From axb224@anugpo.anu.edu.au Mon Jun 24 00:56:06 1996 Received: from anugpo.anu.edu.au for axb224@anugpo.anu.edu.au by www.ccl.net (8.7.5/950822.1) id AAA05480; Mon, 24 Jun 1996 00:02:39 -0400 (EDT) Received: from nicepc.anu.edu.au (nicepc.anu.edu.au [150.203.193.136]) by anugpo.anu.edu.au (8.6.12/8.6.12) with SMTP id OAA26618 for ; Mon, 24 Jun 1996 14:02:38 +1000 Message-Id: <199606240402.OAA26618@anugpo.anu.edu.au> Comments: Authenticated sender is From: "Andrey Blizniuk" Organization: ANU To: chemistry@www.ccl.net Date: Mon, 24 Jun 1996 13:23:25 +0010 Subject: Monte Carlo for Diffusion - Summary Reply-to: Andrey.Bliznyuk@anu.edu.au Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Dear Netters, Thanks to everyone who responded to my question about use of Monte Carlo for diffusion. Some people asked about summary. I am sending them the copy of this message. (1) Several people recommend to look at Monte Carlo Page Unfortunately, I couldn't find anything on the subject in there. But I am still looking :-). (2) Mr. Mark J Biggs sent following references on the diffusion in porous solids: Abbasi et al., AIChE Journal V29, p617, 1983 Havlin and Ben Avraham, Adv in Physics, V36, 695, 1987. Sahimi, J Chem Phys, V92, 5107, 1990 Gusev et al, J Chem Phys, V99, 2221, 1993 Nakano and Evans, J Chem Phys, V78, 2568, 1983 Evans et al, J Chem Phys, V72, 2967, 1980 Tomadakis and Sotirchos, J Chem Phys, V99, 9820, 1993 -----------------------, AIChE J, V39, 397, 1993 they have a few more papers in these Journals as well Melkote and Jensen, AIChE J, V35, 1942, 1989. (3) Dr Kieran F Lim sent the following comments: Monte Carlo (MC) methods imply that the underlying maths has some random event. Brownian dynamics has the *assumption* that the solvent imparts random forces to the molecule (substrate) of interest. Molecular dynamics (MD) incorporates both solvent and substrate motions and so there is nothing random - ie non-MC method. By including everything, the MD calculation is much bigger - hence *many* (not most) prefer MC rather than MD. the choice depends on the nature of the problem, the size of your system and your computer resources. (4) While waiting for the reply from CCL I had a look at the Current Contents. The following papers may be useful: H. Gudbjartsson S. Patz "NMR Diffusion Simulation Based on Conditional Random Walk", IEEE Transactions on Medical Imaging, 1995, 14, 636-642 P.A. Mahama, J.L. Linderman "A Monter Carlo Study of the Dynamics of G-Protein Activation", Biophysical Journal, 1994, 67, 1345-1357. Z. Hong-Dong, L. Jian-Ming, Y. Yu-Liang "Sample duplication Method for Monte Carlo Simulation of Large Reaction-Diffusion System", Science in China, Ser.B., 1994, 37, 385-394. P. Gao "Computer Experiments for Surface Diffusion: The Real Time in Monte Carlo Simulations", Physical Review Letters, 1994, 73, 2595-2598. H. Breuer, W. Huber, F. Petruccione "Fast Monte Carlo algorithm for nonequilibrium systems", Physical Review E, 1996, 4232-4235. Sincerely, Dr. Andrey Bliznyuk Computational Molecular Biology and Drug Design Group Division of Molecular Biology and Biochemistry John Curtin School of Medical Research Australian National University PO Box 334, Canberra, ACT 2601 Australia Email: Andrey.Bliznyuk@anu.edu.au http://biocomp.anu.edu.au/~aab From owner-chemistry@ccl.net Mon Jun 24 01:56:05 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id BAA06018; Mon, 24 Jun 1996 01:49:19 -0400 (EDT) Received: from goliat.eik.bme.hu for zhajnal@goliat.eik.bme.hu by bedrock.ccl.net (8.7.5/950822.1) id BAA19696; Mon, 24 Jun 1996 01:49:17 -0400 (EDT) Received: (from zhajnal@localhost) by goliat.eik.bme.hu (8.7.3/8.7.3) id HAA11782; Mon, 24 Jun 1996 07:49:24 +0200 (MET DST) Date: Mon, 24 Jun 1996 07:49:24 +0200 (MET DST) From: HAJNAL Zoltan To: Computational Chemistry List Subject: Heat of sublimation/ ethylcarbamate Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, could anybody send me or point to data regarding the heat of sublimation of ethylcarbamate? Thank you! Zoltan Hajnal From lankau@blubber.chemie.uni-hamburg.de Mon Jun 24 02:56:09 1996 Received: from blubber.chemie.uni-hamburg.de for lankau@blubber.chemie.uni-hamburg.de by www.ccl.net (8.7.5/950822.1) id CAA06244; Mon, 24 Jun 1996 02:42:26 -0400 (EDT) Received: by blubber.chemie.uni-hamburg.de (AIX 4.1/UCB 5.64/4.03) id AA15094; Mon, 24 Jun 1996 08:29:53 +0200 Date: Mon, 24 Jun 1996 08:29:52 +0200 (DFT) From: Timm Lankau To: chemistry@www.ccl.net Subject: mag. properties of solids Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear collegues, does any one of you have experiences with the calculation of magnetic properties of solids and is willing to share it with us? We are looking for a code (public domain or shareware prefered) for the computation of such properties. Results will collected and posted to the list. Thank you very much. Best wishes Timm ========================================================================== Timm Lankau phone (+)40 4123 3686 Institut fuer Physikalische Chemie fax (+)40 4123 3452 Universitaet Hamburg e-mail lankau@chemie.uni-hamburg.de Bundesstr. 45 20146 Hamburg Germany ----------- End Forwarded Message ----------- From ncapron@ccr.jussieu.fr Mon Jun 24 03:56:27 1996 Received: from shiva.jussieu.fr for ncapron@ccr.jussieu.fr by www.ccl.net (8.7.5/950822.1) id DAA09201; Mon, 24 Jun 1996 03:25:51 -0400 (EDT) Received: from moka.ccr.jussieu.fr (moka.ccr.jussieu.fr [134.157.1.23]) by shiva.jussieu.fr (8.7.5/jtpda-5.2) with ESMTP id JAA25963 for ; Mon, 24 Jun 1996 09:25:37 +0200 (METDST) Received: from (ncapron@localhost) by moka.ccr.jussieu.fr (8.7.5/jtpda-5.2) id JAA171793 for chemistry@www.ccl.net; Mon, 24 Jun 1996 09:25:36 +0200 Date: Mon, 24 Jun 1996 09:25:36 +0200 From: ncapron@ccr.jussieu.fr (Nathalie CAPRON) Message-Id: <199606240725.JAA171793@moka.ccr.jussieu.fr> To: chemistry@www.ccl.net Subject: CCL :Bulk modulus of silicon Dear all, I should need for my study a complete ( or near ) list of the calculations carried out on silicon which give the theoritical values for the elastic constants and especially bulk modulus I have already some papers but I am affraid to miss some important information. Could someone give me the references of these papers ? Thank you in advance Nathalie Capron Laboratoire de Chimie Physique Matiere et Rayonnement 11, rue Pierre et Marie Curie 75231 Paris Cedex 01 ncapron@ccr.jussieu.fr From tp@elptrs7.rug.ac.be Mon Jun 24 06:56:15 1996 Received: from elptrs7.rug.ac.be for tp@elptrs7.rug.ac.be by www.ccl.net (8.7.5/950822.1) id GAA10353; Mon, 24 Jun 1996 06:23:28 -0400 (EDT) Received: by elptrs7.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA19138; Mon, 24 Jun 1996 12:24:21 +0200 Date: Mon, 24 Jun 1996 12:24:21 +0200 (DFT) From: "Park, Tae-Yun" To: Computational Chemistry List Subject: HELP!(urgent):theoretical discrimication & software Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear researchers in computational chemistry, I'm a ph.D. student of State University of Ghent, Belgium. I'm working with zeolite HZSM-5. The goal of my work is to develop a detailed kinetic model for hydrocarbon transformation process over HZSM-5 catalyst. I have some urgent questions for my ph.D. work, which have been discussed with many people who were in the field of chemical engineering/organic chemistry/electrical chemistry in my university or in the internet. So far, I could not get reliable solutions, which have stuck me for relatively long time. During searching for the solutions, I realized that the best people who can give me an advice are in the field of computational chemistry. Please take some time to read the following questions and give me some informaion/advice if it doesn't bother you too much. *** About the structure of surface carbenium ions and symmetry number *** First thing I have to calculate is the symmetry number of surface carbenium ions on the zeolite surface, which is formed by protonation of various olefins. 1. How can we describe the bonding of carbenuim ions to the surface? Is the bonding more ionic or covalent? I know the proton is surely covalently bound, but it is less clear for the case of hydrocarbons(more exactly olefins) adsorbed on zeolite. 2. What is the symmetry number for such surface carbenium ions comparing with corresponding gas phase carbenium ions? In most cases, I believe, the symmetry number of surface ions are identical with those in gas phase, if there is no 2-fold axes. Consider the following examples. C \ C-C+-C (secondary ion in gas phase) / C symmetry number=3*3*3=27 C \ C-C-C (secondary ion on the surface) / | C | --(+)-- symmetry number=3*3*3=27 If there is two-fold axes, however, C \ 2-fold axes.....C+-C-C (tertiary ion in gas phase) / C symmetry number=(3*3*3)*2=54 C \ Not a 2-fold axes(?)...C+-C-C (tertiary on the surface) /| C | --(+)-- symmetry number=3*3*3=27 I think the surface ion loose its 2-fold axes due to the bonding to the catalyst surface. I just want to know whether those approach to calculate the symmetry number of surface carbenium ions is theoretically correct. To check this point, I think, the bonding of carbenium ions to the surface should be defined first, in a certain way of theoretical approach. **** About the structure of activated complex ****** Next problem that I have to solve is concerning the structure of activated complex in transition state for beta-scission. That is, an elementary step representing beta-scission, R1 ---> (Transition State) ----> R2 + O where R1 and R2 are the reactant and product carbenium ion, respectively, and O is the product olefin. What I want to know is the structure of the activated complex in the transition state, as detailed as possible in a certain theoretical way; how many bonds are related, which bonds are to be broken, which bond will be formed, and what does the activated complex look like(is it more like carbenium ion or more like olefin?), etc. Is there any reference/software to describe the structure of activated complex for this reaction in a theoretical way? **** About heat of formation for gas phase carbenium ions *** My final question is about the calculation of thermodynamic data, more exactly, the heat of formation of gas-phase carbenium ions. The reason is the following: To develop a detailed kinetic model, a complex reaction network containing a lot of elementary steps has to be considered. Large number of different carbenium ions are involved in the elementary steps, which produces large number of kinetic parameters that have to be estimated by a certain optimization method. Recently, a solution to solve the problem associated with the large number of the parameters has been considered, i.e, by applying the "Polanyi relation". This relation needs only relative differences in heat of reactions in each elementary steps. This means that the heat of formation for the surface carbenium ions are not necessary, but, at least, heat of formation of gas-phase carbenium ions appearing in the reaction network should be given. Unfortunately, only limited amount of data can be found in the literature, so that some analytical method to calculate the heat of formation is necessary. Benson's group contribution method has been known as one of the most approprate way to calculate the thermodydamic properties. The group contribution value of positively-charged carbon atom involved in the carbenium ions is, however, not available at the moment. The only solution I found recently is using a certain quantum chemistry package such as "MOPAC". My question is that is this a suitable package (accurate enough) to calculate the heat of formation data I need? If so, how can I obtain a copy of this package? If not, is there any other software in the field of computational chemistry to calculate these data? *************** End of my questions ************************* Thank you very much for reading my long message. Since I'm not familar with computational chemistry field, some of my questions would make you feel boring or make you think that this is too basic/stupid questions. I'm really sorry if it is really so. Any suggestions/informations will be greatly appreciated. Particularly, infomation on some computational chemistry softwares (name of the software/how to get it) which give some theoretical point of view on these problems will give me a great help. Thanks again for your patience and I am highly looking forward to hearing any news from you soon. Sincerely, Park, TAE-YUN =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Laboratorium voor Petrochemische Techniek Krijgslaan 281, Blok S5 9000 Gent, Belgium TEL:+(32)-0(9)-264-4527 FAX:+(32)-0(9)-264-4999 e-mail: tp@elptrs7.rug.ac.be =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From Darren.Andrews@man.ac.uk Mon Jun 24 07:56:11 1996 Received: from nessie.mcc.ac.uk for Darren.Andrews@man.ac.uk by www.ccl.net (8.7.5/950822.1) id HAA10752; Mon, 24 Jun 1996 07:52:54 -0400 (EDT) Received: from [130.88.12.235] (actually femt03.ch.man.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Mon, 24 Jun 1996 12:52:17 +0100 X-Sender: mbcdpa@130.88.200.20 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 24 Jun 1996 12:53:38 +0100 To: chemistry@www.ccl.net From: Darren.Andrews@man.ac.uk (Darren Andrews) Subject: MD of ET in solution A little while ago I posted a question about molecular dynamics simulations of electron transfer reactions in solution. These are the replies I got. Status: Dear Darren, I think you should contact Daniel BORGIS at Laboratoire de Physique Theorique des Liquides Universite Pierre et Marie Curie 4 place Jussieu 75252 Paris cedex e-mail: borgis@lptl.jussieu.fr Yours sincerely, -- ============================================================= Dr HERVE TOULHOAT Group Leader Molecular Modeling and Computational Chemistry Division of Computer Science and Applied Mathematics INSTITUT FRANCAIS DU PETROLE 1 & 4 Avenue de Bois-Preau BP 311 92506 RUEIL-MALMAISON Cedex FRANCE TEl: +33-1-47-52-73-50 FAX: +33-1-47-52-70-22 Email: herve.toulhoat@ifp.fr (or toulhoat@irsil47.ifp.fr) ============================================================== Status: >I am looking for a program that will calculate molecular dynamics for >solvent/solute systems where a reaction (electron transfer) occurs. Is >there a general code for the liquid dynamics bit and is there a standard >way of modelling the reaction? > Hi Darren, Good question, and sine I don't know any answers could you send me a summary. My initial thought not knowing much about the systems that you're interested in is that you would need some kind of mixed mode code. see for example M.J. Field, P.A. Bash, M. Karplus. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations; J Comp Chem 1990, 11(6) :700-33. But I don't know of anything created specifically for electron transfer modeling. Iain. _____________________________________________________________ "Nice? It's the only thing," said the Computer Rat solemnly. " Believe me, my young friend, there is nothing - absolutley nothing - half so much worth doing as simply messing about with computers. Simply messing !" -- Appologies to Kenneth Grahame _____________________________________________________________ Iain McVey Graduate Student Department of Chemistry Kent State University Kent, Ohio, USA imcvey@scorpio.kent.edu _________________________________________________________________ Status: Hi! The only way I can think to do this is in a QM/MM environemt - try Charmm. Cheers Alex +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+ Status: Darren Andrews wrote: > > I am looking for a program that will calculate molecular dynamics for > solvent/solute systems where a reaction (electron transfer) occurs. Is > there a general code for the liquid dynamics bit and is there a standard > way of modelling the reaction? I vaguely recall that Michiel Sprik did some work somewhat similar to this. Try a BIDS search on his name, and you might turn up something. And he and Mike Klein (I think) did some Feynmann path-integral MD on solvation of an electron. sincerely Keith Refson -- ------------------------------------------------------------------------------ | Email : keith@earth.ox.ac.uk | Dr Keith Refson, Dept of Earth Sciences| | TEL(FAX): +44 1865 272026 (272072)| Parks Road, Oxford OX1 3PR, UK | ------------------------------------------------------------------------------ From Steven.Creve@chem.kuleuven.ac.be Mon Jun 24 11:56:13 1996 Received: from hartree.quantchem.kuleuven.ac.b for Steven.Creve@chem.kuleuven.ac.be by www.ccl.net (8.7.5/950822.1) id LAA11995; Mon, 24 Jun 1996 11:46:07 -0400 (EDT) Received: by hartree.quantchem.kuleuven.ac.be id AA24466 (5.67b/IDA-1.5 for Computational Chemistry List ); Mon, 24 Jun 1996 17:45:50 +0100 Date: Mon, 24 Jun 1996 17:45:48 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL: BHandH in G94 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Does anyone know how to specify the Becke-Half-and-Half/LYP Density Functional in G94 ? (In G92/DFT it was just a simple keyword: BHandHLYP) Thanks -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie steven@hartree.quantchem.kuleuven.ac.be Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From mhurley@shs2.chem.nd.edu Mon Jun 24 12:56:13 1996 Received: from shs2.chem.nd.edu for mhurley@shs2.chem.nd.edu by www.ccl.net (8.7.5/950822.1) id MAA12129; Mon, 24 Jun 1996 12:06:42 -0400 (EDT) Received: by shs2.chem.nd.edu (AIX 4.1/UCB 5.64/4.03) id AA17030; Mon, 24 Jun 1996 11:06:43 -0500 Date: Mon, 24 Jun 1996 11:06:43 -0500 From: mhurley@shs2.chem.nd.edu (Margaret Mary Hurley) Message-Id: <9606241606.AA17030@shs2.chem.nd.edu> To: CHEMISTRY@www.ccl.net Subject: constraint dynamics Hi Netters. I am interested in using Ciccotti, Ferrario, and Ryckaert's constraint dynamics algorithm (Mol. Phys. 1982, 47, 1253-1264) for rigid systems. Does anyone out there have a code which uses this? I'm currently using a velocity verlet integration scheme, but I'll take any application of the constraint algorithm that's out there. I'm working with a linear triatomic solvent, so standard SHAKE or RATTLE don't help me much. Any help is appreciated. Maggie Hurley mhurley@shs3.chem.nd.edu From topper@cooper.edu Mon Jun 24 13:15:23 1996 Received: from magnum.cooper.edu for topper@cooper.edu by www.ccl.net (8.7.5/950822.1) id LAA12085; Mon, 24 Jun 1996 11:59:20 -0400 (EDT) Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA29447 (5.65c/IDA-1.4.4 for ); Mon, 24 Jun 1996 12:01:25 -0400 Received: by zeus.cooper.edu id AA26531 (5.67b/IDA-1.5); Mon, 24 Jun 1996 11:58:01 -0400 From: TOPPER ROBERT Message-Id: <199606241558.AA26531@zeus.cooper.edu> Subject: Re: CCL:Monte Carlo for Diffusion - Summary To: Andrey.Bliznyuk@anu.edu.au Date: Mon, 24 Jun 1996 11:58:00 -0400 (EDT) Cc: chemistry@www.ccl.net In-Reply-To: <199606240402.OAA26618@anugpo.anu.edu.au> from "Andrey Blizniuk" at Jun 24, 96 01:23:25 pm X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi all, I will put a copy of Andrew's summary on the Molecular Monte Carlo home page. Just FYI. best, robert ************************************************************************ Robert Q. Topper email: topper@cooper.edu Asst. Prof. of Chemistry phone: (212) 353-4378 The Cooper Union FAX: (212) 353-4341 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 USA or the N/R to 8th St/NYU http://www.cooper.edu/engineering/chemechem/depts_info/topper.html ************************************************************************ Check out the Molecular Monte Carlo home page! http://www.cooper.edu/engineering/chemechem/monte.html ************************************************************************ From jdurant@mephisto.ca.sandia.gov Mon Jun 24 13:56:14 1996 Received: from mephisto.ca.sandia.gov for jdurant@mephisto.ca.sandia.gov by www.ccl.net (8.7.5/950822.1) id NAA12623; Mon, 24 Jun 1996 13:50:41 -0400 (EDT) Received: by mephisto.ca.sandia.gov (931110.SGI/890607.SGI) (for chemistry@www.ccl.net) id AA17276; Mon, 24 Jun 96 10:50:37 -0700 From: jdurant@mephisto.ca.sandia.gov (Joe Durant) Message-Id: <9606241750.AA17276@mephisto.ca.sandia.gov> Subject: Re: CCL:G:BHandH in G94 To: chemistry@www.ccl.net Date: Mon, 24 Jun 1996 10:50:37 -0800 (PDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi! At the risk of getting flamed by the folks at Gaussian I present my hack to get g94 to run Becke-Half-and-Half/LYP calculations by explicitly setting the options. Caveat Emptor! I have no control over what the folks at Gaussian do with their codes, so I would be sure to verify that it gives the expected answer with your revision before plunging in. # BLYP 6-31G* iop(5/45=10000500, 5/46=05000500, 5/47=10001000) BHANDHLYP, explicitly called out 0,1 H H,1,HH Variables: HH=1.387 Hope this helps! BTW, in my experience BHANDHLYP has proven to be the best functional to use for transition state calculations.... the others that Gaussian provides give surfaces which are too attractive and barriers which are too low.... Joe -- #################################################################### # Joe Durant voice: (510) 294-3343 # # Mail Stop 9057 FAX: (510) 294-2276 # # Sandia National Laboratories jdurant@ca.sandia.gov # # Livermore, CA 94551 http://mephisto.ca.sandia.gov # #################################################################### From branch@acetsw.amat.com Mon Jun 24 14:56:14 1996 Received: from cressida.mis.amat.com for branch@acetsw.amat.com by www.ccl.net (8.7.5/950822.1) id OAA12882; Mon, 24 Jun 1996 14:30:44 -0400 (EDT) Received: from cressida.mis.amat.com (daemon@localhost) by cressida.mis.amat.com (8.6.12/8.6.12) with ESMTP id LAA07935 for ; Mon, 24 Jun 1996 11:16:54 -0700 Received: from romeo.mis.amat.com (romeo.mis.amat.com [152.135.118.219]) by cressida.mis.amat.com (8.6.12/8.6.12) with ESMTP id LAA07931 for ; Mon, 24 Jun 1996 11:16:54 -0700 Received: from cvd17 ([152.135.245.177]) by romeo.mis.amat.com with SMTP (1.37.109.16/16.2) id AA002601775; Mon, 24 Jun 1996 11:42:55 -0700 Date: Mon, 24 Jun 1996 11:30:06 -0700 (PDT) From: "Michael A. Branch" X-Sender: branch@cvd17 To: CCL Subject: graph to table software Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi, does anybody know of a software package (public domain) that converts graphs to tables? thanks, Mike --------------------------------------------------------- Michael A. Branch "I turn big problems into Process Engineer, HDP-CVD little problems." Applied Materials, Inc. (408) 563-0689 Santa Clara, CA 95051 mbranch@hammerhead.eecs.berkeley.edu --------------------------------------------------------- From arno@alnitak.usc.edu Mon Jun 24 15:03:30 1996 Received: from alnitak.usc.edu for arno@alnitak.usc.edu by www.ccl.net (8.7.5/950822.1) id OAA12905; Mon, 24 Jun 1996 14:32:18 -0400 (EDT) Received: (from arno@localhost) by alnitak.usc.edu (8.7.2/8.7.2/usc) id LAA15365 for CHEMISTRY@www.ccl.net; Mon, 24 Jun 1996 11:31:01 -0700 (PDT) From: Arno Papazyan Message-Id: <199606241831.LAA15365@alnitak.usc.edu> Subject: Re: MD of ET in solution To: CHEMISTRY@www.ccl.net Date: Mon, 24 Jun 1996 11:31:00 -0700 (PDT) In-Reply-To: from "Darren Andrews" at Jun 24, 96 12:53:38 pm X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Darren Andrews asked about simulating electron transfer reactions in MD: I waited to see whether someone else would point out Arieh Warshel's Empirical Valence Bond (EVB) approach, before jumping in. Since I haven't seen any, I should say that the EVB approach represents a quite reliable and feasible method to incorporate reactions (not only electron transfer) into computer simulations. It is a no-nonsense, result-oriented method. His book "Computer modeling of chemical reactions in enzymes and solutions" contains enough information about the method, with references included. I would definitely recommend you to take a look. Arno Papazyan arno@usc.edu From chem8@unix.york.ac.uk Mon Jun 24 15:56:21 1996 Received: from lendal.york.ac.uk for chem8@unix.york.ac.uk by www.ccl.net (8.7.5/950822.1) id OAA13061; Mon, 24 Jun 1996 14:56:19 -0400 (EDT) Received: from ebor.york.ac.uk by lendal.york.ac.uk with SMTP (PP); Mon, 24 Jun 1996 19:53:53 +0100 Received: by ebor.york.ac.uk (950511.SGI.8.6.12.PATCH526/940406.SGI) id TAA10722; Mon, 24 Jun 1996 19:55:44 +0100 Date: Mon, 24 Jun 1996 19:55:43 +0100 (BST) From: John Waite To: chemistry@www.ccl.net Subject: Clustered HPs? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Netters, Does anyone know of an academic or research establishment that has a cluster of Hewlett-Packard workstations and/or servers, used for scientific purposes? If so I'm interested in finding out: Where these are, What configuration is used (ie how many HPs, models, approximate amounts of memory and disk per machine), How they are clustered (ie type of communication between the computers) and what types of code are (mainly) run on the cluster? Thanks, John Dr. John Waite, e-mail: chem8@york.ac.uk or The National Hellenic Research Foundation, rosen@cyclades.nrcps.ariadne-t.gr Organic and Pharaceutical Institute, phone: ++30-1-7238958 (direct) Vas. Konstantinou 48, phone: ++30-1-7247913(secrtry. Mary) Athens 116-35, fax: ++30-1-7247913 Greece or NCRS "Democritos", phone: ++30-1-6513112-5 X219 c/o Dr. G.Kordas, e-mail john@john.nrcps.ariadne-t.gr Material Science Institute, Aghia Paraskevi, Attikis, Athens 153-10, Greece From tp@elptrs7.rug.ac.be Mon Jun 24 18:56:15 1996 Received: from elptrs7.rug.ac.be for tp@elptrs7.rug.ac.be by www.ccl.net (8.7.5/950822.1) id SAA14427; Mon, 24 Jun 1996 18:23:08 -0400 (EDT) Received: by elptrs7.rug.ac.be (AIX 4.1/UCB 5.64/4.03) id AA07484; Tue, 25 Jun 1996 00:24:48 +0200 Date: Tue, 25 Jun 1996 00:24:47 +0200 (DFT) From: "Park, Tae-Yun" To: Computational Chemistry List Subject: Graphical interface for MOPAC6.0 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, all! Can anyone give me any information on a suitable graphical interface (CAChe) for MOPAC6.0 (name/how to get it) ? Thanks in advance. Sincerely, Park, TAE-YUN =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Laboratorium voor Petrochemische Techniek Krijgslaan 281, Blok S5 9000 Gent, Belgium TEL:+(32)-0(9)-264-4527 FAX:+(32)-0(9)-264-4999 e-mail: tp@elptrs7.rug.ac.be =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=