seems to be a considerable gap between the physicists and chemists > working in this field. That is certainly true! Can I add one comment which might avoid misunderstandings. The term "bandstructure calculation" would usually refer to a computation of the eigenvalues (and wavefunctions), ie spectroscopy only. The term "total energy calculation" is often used to subsume all QM calculations of the total energy, forces, optimization etc. One reason for making the distinction is that good bandstructure methods (such as KKR, GW) can not compute total energies(*), and good total energy methods (ie DFT) are poor for bandstructures! > Following the chemical literature little meaning > is assigned to DFT orbital energies and, to my knowledge, there is no > physical justification do interpret them as IPs and EAs. Well, hmm. It's not quite true that Kohn-sham eigenstates have no physical significance. They are "quasiparticle" states and their eigenvalues are formally the derivatives of total energy with respect to occupation. However there is no formal way of constructing a many-body wave-function from Kohn-Sham eigenstates so they are NOT orbitals in the same sense as Hartree-Fock orbitals. *BUT* and surprisingly at first, because of the lack of formal justification, the LDA Kohn-Sham eigenstate spectrum *sometimes* does look *very* like the true (using advanced methods) excitation spectrum, with the proviso that the band gap (in insulators) is underestimated by 30-50%. The proviso is that this applies to weakly-correlated systems only. In a strongly-correlated system ( narrow d-band transition metal compounds) such as NiO the LSDA/GGA band structure is badly wrong. > > However, there are all these DFT band structure codes which determine > band gaps. Formally they must compute eigenvalues in order to evaluate the total energy. That doesn't mean you have to believe the eigenvalues of excited states! > The band gap problem but not the fundamental question whether > DFT eigenenergies should be used at all has been discussed. Oh yes it has! At every electronic structure meeting I have ever been to! > it appeared to me that DFT orbital energies have > physical meening although the matter is by far not settled. I think the question is *what* physical meaning and in which circumstances. There's a very nice paper by Uwe Schonberger, Phys Rev B 52 (1995) 8788-8793. He does GW calculations on MgO and compares the band structure with LSDA and with other methods. What is *very* interesting is that the LSDA band structure is quantitatively and qualitatively correct apart from too narrow a band gap. In other words, if you simply shift the LSDA excited states upwards by 3 eV they match the GW ones very well. This suggests that the narrow gap is a fault of the LSDA rather than some (hypothetical?) exact DFT. I think it was Perdew who showed there must be a discontinuity in the exchange-correlation potential at the fermi energy in exact DFT which is not found in the LSDA (+GGA) approximations. One thing I have wondered but never investigated is whether the bandgap error is systematic enough to make a correction for. Does anyone know whether this has been looked at seriously? > > I am trying to obtain band gaps by extrapolating oligomer HOMO-LUMO gaps > using DFT and run into considerable problems with reviewers (most likely > chemists) who usually point out that DFT can not be used for this. I would hope that physicists would give you a hard time for this too! > As far as I understand band structure calculations, the band gaps are > analogous to HOMO-LUMO gaps in molecules. Almost exactly. Except that you must specify (or assume) the G-vectors at the band edges because of the dispersion. > Is there a fundamental difference between the > DFT eigenenergies of molecules and of solids? Any comments would be > greatly appreciated. No. Except for the existence of dispersive bands at all! Take a look at Peter Bloechl's PAW calculation of a Ferrocene molecule or Graham Acklands calculations of small liquid crystal molecules using plane-waves and pseudopotentials! > > Concerning the comment on ab initio codes in Georg Schreckenbach's summary: > there is also a Hartree-Fock solid state program in Erlangen/Germany. > This program seems to be able to do MP2 corrections. Moreover, W. > Foerner (also formerly in Erlangen) et al. published a paper in J. Chem. > Phys., 1997, 106, pp. 10249 on coulped cluster theory applied to polymers. I wasn't aware of these. Are there any more details? One new code I ought to add to the list is SIESTA, which is a periodic boundary-conditions, DFT code with a local-orbital basis set. It does forces, optimizations MD and is apparently order N in scaling. It is being developed in Madrid and we are hoping to import it to the UK to try out some large-scale calculations on minerals. See P. Ordejon et al Phys. Rev B51 (1995) 1456-1476 and Phys. Rev. B53 (1996) 10441-10444 (*) I had better put this in in case I am contradicted. I do expect this comment to be out of date soon. There is a plethora of work on postLDA and post-density-functional methods. I recently saw a paper claiming total energies from KKR methods and there is certainly work done in Materials Science at Oxford using LDA+Hubbard U which seems to give good bandstructures for NiO and UO2 surfaces! It's an exciting time in the field and it will be interesting to see what methods we are all using in 5 years! Keith Refson