From smori@chem.s.u-tokyo.ac.jp Tue Nov 5 02:18:57 1996 Received: from utsc.s.u-tokyo.ac.jp for smori@chem.s.u-tokyo.ac.jp by www.ccl.net (8.8.2/950822.1) id CAA27669; Tue, 5 Nov 1996 02:08:57 -0500 (EST) Received: from [133.11.6.112] (smori.chem.s.u-tokyo.ac.jp [133.11.6.112]) by utsc.s.u-tokyo.ac.jp (8.7.6+2.6Wbeta7/3.4W2) with SMTP id QAA08219; Tue, 5 Nov 1996 16:06:34 +0900 (JST) Message-Id: <199611050706.QAA08219@utsc.s.u-tokyo.ac.jp> X-Sender: smori@utsc3.chem.s.u-tokyo.ac.jp X-Mailer: Macintosh Eudora Pro Version 2.1.4-J Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-2022-JP" Date: Tue, 5 Nov 1996 16:08:44 +0900 To: hutschka@quantix.u-strasbg.fr From: smori@chem.s.u-tokyo.ac.jp (Seiji Mori) Subject: Re: CCL:G:G92,HF MP2 densities in CHK file Cc: chemistry@www.ccl.net At 3:42 PM 96.10.31, wrote: > hello, > > I am using gaussian92 to fit atomic charges with potential > derived methods. > To save computer time the electronic density can be read > from the checkpoint file to avoid to calculate it several time > if you want to use it for different calculations. > By default, the HF density is saved in the CHK file. > Since I want to use the MP2 density, could somebody tell me if > there is a way to save the MP2 density in the CHK file and if > so, how to do it ?? Hi. By default, even in the MP2 calculations, SCF density was shown in the output file and stored in chkpoint file. To show and store MP2 density to checkpoint file, you need to add the option , "density=MP2" or "density=current", that is OK. > More is it possible to save both the HF and the MP2 densities in the > same CHK file?? Of course, you can split to two jobs (SCF and MP2 density calculations) but I do not know . Seiji Mori #################################################### Seiji Mori Graduate student Lab. of Physical Organic Chemistry Department of Chemistry The University of Tokyo Hongo 7-3-1, Bunkyou-ku, Tokyo 113, JAPAN. email:smori@utsc.s.u-tokyo.ac.jp smori@utsc3.chem.s.u-tokyo.ac.jp --- http://www.chem.s.u-tokyo.ac.jp/Students/smori.html #################################################### From neuber@exp.bessy.de Tue Nov 5 10:18:54 1996 Received: from metaxa.exp.bessy.de for neuber@exp.bessy.de by www.ccl.net (8.8.2/950822.1) id JAA01569; Tue, 5 Nov 1996 09:31:18 -0500 (EST) Received: by exp.bessy.de (MX V4.1 VAX) id 4; Tue, 05 Nov 1996 15:29:12 MET Sender: neuber@exp.bessy.de Date: Tue, 05 Nov 1996 15:29:11 MET From: Michael Neuber To: chemistry@www.ccl.net Message-ID: <009AAEB6.8EA72DB1.4@exp.bessy.de> Subject: pi-pi-interaction ? Dear all, in "Semiempirical Molecular Orbital Methods" (Rev.Comp.Chem. 2(1990)pp 45-81) J.J.P. Stewart describes 'strong and weak points of NDDO semiempirical methods'. What I am interested in is whether there is any further reference regarding the value of semiempiric methods (AM1, PM3, also ZINDO-1) especially for the description of intermolecular pi-pi interaction of aromatic molecules. I would appreciate any hint on reported results or experience with that, will summarize if it seems appropriate. Greetings Michael Neuber @ Berlin From dimitris@3dp.com Tue Nov 5 12:18:56 1996 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.8.2/950822.1) id LAA02618; Tue, 5 Nov 1996 11:37:51 -0500 (EST) Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA16940; Tue, 5 Nov 96 11:19:40 -0500 Received: by europa.3dp.com (950413.SGI.8.6.12) id LAA24315; Sat, 5 Oct 1996 11:35:57 -0400 From: "Dimitris Agrafiotis" Message-Id: <9610051135.ZM24313@europa.3dp.com> Date: Sat, 5 Oct 1996 11:35:53 -0400 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: VRML in HTML Cc: chemweb@ic.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii I have a simple question. How can I insert an Open Inventor (VRML) file into a HTML document? Your help would be greatly appreciated (I need it by 5 pm tonight...). Thanks, -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (610) 458-6045 665 Stockton Drive, Suite 104 | fax: (610) 458-8249 Exton, PA 19341 From robinb@cursci.co.uk Tue Nov 5 12:24:30 1996 Received: from styx.cursci.co.uk for robinb@cursci.co.uk by www.ccl.net (8.8.2/950822.1) id LAA02561; Tue, 5 Nov 1996 11:24:10 -0500 (EST) Received: from gateway.cursci.co.uk (gateway.cursci.co.uk [193.112.129.238]) by styx.cursci.co.uk (8.7.3/8.7.3/ep (2.1)) with SMTP id QAA29263 for ; Tue, 5 Nov 1996 16:23:36 GMT Message-Id: <199611051623.QAA29263@styx.cursci.co.uk> Date: Tue, 5 Nov 1996 16:21:00 +0000 From: Robin Boyett Subject: A World Wide Community for Chemists To: "'Computational Chemistry List'" X-Mailer: Worldtalk (NetConnex V4.00a)/MIME List members may wish to sample ChemWeb.com, another forum for discussion and interchange. ChemWeb.com provides single point access to discussion groups and electronic meeting rooms, a rich library of journals and other data sources, a job exchange, and shopping mall all aimed at the global chemical community.Titles in the library include new journals such as"Current Opinion in Colloid and Interface Science" which recently received and excellent review in Nature (Vol 383 page 4 Sept 5th). New content will be continuously added, including the Available Chemicals Directory from MDL. Many other publishers are expected to add their journals and databases to the Library over the coming months. Anyone with a focus on biological or medical issues may be familiar with the BioMedNet site (http://BioMedNet.com). ChemWeb.com is closely modelled on BioMedNet. Membership in the ChemWeb.com community is open to all at no charge. Members will be able to search the site through text and chemical structure. Currently, during a special introductory period, all articles are free. So it's a great time to take a look around! From rochus@felix.anorg.chemie.tu-muenchen.de Tue Nov 5 12:27:20 1996 Received: from felix.anorg.chemie.tu-muenchen.de for rochus@felix.anorg.chemie.tu-muenchen.de by www.ccl.net (8.8.2/950822.1) id LAA02627; Tue, 5 Nov 1996 11:39:47 -0500 (EST) Received: by felix.anorg.chemie.tu-muenchen.de (940816.SGI.8.6.9/930416.SGI) id RAA23543; Tue, 5 Nov 1996 17:39:34 +0100 From: "Rochus Schmid" Message-Id: <9611051739.ZM23541@felix> Date: Tue, 5 Nov 1996 17:39:33 +0100 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: MD/MM combination Cc: rochus@felix.anorg.chemie.tu-muenchen.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Netters: Please forgive me for this rather simple but long question. I really tried hard to understand the subject, but it appeared to be more complex than I have expected (and my knowledge about physical chemistry is too limited). I would be glad about any explanation or hint. Question 1: What kind of "information" do I get, when performing MD simulations with certain parts of the system kept frozen on its position? Let's consider the following example: We have a rather flexible molecule which has functional groups allowing the formation of hydrogen bonds. Now we put it in a box of water molecules and calculate the potential energy of the system with a forcefield. If we do an MD calculation with a fixed geometry of the molecule (just the solvent is moving) we'll get an ensemble and we can average the potential energy. Now that's the problem: if I want to compare the energy of two conformations of the molecule in solution, it doesn't make sense to minimize the whole systems since there are heaps of local minima of different solvent arrangements. So it seems a natural choice to take the internal energy of the molecule plus the average of the solvent energies, right? As a consequence, the energy difference between the two confromations is now temperature dependent, right? My conclusion is: at a given temperature (and sufficient sampling) these energies form a potential energy surface of the molecule which includes temperature and solvent effects "somehow"? But I don't undestand, what kind of thermodynamic function this really representates. Question 2: If I calculate all internal forces on the atoms of the molecule and average all forces excerted by the solvent on the molecule, I'll get the gradient on that potential energy surface mentioned above. (Right?) That means, I can optimize the structure of the molecule including the tempearture and solvent effects. Question 3: As far as I understood the Thermodynamic Integration method and related methods, the free energy difference can be calculated by defining a reaction coordinate and integrating over the averaged forces along that reaction coordinate. I'm not quite clear, where this deviates from the aproach above. If I asume the reaction coordinate to be the way the optimizer walks from a starting structure to the minimum, then I always have an averaged force along each step (which includes however only a sampling over the solvent). That would imply, that I get something like a free energy "surface". But I'm somehow not convinced. There must be a "bug" in my thinking, but I couldn't find it. It would be very, very helpfull for me if someone could tell me where it is. Thanx for your patience. I will summarize if there interest (and it is not too embarassing for me :-). Best greetings to all of you and especially to Jan Labanowski. Rochus -- ******************************************************************************** Rochus Schmid Technische Universitaet Muenchen Tel. ++49 89 2891 3140 Lehrstuhl f. Anorganische Chemie 1 Fax. ++49 89 2891 3088 Prof. W. A. Herrmann E-mail: Lichtenbergstrasse 4 rochus@felix.anorg.chemie.tu-muenchen.de 85747 Garching ******************************************************************************** From jkl@ccl.net Tue Nov 5 13:44 EST 1996 Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.8.2/950822.1) id NAA24927; Tue, 5 Nov 1996 13:44:53 -0500 (EST) Received: for jkl@ccl.net by krakow.ccl.net (8.6.10/920428.1525) id NAA01115; Tue, 5 Nov 1996 13:44:53 -0500 From: Jan Labanowski Date: Tue, 5 Nov 1996 13:44:53 -0500 Message-Id: <199611051844.NAA01115@krakow.ccl.net> To: chemistry@www.ccl.net Subject: FUTURE OF CCL Just a short note: I will be out of town until the end of this week... So try to be patient, I will answer my mail piece by piece when I return. My contact with the live wire may be unfortunately quite rare for a few days. Thank you very much for your contributions... Some of you really sent your checks promptly. It feels realy nice to see that I can count on you, and we can do a lot together. I will thank you personally when I am back, and I am sure I will have more to say about how things are going at the end of the next week. Thanks again for your patience and trust... Jan Labanowski CCL Admin. jkl@ccl.net From stuchebr@indigo.ucdavis.edu Tue Nov 5 16:11:41 1996 Received: from indigo.ucdavis.edu for stuchebr@indigo.ucdavis.edu by www.ccl.net (8.8.2/950822.1) id QAA04630; Tue, 5 Nov 1996 16:03:47 -0500 (EST) Received: from [128.120.7.242] by indigo.ucdavis.edu via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id NAA10039; Tue, 5 Nov 1996 13:06:38 -0800 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 5 Nov 1996 13:08:48 -0800 To: chemistry@www.ccl.net From: stuchebr@indigo.ucdavis.edu (Alexi Stuchebrukhov) Subject: POSTDOC POSITION IN THEOR CHEMISTRY AT UC DAVIS First Principles Molecular Dynamics Calculations of Complex Systems POSTDOCTORAL POSITION IN THEORETICAL CHEMISTRY AT UC DAVIS A position is available for a postdoctoral associate to conduct theoretical research in the field of dynamics of charge transfer in organic and biological materials (proteins, DNA, molecular wires, molecular electronic devices). Preference will be given to a candidate with research background in ab-initio molecular dynamics and electronic structure calculations (including Car-Parrinello and other modern first principle methods) of organometallic, biological, or other complex systems. Ability to program from scratch is mandatory. Knowledge of C is desirable. Please send CV, publication list and up to three names of references to A. A. Stuchebrukhov, Chemistry, University of California, Davis, CA 95616. One can also respond by e-mail: stuchebr@chem.ucdavis.edu. Alexi Stuchebrukhov Department of Chemistry University of California, Davis From echamot@xnet.com Tue Nov 5 20:11:36 1996 Received: from mail.xnet.com for echamot@xnet.com by www.ccl.net (8.8.2/950822.1) id TAA05697; Tue, 5 Nov 1996 19:26:39 -0500 (EST) Received: from echamot.xnet.com by mail.xnet.com (8.7.5/XNet-2.1R) with SMTP id SAA10041; Tue, 5 Nov 1996 18:27:44 -0600 (CST) Message-ID: Date: Tue, 5 Nov 96 18:25:37 EST From: "Ernest Chamot" Subject: Re: CCL:MD/MM combination To: "Rochus Schmid" , chemistry@www.ccl.net X-Mailer: VersaTerm Link v1.1.6 Dear Netters: In his query to the CCL, Rochus Schmid asked: >What kind of "information" do I get, when performing MD simulations with >certain parts of the system kept frozen on its position? And goes on to ask about: >My conclusion is: at a given temperature (and sufficient sampling) these >energies form a potential energy surface of the molecule which includes >temperature and solvent effects "somehow"? But I don't undestand, what kind of >thermodynamic function this really representates. Now I have a question. What "temperature" is this type of MD going to simulate? Temperature normally just reflects the average kinetic energy of the system, so it can be calculated from the velocities. But if part of the system is frozen, should those atoms be included in the "average"? Obviously, if all atoms are included, it will add a bunch of zero velocities, so the calculated temperature will be lower than what is reflected by the movement of molecules actually allowed to move. But would the "temperature" calculated only by averaging the moving molecules have any more meaning? I suppose that either way this is just an artificial situation, but if there is something that corresponds to temperature, I hope any answer to Rochus's question can also answer my question. Thanks. EC -- Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 Phone/Fax: (630) 637-1559 echamot@xnet.com http://www.xnet.com/~chamotlb