From hinsen@ibs.ibs.fr Mon Nov 4 04:20:03 1996 Received: from ibs.ibs.fr for hinsen@ibs.ibs.fr by www.ccl.net (8.8.2/950822.1) id DAA18938; Mon, 4 Nov 1996 03:35:09 -0500 (EST) Received: from lmshp2.ibs.fr (lmshp2.ibs.fr [192.134.36.228]) by ibs.ibs.fr (8.6.12/8.6.12) with SMTP id KAA24672; Mon, 4 Nov 1996 10:36:32 +0100 Message-Id: <199611040936.KAA24672@ibs.ibs.fr> Received: by lmshp2.ibs.fr (1.37.109.4/16.2) id AA23629; Mon, 4 Nov 96 09:35:49 +0100 Date: Mon, 4 Nov 96 09:35:49 +0100 From: Konrad Hinsen To: bruce@nmr.utmb.edu Cc: CHEMISTRY@www.ccl.net In-Reply-To: <9611031228.ZM1335@cosy.utmb.edu> (bruce@cosy.utmb.edu) Subject: Re: CCL:Fitting point charges to ESP with Spartan > Do you have a reference or some corroborating evidence for your remarks > regarding CHELPG? Do you believe the same is true for CHELP? Yes, there is no difference as far as the actual fitting procedure is concerned. CHELP and CHELPG differ only in the selection of evaluation points for the potential. As for the potential instability, CHELP and CHELPG find the least-squares fit by solving the so-called "normal equations". Any text book on matrix computations or least-squares fitting will explain in detail why this approach is unstable for all but trivial problems. Essentially, the matrix describing the least-squares problem is ill-conditioned, and forming the normal equations aggravates this problem by effectively squaring the condition number. A much better approach is to use singular value decomposition. There was a paper in J. Comp. Chem. earlier this year (I think March) that demonstrated the problem for charge fitting. I don't agree with all its conclusions, but it clearly shows the risks of normal-equation based solution schemes. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-76.88.99.28 Institut de Biologie Structurale | Fax: +33-76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From gmercier@mail.med.upenn.edu Mon Nov 4 08:18:51 1996 Received: from mail.med.upenn.edu for gmercier@mail.med.upenn.edu by www.ccl.net (8.8.2/950822.1) id HAA20151; Mon, 4 Nov 1996 07:54:19 -0500 (EST) Received: (from gmercier@localhost) by mail.med.upenn.edu (8.6.12/8.6.12) id HAA19729 for chemistry@www.ccl.net; Mon, 4 Nov 1996 07:54:20 -0500 From: "Gustavo A. Mercier Jr" Message-Id: <199611041254.HAA19729@mail.med.upenn.edu> Subject: NPT ensemble and P fluctuations To: chemistry@www.ccl.net Date: Mon, 4 Nov 1996 07:54:19 -0500 (EST) X-Mailer: ELM [version 2.4 PL23-upenn3.1] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi! I am running an NPT ensemble using the Berendsen method to scale the Temperature and Pressure. In 25ps the temperature has stabilized within 2-3deg from the 300K target. The energy is pretty stable (although I know it should not be conserved). The dimensions of the periodic box have also stabilized (although the box volume is not meant to be conserved). The density is also stable at 0.98-0.99 (Solvent is water.) The solute is a generation 2 PAMAM dendrimer and it is in a box with 3500 water molecules. I am using the module SANDER from AMBER 4.1 with all patches up to bugfix.77. **Problem**: The pressure is converging very slowly... It fluctuates widely 80-100kbars with the average close to -1.0-+5.0kbars. Right now the coupling constants are 0.1ps for both temp and pressure. **Question**:Are there any tricks to speed up the equilibration of the pressure? I will summarize to the net if there is interest. Thanks for your kind reply! -- ("`-/")_.-'"``-._ Gustavo A. Mercier,Jr.,MD,PhD (. . `) -._ )-;-,_() Division of Nuclear Medicine (v_,)' _ )`-.\ ``- Dept. of Radiology _;- _,-_/ / ((,' University of Pennsylvania ((,.-' ((,/ 3400 Spruce St. gmercier@mail.med.upenn.edu Philadelphia, PA 19104 215-662-3069/3091 fax: 215-349-5843 From ep7@dent.okayama-u.ac.jp Thu Oct 31 20:17:55 1996 Received: from deews1.dent.okayama-u.ac.jp for ep7@dent.okayama-u.ac.jp by www.ccl.net (8.8.2/950822.1) id TAA18372; Thu, 31 Oct 1996 19:37:39 -0500 (EST) Received: from [150.46.140.80] (yobou2.dent.okayama-u.ac.jp) by deews1.dent.okayama-u.ac.jp (5.67+1.6W/6.4JAIN-1.1) id AA06550; Fri, 1 Nov 96 09:37:01 JST Message-Id: <9611010037.AA06550@deews1.dent.okayama-u.ac.jp> Date: Fri, 1 Nov 1996 09:45:39 +0900 To: chemistry@www.ccl.net From: ep7@dent.okayama-u.ac.jp Subject: CCL:SUMMARY:BSSE I send you a summary of answers about BSSE.　I would like to thank eve rybody for many advices. I hope this summary will help everybody. Masao Masamura Masao Masamura: Dear Sir: I would like to ask about BSSE. (1) In large basis set, how large is BSSE ? (2) In chemical physics letters, 217(1994)48 written by Ernest R. Davidson and Subhas J. Chakravorty, an explanation is provided for the tendency in water and HF dimers for the counterpoise-corrected correlation energy to seem worse than the uncorrected energy. Do you know related paper ? (3) Do you know best method for removing BSSE ? Thank you. ============================================================================ ===== Masao Masamura Okayama University Dental School Department of Preventive Dentistry Fax: 81-86-225-3724 e-mail: ep7@dent.okayama-u.ac.jp ============================================================================ ===== you might find our article on the HF dimer of use: K.A. Peterson and T.H. Dunning, Jr., J. Chem. Phys. 102, 2032 (1995). I believe there is now a general consensus in the literature that the function counterpoise method of Boys and Bernardi is the best way to remove BSSE. best regards, Kirk Peterson -- Kirk A. Peterson Assistant Professor Affiliate Scientist Department of Chemistry & Theory, Modeling, and Simulation Washington State University Environmental Molecular Sciences Laboratory Richland, WA Pacific Northwest National Laboratory Office: (509) 375-6350, (509) 372-7282 Fax: (509) 375-6631 ka_peterson@pnl.gov http://www.tricity.wsu.edu/~kipeters/ Date: Thu, 17 Oct 96 17:19:44 -0230 From: cory@bohr.chem.mun.ca (Cory C. Pye) To: ep7@dent.okayama-u.ac.jp Subject: BSSE 1) Usually not very big. 2) I am not familiar with this paper, but I will look it up. 3) I personally feel that the CHA method is the best way to remove BSSE. You may wish to have a look at C. C. Pye et al, JMS (Theochem), 307 (1994) 239 where we calculate BSSE for 46 basis sets from STO_3G up to quadruple zeta for 8 systems, using both CHA and Boys-Bernardi counterpoise method. There are a few references in here that may be useful. -Cory ************* ***************** ! Cory C. Pye *** ** ** ** ! Graduate Student and Unpaid Sys Admin ** * **** ! Theoretical and Computational Chemistry ** * * ! cory@bohr.chem.mun.ca ** * * ! http://www.ucs.mun.ca/~cory/index.html *** * * ** ! ***************** ! Les Hartree-Focks ************* ! (Apologies to Montreal Canadien Fans) Date: Thu, 17 Oct 1996 22:03:03 +0100 From: Marc Prosenc Apparently-To: ep7@dent.okayama-u.ac.jp hi masao, to avoid BSSE try to maximize your base-set. if you already know which atoms have a superposition error, put polarisation functions to these atoms to describe the electron distribution correct. greetings marc From: David Heisterberg Date: Thu, 17 Oct 1996 17:34:57 -0400 To: Chemistry@www.ccl.net, ep7@dent.okayama-u.ac.jp Subject: CCL:BSSE Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk Masao Masamura writes: > I would like to ask about BSSE. There is an interesting paper by van Duijneveldt et.al. in Chemical Reviews 94, 1873 (1994). They argue rather strongly that counterpoise correction is the way to go. They are also "forced to conclude that this new definition of BSSE [Davidson and Chakravorty] is superfluous, and one may only hope that its introduction will not further increase the confusion surrounding the CP recipe." It's a spirited review! Dave Heisterberg -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: djh@ccl.net -- Original Sender From: Address: djh@ccl.net 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 Date: Fri, 18 Oct 1996 09:28:33 +0200 From: hutschka@quantix.u-strasbg.fr To: ep7@dent.okayama-u.ac.jp Subject: Re: CCL:BSSE Masao, In theory, the larger your basis set is the smaller will be the counterpoise correction to the interaction energy between your fragments. At my knowledge, the counterpoise correction is the most accepted correction to avoid BSSE. Ypu can take a look at the review by Van Duijneveldt: State of the art in countepoise theory, Van Duijneveldt et al., Chem. Rev., 1994, 1873-1885. Regarding to the paper of Davidson et al. you can take a look at: Kallies, Mitzner, J. Mol. Model., 1995, 1, 68-78 The paper deal with proton transfer in hydrogen bonded system and talk about BSSE evaluated at various level including MP2. http://derioc1.organik.uni-erlangen.de/info/JMOLMOD/papers/papers.html I hope this will help you. Francois ============================================================================= Fran苡is HUTSCHKA Ph.D. Student in Quantum Chemistry Laboratoire de Chimie Quantique UPR 139 du CNRS 4, rue Blaise Pascal Phone: (33).88.41.60.32 67000 STRASBOURG Fax: (33).88.61.20.85 FRANCE E-Mail: hutschka@quantix.u-strasbg.fr ============================================================================ = Date: Fri, 18 Oct 96 10:23:45 +0200 From: aldert@chemde4.leidenuniv.nl (Aldert Westra Hoekzema) To: Subject: Re: CCL:BSSE Hi Masao, Regarding your questions about BSSE I do not consider myself qualified to give my opinion, but I can recommend the following article: "State of the Art in Counterpoise Theory" F.B. van Duijnevelt, J.G.C.M. van Duijnevelt & J.H. van Lenthe, Chem. Rev. 94 (1994), 1873-1885. Kind greetings, Aldert ------------------------------------------- A.J.A. Westra Hoekzema Conformational Analysis (Organic Chemistry) Leiden Institute of Chemistry, Gorlaeus Laboraties, Leiden University P.O. Box 9502, 2300 RA Leiden The Netherlands Phone : +31 715274505 Fax : +31 715274488 E-mail: aldert@chemde4.LeidenUniv.nl ------------------------------------------- From: mbdpsrl Subject: BSSE To: ep7@dent.okayama-u.ac.jp Date: Fri, 18 Oct 1996 09:38:01 +0100 (BST) X-Mailer: ELM [version 2.4 PL24alpha3] Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 719 Dear Dr. Masamura, I hope you don't mind me emailing you directly. I was in a similar position to you last year, as I did not know very much about BSSE.Also I am not a specialist in computational chemistry which made things very difficult to understand. I did alot of reading about this as it directly affected my work but there is a GREAT deal of controversy over BSSE and how it is dealt with. If you wish I will send you a list of my papers that I found regarding the subject, also please search through the archives of the CCL lists and there should be some information there. Best wishes, Robert V. Law, Dept. of Chemistry, University of Manchester, Manchester M13 9PL U.K. email:mbdpsrl@afs.mcc.ac.uk Date: Fri, 18 Oct 1996 08:56:12 -0400 (EDT) From: "Subhas J. Chakravorty" X-Sender: rahsjc@walrus.sh.rohmhaas.com To: Chemistry@www.ccl.net Subject: CCL:BSSE Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk On Thu, 17 Oct 1996, David Heisterberg wrote: > Masao Masamura writes: > > I would like to ask about BSSE. > > There is an interesting paper by van Duijneveldt et.al. in > Chemical Reviews 94, 1873 (1994). They argue rather strongly > that counterpoise correction is the way to go. They are also > "forced to conclude that this new definition of BSSE [Davidson > and Chakravorty] is superfluous, and one may only hope that its > introduction will not further increase the confusion surrounding > the CP recipe." It's a spirited review! > > Dave Heisterberg There are a couple of comments and replies on our paper in CPL which may be of interest. Feller, DelBene and Dunning groups have been studying the dimers, their studies and results are relevant. Subhas J. Chakravorty, sjchakravorty@rohmhaas.com (215)-619-5481 Rohm and Haas Company Spring House, PA-19447 ************************************************************************** Disclaimer : Opinions in the above text are not of Rohm and Haas Company + ************************************************************************** -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: rahsjc@rohmhaas.com -- Original Sender From: Address: rahsjc@rohmhaas.com 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 cdac.ernet.in!gadre@parcom.ernet.in Thu Oct 31 10:18:02 1996 Received: from sangam.ncst.ernet.in for cdac.ernet.in!gadre@parcom.ernet.in by www.ccl.net (8.8.2/950822.1) id KAA14634; Thu, 31 Oct 1996 10:09:44 -0500 (EST) Received: (from root@localhost) by sangam.ncst.ernet.in (8.7.5) id UAA03241 for CHEMISTRY@www.ccl.net; Thu, 31 Oct 1996 20:43:37 +0530 (GMT+05:30) Received: from parcom.UUCP by iucaa (4.1/SMI-4.1) id AA18000; Thu, 31 Oct 96 09:42:01+050 Received: from parcom by sangam.ncst.ernet.in; Thu, 31 Oct 1996 20:43 GMT Received: from parcom.UUCP by iucaa (4.1/SMI-4.1) id AA18000; Thu, 31 Oct 96 09:42:01+050 Received: by parcom.cdac.ernet.in (4.1/SMI-4.1) id AA26175; Thu Oct 31 09:26:05 1996 (GMT + 0530) Date: Thu Oct 31 09:26:05 1996 (GMT + 0530) From: gadre@cdac.ernet.in Message-Id: <9610310356.AA26175@parcom.cdac.ernet.in> To: CHEMISTRY@www.ccl.net Subject: Packing in hydrocarbons Dear Sirs : Do you have a guess or explanation for the fact that the paraffins pack with their skeletons almost parallel. Further, what is a simple explanation for the fact that even n paraffins have higher MP's than the next odd n-ones? I'll be grateful for your response and references related to my query. Thanks...................................Shridhar Gadre 31.10.96. From joubert@ext.jussieu.fr Thu Oct 31 10:37:02 1996 Received: from shiva.jussieu.fr for joubert@ext.jussieu.fr by www.ccl.net (8.8.2/950822.1) id JAA14446; Thu, 31 Oct 1996 09:33:44 -0500 (EST) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.7.6/jtpda-5.2) with ESMTP id PAA03110 for ; Thu, 31 Oct 1996 15:32:29 +0100 (MET) Received: from [134.157.11.17] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Thu, 31 Oct 1996 15:32:22 +0100 X-Sender: joubert@idf.ext.jussieu.fr Message-Id: Date: Thu, 31 Oct 1996 16:38:05 +0200 To: chemistry@www.ccl.net From: joubert@ext.jussieu.fr (Laurent Joubert) Subject: G94 Cube files visualization Dear Netters, There have been many questions regarding visualization of the data generated by Gaussian 94 Cube files. One way to visualize these files, is to get a great FREEWARE called "SciAn" which is a scientific visualization and animation program for SGI and IBM Risc6000 workstations. You can get it at the following ftp address : ftp.scri.fsu.edu (/pub/SciAn) The last version is a beta one : /pub/SciAn/beta/scian120.tar.Z (This is the one I use). Once you have installed the software, it is easy to convert cube files to the "stf" file format which is readable by SciAn (I have written a small program which can do it, in order to visualize density, electrostatic potential or molecular orbitals). If you have any problem, do not hesitate to contact me. Laurent Joubert ******************************************************** * Laurent JOUBERT (PhD student) * * * * Ecole Nationale Superieure de Chimie de Paris * * Laboratoire d'Electrochimie et de Chimie Analytique * * 11, rue Pierre et Marie Curie * * 75231 PARIS CEDEX 05- FRANCE * * * * Tel : 44-27-66-94 * * Fax : 44-27-67-50 * * * * E-Mail : joubert@ext.jussieu.fr * * http://www.enscp.jussieu.fr * ******************************************************** From PEARLMAN@VAX.PHR.UTEXAS.EDU Thu Oct 31 12:22:32 1996 Received: from VAX.PHR.UTEXAS.EDU for PEARLMAN@VAX.PHR.UTEXAS.EDU by www.ccl.net (8.8.2/950822.1) id MAA15708; Thu, 31 Oct 1996 12:08:39 -0500 (EST) From: Date: Thu, 31 Oct 1996 11:08:37 -0600 (CST) To: CHEMISTRY@www.ccl.net Message-Id: <961031110837.7300@VAX.PHR.UTEXAS.EDU> Subject: What *YOU* can do to help with the future of the CCL Greetings -- Jan Labanowski recently posted a message regarding the future of the CCL. He specifically asked that we NOT take up "CCL-bandwidth" by discussing the various issues "on-line" and I certainly do not intend to ignore his request!! However, Jan made a second request in his message which I fear some CCL-readers might not have seen. "Buried" under 222 lines of very good (but lengthy) justifications was the text: >So now is the reality check... Please contribute as individuals now... >I will of course remind you about the CCL Drive several times. Send the >checks with the amount you consider reasonable to me: > > Jan Labanowski > Ohio Supercomputer Center > 1224 Kinnear Rd > Columbus, OH 43212-1163 > >and make the checks payable to: > > OSC Development Fund (CCL) > >(Not to me personally, since I will not be able to cash them!!!) >You will receive a THANK YOU letter, which you need to keep for your >records, since the contribution IS TAX DEDUCTIBLE and you should deduct >it on your income tax return (Yes, I checked this!!!). Jan also pointed out that the CCL's annual costs (approximately $200,000) could be met if EVERY subscriber contributed $100. Of course, it is not possible for all subscribers to contribute but it provides an indication of the dollar amounts he he hoping to receive from those of us who can make such contributions. I'm sure that contributions in *any* amount will be appreciated. -- Bob Pearlman From rabe@fu-berlin.de Mon Nov 4 09:18:42 1996 Received: from ki1.chemie.fu-berlin.de for rabe@fu-berlin.de by www.ccl.net (8.8.2/950822.1) id JAA20727; Mon, 4 Nov 1996 09:12:22 -0500 (EST) Received: by ki1.chemie.fu-berlin.de (Smail3.1.28.1) from waller.chemie.fu-berlin.de (160.45.26.6) with smtp id ; Mon, 4 Nov 96 15:11 MET Received: by waller.chemie.fu-berlin.de (Smail3.1.28.1) from Waller.Chemie.FU-Berlin.DE (127.0.0.1) with smtp id ; Mon, 4 Nov 96 15:11 MET Sender: rabe@www.ccl.net Message-ID: <327DF9AC.446B@fu-berlin.de> Date: Mon, 04 Nov 1996 15:11:56 +0100 From: Bjoern Rabenstein Organization: Freie Universitaet Berlin, Germany X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 5.3 IP20) MIME-Version: 1.0 To: Computational Chemistry Mailing List Subject: Summary: Fitting point charges to ESP with Spartan Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I got many replies, of which some were already posted to the list. Among them were also mails from Philip E. Klunzinger from Wavefunction and even Curt Breneman himself. (: Conclusions: Spartan IS essentially using a CHELPG-approach, i.e. points are on a grid and not on atom centered shells. The slightly different results compared to stand alone CHELPG or CHELP included in Gaussian9x could be explained by the following: - number of used points - default set of atomic exclusion radii - how far away from atoms reaches region included in calculation (in neutral molecules charges will approach to zero if too many points too far away are included) - instability of least square fitting (alternative would be singular value decomposition, see posting of Konrad Hinsen) -- Bjoern Rabenstein * Freie Universitaet Berlin * Inst. f. Biochemie Inst. f. Kristallographie * AG Knapp * Takustrasse 6 * D-14195 Berlin [Telephon] +49-30-838-3484 [Telefax] +49-30-838-3464 [email] rabe@fu-berlin.de [WWW] http://www.chemie.fu-berlin.de/~rabe/ From qojskd@uscmail.usc.es Thu Oct 31 04:17:54 1996 Received: from uscmail.usc.es for qojskd@uscmail.usc.es by www.ccl.net (8.8.2/950822.1) id EAA12414; Thu, 31 Oct 1996 04:15:56 -0500 (EST) Received: from [193.144.74.36] (qolera.usc.es) by uscmail.usc.es (5.67b/1.34) id AA14419; Thu, 31 Oct 1996 10:14:40 +0100 Date: Thu, 31 Oct 1996 10:14:40 +0100 Message-Id: <199610310914.AA14419@uscmail.usc.es> From: "F. Javier Sardina" To: CHEMISTRY@www.ccl.net Subject: Freeware for NMR data processing Dear fellow netters: The newest versions of the freeware NMR data processing programs SwaN-MR (3.2.4 for PowerMacintosh) and MestRe-C (1.1.1 for Windows 95) have just been released. They can be retrieved from any of the following anonymous ftp repositories: SwaN-MR 3.2.4 (for PowerMacintosh): qobrue.usc.es/nmr/SwaN-MR/Swan_mr_324 ftp.uniovi.es/pub/Mac/nmr ftp.rediris.es/software/incoming/science/nmr/swan-mr www.ccl.net/pub/chemistry/software/MAC/Swan-NR For more information check SwaN-MR WWW home page: http://qobrue.usc.es/jsgroup/swan/home.htm MestRe-C 1.1.1 (for PC's with Windows 95): ftp://qobrue.usc.es/pub/nmr/MestRe-C ftp.uniovi.es/pub/win95/nmr ftp.rediris.es/software/incoming/science/nmr/mestrec111 ftp://www.ccl.net/pub/chemistry/software/MS-WINDOWS95/MestRe-C For more information check MestRe-C WWW home page: http://qobrue.usc.es/jsgroup/MestRe-C/MestRe-C.html Happy NMR data processing F. Javier Sardina F. Javier Sardina Phone: 34-81-591085 Departamento de Quimica Organica 34-81-563100. Ext 14234 Universidad de Santiago de Compostela Fax: 34-81-595012 or 34-81-591091 15706 Santiago de Compostela e-mail: qojskd@usc.es SPAIN http://qobrue.usc.es/jsgroup/Js-eng.html From ccl@www.ccl.net Thu Oct 31 14:30:48 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.2/950822.1) id OAA16485; Thu, 31 Oct 1996 14:01:04 -0500 (EST) Received: from adams.patriot.net for eslone@patriot.net by bedrock.ccl.net (8.8.2/950822.1) id OAA04692; Thu, 31 Oct 1996 14:01:02 -0500 (EST) Received: from eslone.erols.com (th-0-25.patriot.net [206.151.9.35]) by adams.patriot.net (8.7.4/8.7.3) with SMTP id NAA20398; Thu, 31 Oct 1996 13:58:53 -0500 Message-ID: <3278F750.5DCA@patriot.net> Date: Thu, 31 Oct 1996 14:00:32 -0500 From: "J. Eric Slone" Reply-To: eslone@patriot.net Organization: Scientific Consulting Services To: chemistry@ccl.net, CHMINF-L@IUBVM.UCS.INDIANA.EDU Subject: Free Molgen Copy Now ONLINE! Hello again: Molgen is now available from CCL archives as: ftp://www.ccl.net/pub/chemistry/software/MS-DOS/molgen You can also get there via Web http://www.ccl.net/chemistry.html -> CC Archive -> software -> MS-DOS -> molgen A copy of the Users Manual in MS Word 7 format is available >from my homepage at: http://www.patriot.net/users/eslone Please feel free to download and distribute this program and manual as you wish (as long as it's for FREE). Although I will not provide technical support on a free program, I am happy to receive comments and suggestions. Please re-post this message on any other chemistry related lists you belong to. Thanks! Eric ___________________________________________________________________ J. Eric Slone 10 years of Serving Scientific Consulting Services the Technical Community 5500 Holmes Run Parkway, Suite 501 Alexandria, Virginia 22304-2851 Phone: (703) 461-7078 mailto:eslone@patriot.net Fax: (703) 751-6639 http://www.patriot.net/users/eslone ___________________________________________________________________ Visit the Tuva Trader Online on our site at: http://www.patriot.net/users/eslone/tuva.htm ___________________________________________________________________ Freelance Technical Writing Software and Multimedia Development Specializing in the Sciences ___________________________________________________________________ From harmonic@world.std.com Fri Nov 1 22:18:07 1996 Received: from europe.std.com for harmonic@world.std.com by www.ccl.net (8.8.2/950822.1) id VAA25631; Fri, 1 Nov 1996 21:51:39 -0500 (EST) From: Received: from world.std.com by europe.std.com (8.7.5/BZS-8-1.0) id VAA11346; Fri, 1 Nov 1996 21:51:39 -0500 (EST) Received: by world.std.com (5.65c/Spike-2.0) id AA01921; Fri, 1 Nov 1996 21:51:38 -0500 Date: Fri, 1 Nov 1996 21:51:38 -0500 Message-Id: <199611020251.AA01921@world.std.com> To: chemistry@www.ccl.net Subject: Free, downloadable version of O-Matrix Harmonic Software Inc. has released O-Matrix 3.1 for Windows, a RAD environment (Rapid Application Development), for scientific and engineering applications. The new version of O-Matrix includes extensive capabilities for developing visually-oriented, easy-to-use technical applications. This enables the development of user-friendly applications significantly faster than traditional visually-oriented compilers and with performance that is dramatically faster than typical interpreted matrix languages. In addition O-Matrix version 3.1 includes an improved user interface for more productive application development and simplified interactive usage. Many functions have been added including routines for Kalman filtering, wavelet analysis and advanced statistics. Download a free copy of O-Matrix at http://world.std.com/~harmonic/download.html O-Matrix for Windows is compatible with Windows 3.1, Windows 95 and Windows NT. Individual copies are priced at $395.00. Currently registered students and faculty may purchase the complete package for $49.95. Harmonic Software Inc. 1-800-895-4546 12223 Dayton Avenue North FAX: 1-206-367-1067 Seattle, WA 98133 E-mail: harmonic@world.std.com http://world.std.com/~harmonic From tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de Mon Nov 4 07:18:40 1996 Received: from ns1.DKFZ-Heidelberg.de for tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de by www.ccl.net (8.8.2/950822.1) id GAA19882; Mon, 4 Nov 1996 06:40:57 -0500 (EST) Received: from mbp-sgi7.inet.dkfz-heidelberg.de (mbp-sgi7.inet.dkfz-heidelberg.de [193.174.48.96]) by ns1.DKFZ-Heidelberg.de (8.7.3/DKFZ-8.6.4) with ESMTP id MAA03044 for ; Mon, 4 Nov 1996 12:36:05 +0100 (MET) Received: (tajkhors@localhost) by mbp-sgi7.inet.dkfz-heidelberg.de (940816.SGI.8.6.9/DKFZ-8.6.4) id NAA25004 for chemistry@www.ccl.net; Mon, 4 Nov 1996 13:38:35 +0100 From: "Emadeddin Tajkhorshid" Message-Id: <9611041338.ZM25000@mbp-sgi7.inet.dkfz-heidelberg.de> Date: Mon, 4 Nov 1996 13:38:34 +0100 Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de To: chemistry@www.ccl.net (Computational Chemistry List) Subject: Summary: Quntom Chem. MD Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="PART-BOUNDARY=.19611041338.ZM25000.inet.dkfz-heidelberg.de" --PART-BOUNDARY=.19611041338.ZM25000.inet.dkfz-heidelberg.de Content-Description: Text Content-Type: text/plain ; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Zm-Decoding-Hint: mimencode -q -u Dear Netter Enclosed I collect the responses to my question about quantom chemical molecular dynamics. Thanx all for their answers. The question: ************* I want to know if there is any program applying semiempirical and/or ab i= nitio quantom chemical calculation in molecular dynamics simulation. Any relate= d information and comments is highly appreciated. *************************************************************************= *** Recent academic versions of CHARMM have both AM1 (semi-empirical) and GAMESS (ab-initio) interfaces and code; distribution is arranged through Prof. Martin Karplus's group at Harvard for a modest fee to non-profit research organizations. -- Rick Venable =3D=3D=3D=3D=3D\ |=3D| "Eschew Obfus= cation" FDA/CBER Biophysics Lab |____/ |=3D| Bethesda, MD U.S.A. | \ / |=3D| ( Not an official stateme= nt or rvenable@deimos.cber.nih.gov \/ |=3D| position of the FDA; fo= r that, http://nmr1.cber.nih.gov/venable.html |=3D| see http://www.fda.go= v ) *************************************************************************= ** Hi! Charmm will do just that. Charmm 24b2 should do the ab-initio stuff - bu= t I found a bunch of routines missing when I tried to compile. The am1 method is quite stable now. There are numberous others - but that one is availible commercially (for the am1 at least) and straight forward. Good luck Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- *************************************************************************= ** You might have a look at: Bash P. A., Ho L. L., MacKerell A., Levine D., Halstrom P., =93Progress Toward Chemical Accuracy in Computer Simulations of Condense= d Phase Chemical Reactions=94, Proc. Nat. Acad. Sci., 93, 3698, 1996 Ho L. L., MacKerell, A., Bash P. A. =93Proton and Hydride Transfers in Solution: Hybrid QM/MM Free Energy Perturbation Study=94, J. Phys. Chem., 100, 4466, 1996 Paul Bash ________________________________________ Paul A. Bash Argonne National Laboratory Bldg 202/A349 9700 S. Cass Avenue Argonne, IL. 60439 pabash@anl.gov Work Phone: 708-252-8631 Home Phone: 312-642-3029 Fax: 708-252-3387 ---------------------------------------- *************************************************************************= ** There are probably more, but the two I am aware of off hand are Carr-Parinello, which does dynamics with the local density functional approximate ab initio code, and some work by Dave Dixon, while at Dupont,= which he as reported at ACS meetings. It's been some time, but the Corne= ll Theory Center had the Carr-Parinello code, and Dave Dixon is now at Pacif= ic Northwest Laboratories I believe. I would be interested in hearing a summary, if there isn't already one in= the CCL archives. 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 *************************************************************************= ** HyperChem 4 (semiempirical level), 4.5-5 both ab initio and semiempirical= - but of cours it's comercial. If it's still interesting I can ad some comm= ents. regards, Krzys Radacki _________________________-----------------------------------------------= ----- ------------------------- e-mail: Krys.Radacki@ac.RWTH-Aachen.DE= --- ------------------------------------------------------------------------= ----- *************************************************************************= ** Try HyperChem (available for both IBM-compatible PC and for SGI). The URL is http://www.hyper.com Dan Berger bergerd@bluffton.edu *************************************************************************= ** Hi Emad, I am not entirely sure what you mean with your request... However, I know that "combined QM/MM" (a method where the most interestin= g part of the molecule is being treated by QM, e.g. DFT, the rest by MM) is very actively under study these days. No references, though. On the other hand, there is the "ab initio molecular dynamics", as has been developed by Car and Parinello. References that I would have on hand would be P.E. Blochl, Phys.Rev.B.50 (1994), 17953 and other papers by Blochl (the name contains an "Umlaut o"). D.K.Remler, P.A.Madden, Mol. Phys. 70 (1990), 921 (review paper). Look, of course, also for papers by M.Parinello and / or R.Car. Hope this helps a bit.... Please summarize! Yours, Georg This is a P.S. to my message that I sent before: one should call the Car-Parinello approach "first principle molecular dynamics" since it is a DFT based method rather then an "ab initio" method. G. -- =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D Georg Schreckenbach Tel: (Canada)-403-220 8204 Department of Chemistry FAX: (Canada)-403-289 9488 University of Calgary Email: schrecke@zinc.chem.ucalga= ry.ca 2500 University Drive N.W., Calgary, Alberta, Canada, T2N 1N4 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D *************************************************************************= ** HyperChem can do this; I can send you more information, or put you in contact with a local dealer, if you wish. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-404= 0 Info requests to: info@hyper.com Support questions to: support@hyper.c= om Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ *************************************************************************= ** Contact or search for papers by Paul Bash at Argonne National Laboratory,= Argonne, IL, USA. He has been doing work in that area for years. -- Jeff Nauss *********************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: Jeffrey.Nauss@UC.Edu * * CCCCCCC URL http://www.che.uc.edu/~nauss * *********************************************************************** *************************************************************************= ** Dear Emad, I read your note on Computational Chemistry List (CCL). I am presently applying ab initio molecular dynamics on biological systems. The method, who allow you to solve the time-dependent Sro equation in simulations a smart way, was devised 11 years ago by Car and Parrinello, If you're interested, I can send you some reprints. Sincerely yours Paolo -- Paolo Carloni IBM Zurich Research Laboratory Saeumerstrasse 4 CH-8803 Rueschlikon/Switzerland Internet: cap@zurich.ibm.com Phone: +41-1-724-8490 Fax: +41 1-724 0809 *************************************************************************= ** Thanx again. -- = Emad ********************************************************************* E. Tajkhorshid = German Cancer Research Center; DKFZ Tel: +49 6221 42 2339 Dept. Molecular Biophysics (0810) FAX: +49 6221 42 2333 P.O.Box 101949 Email: E.Tajkhorshid@DKFZ-Heidelberg.DE 69009 Heidelberg, FRG *********************************************************************** * A friend may well be reckoned a masterpiece of the nature (Emerson) * *********************************************************************** --PART-BOUNDARY=.19611041338.ZM25000.inet.dkfz-heidelberg.de-- From nila@solidmr.kun.nl Fri Nov 1 05:18:41 1996 Received: from wn1.sci.kun.nl for nila@solidmr.kun.nl by www.ccl.net (8.8.2/950822.1) id EAA20187; Fri, 1 Nov 1996 04:49:28 -0500 (EST) Received: from bloch.solidmr.kun.nl by wn1.sci.kun.nl via bloch.solidmr.kun.nl [131.174.41.1] with SMTP for id KAA06265 (8.7.6/3.11); Fri, 1 Nov 1996 10:49:21 +0100 (MET) Received: from stern.solidmr.kun.nl by bloch.solidmr.kun.nl (SMI-8.6/SMI-SVR4) id KAA08355; Fri, 1 Nov 1996 10:49:20 +0100 Received: by stern.solidmr.kun.nl (SMI-8.6/SMI-SVR4) id KAA11098; Fri, 1 Nov 1996 10:49:19 +0100 Date: Fri, 1 Nov 1996 10:49:19 +0100 From: nila@solidmr.kun.nl (Niels van der Laag) Message-Id: <199611010949.KAA11098@stern.solidmr.kun.nl> To: chemistry@www.ccl.net Subject: Summary: algorithm for eigenvalues Dear CCL-ers, Last week I posted a question about eigenvalaues of a large banded hermitian matrices. I got several responses which I summarized here below. The best way to do this is to use the Householder reduction and after that an QR method. With all the answers I recieved,I will try to modify the algorithm so it would fit strictly to my problem. For theoretical explenation: Wilkinson, "The Algebraic Eigenvalue Problem", Clarendon Press, Oxford (1965) (there should be a newer edition, but I didn't find it in our library) Press et. al., Numerical recipes in C, Cambridge University Press", Cambridge (1992) (it's now also on the web: http://cftata2.harvard.edu/nr) Burden and Faires, "Numerical Analysis", PWS Publishing Company, Boston (5th ed., 1993) (This is a , IMHO, good introductionary book in numerical analysis, It could be used in such a course for computational chemists.) Wilkinson and Reinsch, "Handbook for Automatic Computation, Vol. II Linear Algebra", Springer-Verlag, Berlin (1971) Many have already implemented the algorithms. They are stored in several packages. Here are some: LAPACK: http://www.netlib.org/lapack EISPACK: http://www.netlib.org/eispack ARPACK: http://www.caam.rice.edu/~kristyn/parpack_home.html Thanks to all who responded, Niels +----------------------------------------------------------+ | Niels J. van der Laag | | Student Computational Chemistry | | Dept. of Physical Chemistry (Solid State NMR) | | University of Nijmegen | | Toernooiveld 1, NL-6525 ED Nijmegen, Netherlands | | phone: ++31-24-3653112 email: nila@solidmr.kun.nl | | nielsl@sci.kun.nl | +----------------------------------------------------------+ From ccl@www.ccl.net Fri Nov 1 17:18:10 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.2/950822.1) id QAA24140; Fri, 1 Nov 1996 16:20:46 -0500 (EST) Received: from tlon.unq.edu.ar for seba@tlon.unq.edu.ar by bedrock.ccl.net (8.8.2/950822.1) id QAA25574; Fri, 1 Nov 1996 16:19:49 -0500 (EST) Received: from pent1.unlp.edu.ar (pent1.unq.edu.ar [170.210.73.72]) by tlon.unq.edu.ar (8.8.0/8.6.10) with SMTP id SAA04274 for ; Fri, 1 Nov 1996 18:21:14 -0300 Date: Fri, 1 Nov 1996 18:21:14 -0300 Message-Id: <199611012121.SAA04274@tlon.unq.edu.ar> X-Sender: seba@tlon.unq.edu.ar To: chemistry@ccl.net From: seba@unq.edu.ar (sebastian fernandez) Subject: protonation using MD Status: RO Hi: Does anybody know how can I study a protonation reaction using Molecular Dynamic or Quantum Mechanic/Molecular Mechanic mixed model? I would be very greatfull if there is anyone that know something about it. Sebasti=E1n Fern=E1ndez Alberti Centro de Estudios e Investigaciones Univ. Nacional de Quilmes Saenz Pe=F1a 180, 1876 Bernal, Prov. Buenos Aires Argentina From toukie@zui.unizh.ch Mon Nov 4 04:18:46 1996 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.2/950822.1) id EAA19133; Mon, 4 Nov 1996 04:10:03 -0500 (EST) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA10439; Mon, 4 Nov 1996 10:14:18 +0100 Message-Id: <1.5.4.32.19961104091045.0066d4dc@zui.unizh.ch> X-Sender: toukie@zui.unizh.ch (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Date: Mon, 04 Nov 1996 10:10:45 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Polarisability in MOPAC Dear Colleagues; Using MNDO with MOPAC 6.0, I obtained an E4 average alpha polaris- ability value for phenol of 11.261823 cubic Angstoms. According to the in- formation available to me, the E4 value is derived from the effect of the applied electric field (electric field gradient of 0.001) on the heat of formation. Is the "electric field gradient of 0.001" abbreviated "del E = 0.001"? Also, what are the units/dimensions of the value "0.001"? Thanks in advance to all responders. Sincerely, S. Shapiro ZH, CH toukie@zui.unizh.ch From vangreve@univ-orleans.fr Mon Nov 4 13:18:52 1996 Received: from centre.univ-orleans.fr for vangreve@univ-orleans.fr by www.ccl.net (8.8.2/950822.1) id MAA22929; Mon, 4 Nov 1996 12:31:05 -0500 (EST) Received: from TOURMALET.univ-orleans.fr (tourmalet.univ-orleans.fr [193.49.95.21]) by centre.univ-orleans.fr (8.6.9/8.6.9) with SMTP id SAA07004 for ; Mon, 4 Nov 1996 18:32:46 +0100 Message-ID: <327E2845.1AEE@univ-orleans.fr> Date: Mon, 04 Nov 1996 18:30:45 +0100 From: Eric VANGREVELINGHE Reply-To: vangreve@univ-orleans.fr Organization: ICOA X-Mailer: Mozilla 3.0Gold (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Sybyl - adding files in database Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netter I failed to contact a sybyl mail list. Does someone know a good address? So, I post my question on CCL. It is stupid but, under Sybyl, i can't add a long list of mol2-files in a database. I can do that manually but with a big number of structures, it's too long. Does exist a SPL-Macro for that? Thanks in advance. Eric VANGREVELINGHE -------- PhD Student e-mail: vangreve@univ-orleans.fr http://web.univ-orleans.fr/ICOA From mfrancl@brynmawr.edu Mon Nov 4 14:18:46 1996 Received: from amelia.brynmawr.edu for mfrancl@brynmawr.edu by www.ccl.net (8.8.2/950822.1) id NAA23509; Mon, 4 Nov 1996 13:25:08 -0500 (EST) Received: from [165.106.10.47] (mpmac7.brynmawr.edu [165.106.10.47]) by amelia.brynmawr.edu (8.6.12/8.6.12) with SMTP id NAA23658 for ; Mon, 4 Nov 1996 13:23:02 -0500 Date: Mon, 4 Nov 1996 13:23:02 -0500 Message-Id: <199611041823.NAA23658@amelia.brynmawr.edu> To: CHEMISTRY@www.ccl.net From: mfrancl@brynmawr.edu (Michelle M Francl) X-Sender: mfrancl@ada.brynmawr.edu Subject: Re: CCL:G:Fitting point charges to ESP with Spartan Wayne Huang notes: >As there is discrepancy on resulting charges from G9x and Spartan, that >would not be surprising. Although based on the same idea, the implementation >could be different. It is somewhat arbitrary in at least two ways, the >number of grid points chosen and the how far the region included. In plain >English, it basically paints a layer of grease on the vdw surface. Too far >beyond the vdw surface would get the charges too small (eventually approach >zero). The extent of the exclusion of the inner volume will also affect the >outcome (too close to the centers results in charges being too large). I would >tend to believe the two implementations should differ by a factor, may or may >not be linearly scalable. > As a clarification, most of these algorithms do not "paint a layer of grease" onthe VDW surface, but take some collection of points outside the VDW. This collection is sometimes a shell around the molecules, othertimes a box. The size of the box is generally much larger than the molecule. Points within the VDW are excluded. The implementation of CHELP in Spartan may be different, I know that the algorithm was recoded for Spartan based on the original CHELP paper. I would tend to believe the last comment regarding the relationship of the magnitude of the charges to the selection of the surface is not correct. For example, when points within 2.0 x the VDW surface are excluded in phenol, the charge on oxygen is 0.95, when points withing 0.75 of the VDW are excluded (more points now selected closer to the atomic centers), the charge actually _drops_ to 0.23. As Konrad Hinsen notes: this type of fitting is VERY unstable, and charges should be used with great care. More discussion can be found in our paper which uses the singular value decomposition or SVD to examine the problem (the paper I think Hinsen is refering to in his last post: J.Comp. Chem., Francl, Carey, Chirlian and Gange, v. 17 pp368-383), as well as in papers by Stouch and Williams. I don't disagree with Dr. Hinsen's contention that computational chemists, in general, have been quite naive in their use of the linear least squares regression for this problem. All I can say is that I was young and foolish when we wrote the first CHELP paper in 1987 which suggested replacing the older iterative methods with a slightly more sophisticated method. _____________________ ____________________ Michelle M. Francl phone: 610.526.5108 Associate Professor FAX: 610.526.5086 Dept. of Chemistry Bryn Mawr College 101 N. Merion Ave. Bryn Mawr, PA 19010 USA Internet: mfrancl@brynmawr.edu WWW: http://fieser.brynmawr.edu/~dept/chemistry.html From ahocquet@tamarugo.cec.uchile.cl Mon Nov 4 16:19:02 1996 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.2/950822.1) id QAA24772; Mon, 4 Nov 1996 16:07:18 -0500 (EST) Received: from ([146.83.10.50]) by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA20000; Mon, 4 Nov 1996 18:06:53 +0400 Message-Id: <327EA11B.4F4D@tamarugo.cec.uchile.cl> Date: Mon, 04 Nov 1996 18:06:19 -0800 From: Alexandre Hocquet X-Mailer: Mozilla 2.02 (Win16; I) Mime-Version: 1.0 To: chemistry@www.ccl.net Cc: ahocquet@tamarugo.cec.uchile.cl Subject: Force fields comparisons in the litterature (francais-castellano-english) Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Message post=E9 en francais-Mensaje enviado en castellano-Message posted in= english Chers CCLeurs, Dans un article r=E9cent du Journal of Computational Chemistry (Cornell et = al., 17, 1996, p1541), les = auteurs estiment que peu d=92=E9tudes comparatives de champs de forces ont = =E9t=E9 men=E9es jusqu=92=E0 pr=E9sent. Je = n=92ai pas l=92article sous les yeux, mais il me semble qu=92ils ne citent = qu=92une r=E9f=E9rence : Hall et al., J: Comput. Chem., 5, 1984, p441. Pour ma part, j=92ai r=E9cemment vu les comparaisons suivantes : Gundertofte et al., J: Comput. Chem., 12, 1991, p200. Gundertofte et al., J: Comput. Chem., 17, 1996, p429. (Et aussi, apparemmen= t, dans le volume 9 des = Reviews in Computational Chemistry) Si vous connaissez un article comparatif de champs de force, (disons post=E9= rieur =E0 1985, pour =E9viter des = comparaisons de champs de force de premi=E8re g=E9neration aujourd=92hui pe= u usit=E9s), je serai tr=E8s int=E9ress=E9 = par la r=E9f=E9rence, et si possible, une br=E8ve description, pour =E9tabl= ir une collection, que je r=E9sumerai = ensuite dans la liste. Je suis aussi int=E9ress=E9 par toute forme de collaboration avec d=92autre= s =E9quipes dans ce domaine. Je me = sp=E9cialise pour ma part dans les champs de force paraissant dans les logi= ciels grand public(MM+, MMX...). Merci d=92avance pour vos r=E9ponses. Estimados CCLeros, En un articulo recien salido en el Journal of Computational Chemistry (Corn= ell et al., 17, 1996, p1541), = los autores se quejan que existen pocos estudios comparativos de campos de = fuerzas. Aunque yo no tenga el = articulo a mano, me parece que citan una sola referencia : Hall et al., J: Comput. Chem., 5, 1984, p441. Por mi lado, encontr=E9 dos mas : Gundertofte et al., J: Comput. Chem., 12, 1991, p200. Gundertofte et al., J: Comput. Chem., 17, 1996, p429. (Y tambien, aparentem= ente, en el noveno volumen de = las Reviews in Computational Chemistry) Si Ud conoce algun articulo comparativo de campos de fuerza, digamos despue= s de 1985 (para eliminar = comparaciones de campos de fuerzas de primera generacion), estaria muy inte= resado por la referencia y , = si puede ser, una breve descripcion, para establecer una lista que podria resumir en la CCL.= Tambien estoy interesado por cualquier forma de colaboracion con otros labo= ratorios en este campo. Por mi = lado, me estoy especialisando en campos de fuerzas disponibles en softwares= para gran publico (MM+, = MMX...). Gracias por sus respuestas. Dear Cclers, In a recent article in the Journal of Computational Chemistry (Cornell et a= l., 17, 1996, p1541), authors = complain about too few comparative studies of force fields published. Thoug= h i dont have the article at = the moment, i think i remember they only quote one reference : Hall et al., J: Comput. Chem., 5, 1984, p441. As for me, i noticed these other two : Gundertofte et al., J: Comput. Chem., 12, 1991, p200. Gundertofte et al., J: Comput. Chem., 17, 1996, p429. (And aparently, in Re= views in Computational = Chemistry, volume 9) If you know about an article involved in force field comparisons, (later th= an, say, 1985 in order to = avoid first generation force fields that are no more used), i would be very= interested in the reference = and, if possible, a short description. I will summarise to the list. I am also interested in any kind of cooperation with other teams involved i= n this field. I am myself = specialising in =93general audience software=94 force fields such as MM+, M= MX... Thanks in advance for your answers. -- = Alexandre HOCQUET Laboratorio de Cristalograf=EDa Facultad de Ciencias F=EDsicas Universidad de Chile Blanco Encalada, 2008 Santiago Chile fax : 56 2 696 73 59 email : ahocquet@tamarugo.cec.uchile.cl From adler@pulsar.cs.wku.edu Mon Nov 4 17:18:53 1996 Received: from axp1.wku.edu for adler@pulsar.cs.wku.edu by www.ccl.net (8.8.2/950822.1) id RAA25352; Mon, 4 Nov 1996 17:01:31 -0500 (EST) Received: from pulsar.cs.wku.edu by axp1.wku.edu (MX V4.3 Alpha) with SMTP; Mon, 04 Nov 1996 15:59:36 CST Received: by pulsar.cs.wku.edu (SMI-8.6/SMI-SVR4) id PAA11996; Mon, 4 Nov 1996 15:59:42 -0600 From: adler@pulsar.cs.wku.edu (Allen Adler) Message-ID: <199611042159.PAA11996@pulsar.cs.wku.edu> Subject: CCL: What *YOU* can do ... To: chemistry@www.ccl.net Date: Mon, 4 Nov 1996 15:59:42 -0600 (CST) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit If a detailed accounting of the costs of operating CCL were made available to the readers, perhaps readers could make their contributions by suggesting some ways to cut costs. There are lots of things that can be done for free on the internet. Naively, Allan Adler adler@pulsar.cs.wku.edu