From cheidel@weizen.mpibpc.gwdg.de Mon Mar 25 05:33:10 1996 Received: from weizen.mpibpc.gwdg.de for cheidel@weizen.mpibpc.gwdg.de by www.ccl.net (8.7.1/950822.1) id EAA27158; Mon, 25 Mar 1996 04:53:43 -0500 (EST) Message-Id: <199603250953.EAA27158@www.ccl.net> Received: by weizen.mpibpc.gwdg.de (1.37.109.16/16.2) id AA125237612; Mon, 25 Mar 1996 10:53:32 +0100 Date: Mon, 25 Mar 1996 10:53:32 +0100 From: Christoph Heidelbach To: chemistry@www.ccl.net Subject: Summary: MD parameters from ab initio calculations Cc: cheidel@gwdg.de Dear CCL'ers, many thanks to all those who answered me. My original question was: I am searching for some information about the evaluation of force field parameters for molecular dynamics from ab initio or semiempirical calculations. What I am looking for is how to fit atomic charges and Lennard-Jones-parameters. Any answers will be greatly appreciated and I will summerize all replies. This is what I got: >From hinsenk@ERE.UMontreal.CA Tue Feb 27 22:04 MEZ 1996 Received: from harfang.CC.UMontreal.CA by weizen.mpibpc.gwdg.de with ESMTP (1.37.109.16/16.2) id AA206815086; Tue, 27 Feb 1996 22:04:46 +0100 Return-Path: Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by harfang.CC.UMontreal.CA with ESMTP id QAA13932 (8.6.11/IDA-1.6 for ); Tue, 27 Feb 1996 16:03:35 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id QAA19296; Tue, 27 Feb 1996 16:03:34 -0500 Received: by cyclone.ERE.UMontreal.CA (950221.405.SGI.8.6.10/5.17) id QAA21209; Tue, 27 Feb 1996 16:03:34 -0500 Date: Tue, 27 Feb 1996 16:03:34 -0500 Message-Id: <199602272103.QAA21209@cyclone.ERE.UMontreal.CA> To: cheidel@weizen.mpibpc.gwdg.de In-Reply-To: <199602271757.MAA10086@www.ccl.net> (message from Christoph Heidelbach on Tue, 27 Feb 1996 18:57:05 +0100) Subject: Re: CCL:MD parameters from ab initio >From: hinsenk@ERE.UMontreal.CA (Konrad HINSEN) Status: RO I am searching for some information about the evaluation of force field parameters for molecular dynamics from ab initio or semiempirical calculations. What I am looking for is how to fit atomic charges and Lennard-Jones-parameters. Ich schreiben gerade an einem Artikel ueber ein solches Projekt (ein Potential fuer quantenmechanische Simulationen von Protonentransfer in Acetylaceton), mit einer recht ausfuehrlichen Abhandlung ueber das Fitten von Ladungen, da meine Methode sich von den ueblichen unterscheidet. Ich kann gerne eine Kopie (auch elektronisch) schicken, wenn alles fertig ist, d.h. voraussichtlich naechste Woche. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- >From eduffy@laplace.csb.yale.edu Tue Feb 27 22:22 MEZ 1996 Received: from laplace.csb.yale.edu by weizen.mpibpc.gwdg.de with SMTP (1.37.109.16/16.2) id AA208516124; Tue, 27 Feb 1996 22:22:04 +0100 Return-Path: Received: from kepler by laplace.csb.yale.edu (NX5.67d/NX3.0M) id AA01528; Tue, 27 Feb 96 16:21:57 -0500 >From: "Erin Duffy" Received: (from eduffy@localhost) by kepler.csb.yale.edu (8.7.4/8.7.3) id QAA20313 for cheidel@weizen.mpibpc.gwdg.de; Tue, 27 Feb 1996 16:21:56 -0500 (EST) Message-Id: <199602272121.QAA20313@kepler.csb.yale.edu> Subject: Re: CCL:MD parameters from ab initio To: cheidel@weizen.mpibpc.gwdg.de (Christoph Heidelbach) Date: Tue, 27 Feb 1996 16:21:56 -0500 (EST) In-Reply-To: <199602271757.MAA10086@www.ccl.net> from "Christoph Heidelbach" at Feb 27, 96 06:57:05 pm X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Status: RO Hi - I'd suggest looking at some of Bill Jorgensen's papers - his group are experts in this area. Here is a small sampling. Please contact me if I can be of further assistance. - Erin Duffy eduffy@franklin.csb.yale.edu Jorgensen, W.L.; Madura, J.D.; Swenson, C.J. "Optimized Intermolecular Potential Functions for Liquid Hydrocarbons." J. Am. Chem. Soc., 1984, v.106, 6638-6646. Jorgensen, W.L.; Tirado-Rives, J. "The OPLS Potential Functions for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin." J. Am. Chem. Soc., 1988, v.110, 1657-1666. Jorgensen, W.L.; Gao, J. "Cis-Trans Energy Difference for the Peptide Bond in the Gas Phase and in Aqueous Solution." J. Am. Chem. Soc., 1988, v.110, 4212. Jorgensen, W.L.; Severance, D.L. "Aromatic-Aromatic Interactions: Free Energy Profiles for the Benzene Dimer in Water, Chloroform, and Liquid Benzene." J. Am. Chem. Soc., 1990, v.112, 4768-4774. Duffy, E.M.; Severance, D.L.; Jorgensen, W.L. "Urea: Potential Functions, logP, and Free Energy of Hydration." Isr. J. Chem., 1993, v.33, 323-330. Carlson, H.A.; Nguyen, T.B.; Orozco, M.; Jorgensen, W.L. "Accuracy of Free Energies of Hydration for Organic Molecules from 6-31G(d)- Derived Partial Charges." J. Comput. Chem., 1993, v.14, 1240-1249. >From v_uk@iris23.biosym.com Wed Feb 28 02:05 MEZ 1996 Received: from bioc1.biosym.com by weizen.mpibpc.gwdg.de with SMTP (1.37.109.16/16.2) id AA225539529; Wed, 28 Feb 1996 02:05:29 +0100 Return-Path: Received: from iris23.biosym.com by bioc1.biosym.com (5.64/0.0) id AA21813; Tue, 27 Feb 96 17:09:46 -0800 Received: by iris23.biosym.com (940816.SGI.8.6.9/930416.SGI) for cheidel@weizen.mpibpc.gwdg.de id RAA27793; Tue, 27 Feb 1996 17:05:16 -0800 Date: Tue, 27 Feb 1996 17:05:16 -0800 >From: v_uk@biosym.com (Masahiko Katagari XPIRE 4-15-96 HOST John Newsam Tohoku University) Message-Id: <199602280105.RAA27793@iris23.biosym.com> To: cheidel@weizen.mpibpc.gwdg.de Subject: MD parameters Status: RO Dear Dr. Christoph Heidelbach, As for the parametrization, we (biosym/msi) parametrize the LJ and partial charge using a nonlinear least-squares fit to the ab-initio data. If you are interested in, please refer, e.g. J.Hill and J.Sauer, Molecular Mechanics Potential for Silica and Zeolite Catalysis Based on ab initio Calculations. 1. Dens and Microporous Silica J. Phys. Chem. 98, 1238 (1994). This method produces the potential which includes many body terms such as distortion. The charges in the forcefield are directly taken from a population analysis of the wavefunctions. The use of charges is somewhat artificial, since potential has its origin in a Taylor series expansion which accounts for all interactions. In this context, point charge interactions are not required, but because of the necessity to describe interactions between atoms or groups which are not directly connected by bonds, but which may come close to each other simulations, they are introduced in potential, too. Frankly speaking, we use the partial charge as a parameter to fit the experimental data. As for the repulsive van der Waals parameters, test particle method is frequently used. See for example, H. Bohm and R. Ahlrichs A Study of short-range repulsions. J. Chem. Phys., 77, 2028 (1982). or H. Bohm, R. Ahlrichs, P. Scharf and H. Schiffer Intermolecular potentials for CH4, CH3F, CHF3, CH3Cl, CH2Cl2, CH3CN and CO2 J. Chem. Phys., 81, 1389 (1984). Best Regards, Masa Katagiri __o__o_o__o __o Masahiko Katagiri __o__o_o__o __o `\<,\<,<,\<,`\<, v_uk@biosym.com `\<,\<,<,\<,`\<, O/ O/ O O/ OO/ O TEL -1-619-546-5389(direct) O/ O/ O O/ OO/ O FAX -1-619-458-0136 e_mail v_uk@biosym.com MSI 9685 Scranton Road San Diego, CA 92121 >From ross@cgl.ucsf.EDU Wed Feb 28 02:13 MEZ 1996 Received: from socrates.ucsf.EDU by weizen.mpibpc.gwdg.de with ESMTP (1.37.109.16/16.2) id AA225590020; Wed, 28 Feb 1996 02:13:40 +0100 Return-Path: Received: (from ross@localhost) by socrates.ucsf.EDU (8.7.3/GSC4.24) id RAA00603 for cheidel@weizen.mpibpc.gwdg.de; Tue, 27 Feb 1996 17:13:37 -0800 (PST) Date: Tue, 27 Feb 1996 17:13:37 -0800 (PST) >From: ross@cgl.ucsf.EDU Message-Id: <199602280113.RAA00603@socrates.ucsf.EDU> To: cheidel@weizen.mpibpc.gwdg.de Subject: Re: CCL:MD parameters from ab initio Status: RO You might want to check out the force field sections of the amber web pages at: http://www.amber.ucsf.edu/amber/ Bill Ross >From hebant@ext.jussieu.fr Wed Feb 28 09:21 MEZ 1996 Received: from shiva.jussieu.fr by weizen.mpibpc.gwdg.de with ESMTP (1.37.109.16/16.2) id AA256975685; Wed, 28 Feb 1996 09:21:25 +0100 Return-Path: Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.7.3/jtpda-5.2) with ESMTP id JAA20491 ; Wed, 28 Feb 1996 09:20:47 +0100 (MET) Received: from [134.157.11.16] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Wed, 28 Feb 1996 09:20:43 +0100 X-Sender: hebant@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 28 Feb 1996 09:19:25 +0100 To: Christoph Heidelbach , chemistry@www.ccl.net >From: hebant@ext.jussieu.fr (Pascal HEBANT) Subject: Re: CCL:MD parameters from ab initio Cc: cheidel@gwdg.de Status: RO At 18:57 27/02/96, Christoph Heidelbach wrote: >Hallo everybody out there, > >I am searching for some information about the evaluation of force field >parameters for molecular dynamics from ab initio or semiempirical calculations. >What I am looking for is how to fit atomic charges and >Lennard-Jones-parameters. >Any answers will be greatly appreciated and I will summerize all replies. > >Best regards. > >Christoph > We have done something like that in our lab : we have computed pair potential function of Born Huggins Mayer type with DMol calculations : Point energies are performed for the 2 atoms involved in the potential with fixed geometry. Then, a curve fitting (with Kaleidagraph) allowed us to obtain the parameters. See e.g. Roullet, G., J. J. Legendre, et al. (1994). "Ab-initio and molecular dynamics studies of molten NaCl Graphite interfaces." Molten Salt Forum 1-2: 105-116. Hope this helps you Pascal ***************************************************************************** Pascal HEBANT Laboratoire d'Electrochimie et de Chimie Analytique Ecole Nationale Superieure de Chimie de Paris 11 rue Pierre et Marie Curie 75005 Paris FRANCE tel: 33 (1) 44 27 66 94 fax: 33 (1) 44 27 67 50 http://alcyone.enscp.jussieu.fr/Pages/LECA/Electrochimie.html ***************************************************************************** >From ferenc@rchsg8.chemie.uni-regensburg.de Wed Feb 28 09:50 MEZ 1996 Received: from comsun.rz.uni-regensburg.de by weizen.mpibpc.gwdg.de with SMTP (1.37.109.16/16.2) id AA262597400; Wed, 28 Feb 1996 09:50:00 +0100 Return-Path: Received: from rchsg8.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA19403 (5.65c/IDA-1.4.4 for ); Wed, 28 Feb 1996 09:49:57 +0100 Received: by rchsg8.chemie.uni-regensburg.de (931110.SGI/URRZ-Sub-1.5-irix) (for cheidel@weizen.mpibpc.gwdg.de) id AA14032; Wed, 28 Feb 96 09:50:12 +0100 >From: "Ferenc Molnar" Message-Id: <9602280950.ZM14030@rchsg8.chemie.uni-regensburg.de> Date: Wed, 28 Feb 1996 09:50:11 +0100 In-Reply-To: Christoph Heidelbach "CCL:MD parameters from ab initio" (Feb 27, 6:57pm) References: <199602271757.MAA10086@www.ccl.net> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: Christoph Heidelbach Subject: Re: CCL:MD parameters from ab initio Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Status: RO Hallo Chrisoph! > What I am looking for is how to fit atomic charges and > Lennard-Jones-parameters. > Any answers will be greatly appreciated and I will summerize all replies. Das wuerde mich auch sehr interessieren! Bitte schick mir doch die Antworten, insbesondere Hinweise auf bestehende Programme! Einige Referenzen kann ich dir geben: 1) N.L. Allinger and J.P. Bowen in Rev.Comp.Chem. 2, K.B. Lipkowitz and D.B. Boyd (Eds.), VCH, 1991, ISBN 3-527-28338-2. 2) U. Dinur and A.T. Hagler (ebd.). 3) AUTHOR = {G. Chalasi\'nski and M.M. Szcze\'sniak}, TITLE = {Origins of Structure and Energetics of van der Waals JOURNAL =Chem. Rev., YEAR = {1994}, VOLUME = {94}, NUMBER = {7}, PAGES = {1723--1765}, KEYS = {van der Waals, ab initio, dispersion, correlation, PES}, 4) AUTHOR = {J.R. Maple and M.-J. Hwang and T.P. Stockfisch and U. Dinur and M. Waldman and C.S. Ewig and A.T. Hagler}, TITLE = {Derivation of Class II Force Fields. I. Methodology and Quantum Force Field for the Alkyl Functional Group and Alkane Molecules}, JOURNAL =J. Comp. Chem., YEAR = {1994}, VOLUME = {15}, NUMBER = {2}, PAGES = {162--182}, KEYS = {derivatives, parameters, ab initio, PES, anharmonicity, intramolecular forces, cross terms, transferability, validity }, Clusters from ab Initio Calculations}, 5) AUTHOR = {D.E. Woon}, TITLE = {Accurate modeling of intermolecular forces: a systematic M\o ller-Plesset study of the argon dimer using correlation consistent basis sets}, JOURNAL = Chem. Phys. Lett., YEAR = {1993}, VOLUME = {204}, NUMBER = {1,2}, PAGES = {29--35}, KEYS = { PES, MP4, augmented correlation consistent basis set, argon, supermolecule approach, BSSE, CP}, Ich habe auch schon einige Parametrisierungsversuche unternommen. Allerdings geraet man sehr schnell an die Grenzen der ab initio Prgramme (Gaussian, Gamess) oder der Optimierungsverfahren (zu viele Parameter). Eine Parametrisierung kann selbst fuer kleine Systeme sehr aufwendig werden! Trotzdem: Have fun! Ferenc >From chemistry-request@www.ccl.net Wed Feb 28 10:07 MEZ 1996 Received: from www.ccl.net by weizen.mpibpc.gwdg.de with ESMTP (1.37.109.16/16.2) id AA263458467; Wed, 28 Feb 1996 10:07:47 +0100 Return-Path: Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.1/950822.1) id DAA20495; Wed, 28 Feb 1996 03:32:24 -0500 (EST) Received: from shiva.jussieu.fr for hebant@ext.jussieu.fr by www.ccl.net (8.7.1/950822.1) id DAA20463; Wed, 28 Feb 1996 03:21:10 -0500 (EST) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.7.3/jtpda-5.2) with ESMTP id JAA20491 ; Wed, 28 Feb 1996 09:20:47 +0100 (MET) Received: from [134.157.11.16] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Wed, 28 Feb 1996 09:20:43 +0100 X-Sender: hebant@idf.ext.jussieu.fr Message-Id: Date: Wed, 28 Feb 1996 09:19:25 +0100 To: Christoph Heidelbach , chemistry@www.ccl.net >From: hebant@ext.jussieu.fr (Pascal HEBANT) Subject: CCL:MD parameters from ab initio Cc: cheidel@gwdg.de Sender: Computational Chemistry List Errors-To: ccl@www.ccl.net Precedence: bulk Status: RO At 18:57 27/02/96, Christoph Heidelbach wrote: >Hallo everybody out there, > >I am searching for some information about the evaluation of force field >parameters for molecular dynamics from ab initio or semiempirical calculations. >What I am looking for is how to fit atomic charges and >Lennard-Jones-parameters. >Any answers will be greatly appreciated and I will summerize all replies. > >Best regards. > >Christoph > We have done something like that in our lab : we have computed pair potential function of Born Huggins Mayer type with DMol calculations : Point energies are performed for the 2 atoms involved in the potential with fixed geometry. Then, a curve fitting (with Kaleidagraph) allowed us to obtain the parameters. See e.g. Roullet, G., J. J. Legendre, et al. (1994). "Ab-initio and molecular dynamics studies of molten NaCl Graphite interfaces." Molten Salt Forum 1-2: 105-116. Hope this helps you Pascal ***************************************************************************** Pascal HEBANT Laboratoire d'Electrochimie et de Chimie Analytique Ecole Nationale Superieure de Chimie de Paris 11 rue Pierre et Marie Curie 75005 Paris FRANCE tel: 33 (1) 44 27 66 94 fax: 33 (1) 44 27 67 50 http://alcyone.enscp.jussieu.fr/Pages/LECA/Electrochimie.html ***************************************************************************** -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: hebant@ext.jussieu.fr -- Original Sender From: Address: hebant@ext.jussieu.fr 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 Darren.Andrews@man.ac.uk Wed Feb 28 11:34 MEZ 1996 Received: from nessie.mcc.ac.uk by weizen.mpibpc.gwdg.de with ESMTP (1.37.109.16/16.2) id AA273343675; Wed, 28 Feb 1996 11:34:35 +0100 Return-Path: Received: from [130.88.12.235] (actually femt03.ch.man.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Wed, 28 Feb 1996 10:34:01 +0000 X-Sender: mbcdpa@nessie.mcc.ac.uk Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 28 Feb 1996 10:38:40 +0000 To: cheidel@weizen.mpibpc.gwdg.de >From: Darren.Andrews@man.ac.uk (Darren Andrews) Subject: Re: CCL:MD parameters from ab initio Status: RO A very basic way to do this would be to use the Mulliken or similar charges from the Ab Initio output and some empirical Lennard-Jones parameters e.g., Lorentz-Berthelot to get a pretty rough set of starting values. If you use a distributed multipole analysis approach (see Anthony Stone circa. '89) which can be calculated using CADPAC you can get a (very) good approximation of the electrostatic part of the interaction. If the system you are looking at is dominated by electrostatic forces then the empirical L-J parameters will be less important. Darren Andrews. University of Manchester, Department of Chemistry, Oxford road, Manchester. M13 9PL. Darren.Andrews@man.ac.uk PGP: 512/62A971A9 Tel: 0161 275 2000 ext.4699. Fax: 0161 275 4598. >From garciae@guarany.cpd.unb.br Wed Feb 28 13:33 MEZ 1996 Received: from guarany.cpd.unb.br by weizen.mpibpc.gwdg.de with SMTP (1.37.109.16/16.2) id AA285770809; Wed, 28 Feb 1996 13:33:29 +0100 Return-Path: Received: by guarany.cpd.unb.br (AIX 3.2/UCB 5.64/4.03) id AA62884; Wed, 28 Feb 1996 09:32:46 -0300 Date: Wed, 28 Feb 1996 09:32:46 -0300 (GRNLNDST) >From: edgardo garcia To: Christoph Heidelbach Subject: Re: CCL:MD parameters from ab initio In-Reply-To: <199602271757.MAA10086@www.ccl.net> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: RO Hi Christoph, CHARGES I'm currently using AM1 CHELP Potential derived charges that reproduce the molecular dipoles with 12% error, usually bigger dipoles. The dipoles are similar to the ones obtained from 6-31G* on the same compounds. I also tried Charge Equilibration Method of Antony Rappe but the results are really bad, not only the dipoles are wrong in absolute values but the trends for a set of molecules is also wrong. The AM1 dipole trends are also correct. The problem with force fields is that you need fixed charges, now charges change with the connectivity environment and also (but much less important) with the 3D environment. I use AM1 charges computed for model compounds and then I symmetrize the charges, by a simple average of the values of topologicaly identical atoms. With this fixed 2D AM1 CHELP charges I then parametrize the Force Field to reproduce energy data. There is no point in trying to be more accurate on that unless you can use hyper-atom-types that embody the atom molecular environment. VdW The vdW parameters are another story :-( I don't really know what is a good method. The points are: - what do you want ? - what is the quality/cost ratio for the method ? Is is worth it ? I'm using OPLS vdW parameters and they are fixed for specific atom types. >From my point of view one of the most serius works for liquid phases. Again for organic molecules, I bet you that the vdW parameters will change a bit depending on the atom environment. It could be that some ab initio procedure can give you a good functional form and good parameters, considering the BSSE was removed, but the problem is : can you really make use of this great accuracy in your force field ? You have to consider that force fields use limited atom types and also there are the vdW combination rules, ad hoc little formulas, who know were they really work ? There is a nice work for noble gases for the ab initio derivation of vdW parameters, functional forms and combination rules. I don't remember the reference now but I can give it to you latter if you are interested. The author is A.T. Hagler from Merk, I think it was on JACS, 1985 - 1993. The big deal will be to find parameters that are independent of the environment, i.e., pure parameteres. The big problem is what are good functional forms, how the parameters change with topological and with 3D environment and how to include this in a usefull Force Field that is able to handdle them to make practical and accurate predictions. Hope this helps, Edgardo Dr.Edgardo Garcia Dpto of Chemistry University of Brasilia, Brasilia DF, Brazil >From cheidel@gwdg.de Thu Feb 29 16:53 MEZ 1996 Received: from gwdu42.gwdg.de by weizen.mpibpc.gwdg.de with SMTP (1.37.109.16/16.2) id AA140329197; Thu, 29 Feb 1996 16:53:17 +0100 Return-Path: Received: from gwdu28.gwdg.de (actually gwdu28-eth.gwdg.de) by gwdu42.gwdg.de with SMTP (PP); Thu, 29 Feb 1996 16:52:44 +0100 Received: by gwdu28.gwdg.de; (5.65v3.2/1.1.8.2/19Jan96-1057AM) id AA08694; Thu, 29 Feb 1996 16:52:42 +0100 >From: cheidel Message-Id: <9602291552.AA08694@gwdu28.gwdg.de> Subject: Re: CCL:MD parameters from ab initio (fwd) To: cheidel@weizen.mpibpc.gwdg.de Date: Thu, 29 Feb 1996 16:52:41 +0100 (MET) X-Mailer: ELM [version 2.4 PL25] Content-Type: text Content-Length: 3637 Status: RO Forwarded message: >From jxh@ibm12.biosym.com Wed Feb 28 23:30:32 1996 Delivery-Date: Wed, 28 Feb 1996 23:30:32 +0100 Message-Id: Date: Wed, 28 Feb 1996 14:25:37 -0800 (PST) >From: Joerg Hill To: cheidel@gwdg.de Subject: Re: CCL:MD parameters from ab initio Hallo, > I am searching for some information about the evaluation of force field > parameters for molecular dynamics from ab initio or semiempirical calculations. > What I am looking for is how to fit atomic charges and Lennard-Jones-parameters. > Any answers will be greatly appreciated and I will summerize all replies. Es gibt eine ganze Serie von Arbeiten ueber die Ableitung von repulsiven van-der-Waals-Parametern aus ab initio Rechnungen von Boehm und Ahlrichs: @article{boe82, author={H.-J.~B{\"o}hm and R.~Ahlrichs}, title={A study of short--range repulsions}, journal={J. Chem. Phys.}, year=1982, volume=77, pages=2028 } @article{boe84:1, author={H.-J.~B{\"o}hm and R.~Ahlrichs and P.~Scharf and H.~Schiffer}, title={Intermolecular potentials for {CH$_4$, CH$_3$F, CHF$_3$, CH$_3$Cl, CH$_2$Cl$_2$, CH$_3$CN, and CO$_2$}}, journal={J. Chem. Phys.}, year=1984, volume=81, pages=1389 } @article{sag87, author={K.~P.~Sagarik and R.~Ahlrichs}, title={A test particle model potential for formamide and molecular dynamics simulations of the liquid}, journal={J. Chem. Phys.}, year=1987, volume=86, pages=5117 } @article{sag86:1, author={K.~P.~Sagarik and R.~Ahlrichs and S.~Brode}, title={ }, journal={Mol. Phys.}, year=1986, volume=57, pages=1247 } @article{boe84:2, author={H.-J.~B{\"o}hm and C.~Meissner and R.~Ahlrichs}, title={ }, journal={Mol. Phys.}, year=1984, volume=53, pages=651 } @article{sag86:2, author={K.~P.~Sagarik and R.~Ahlrichs}, title={ }, journal={Chem. Phys. Letters}, year=1986, volume=131, pages=74 } Ich selbst habe vor kurzem ein Paper bei J. Comp. Chem. eingereicht, in dem auch die dispersiven Parameter aus ab initio Rechnungen abgeleitet werden. Ich hoffe, das ich bald Nachricht ueber die Annahme bekomme. Viele Gruesse nach Deutschland Joerg-R. Hill ------------------------------------------------------------------------------- - Dr. Joerg-Ruediger Hill | Every attempt to employ mathematical methods in the Biosym/MSI | study of chemical questions must be considered pro- 9685 Scranton Road | foundly irrational and contrary to the spirit of San Diego, CA 92121-2777 | chemistry ... If mathematical analysis should ever USA | hold a prominent place in chemistry - an aberration | which is happily almost impossible - it would Phone (619) 546-5508 | occasion a rapid and widespread degeneration of Fax (619) 458-0136 | that science. E-mail jxh@biosym.com | Auguste Comte, Philosophie Positive, Paris, 1838 ------------------------------------------------------------------------------- - The opinions expressed in this message are my personal opinions and no offical statements of Biosym Technologies, Inc. For informations about Biosym products take a look at: http://www.msi.com/. ------------------------------------------------------------------------------- - From jmanrique@beilstein.com Mon Mar 25 08:18:39 1996 Received: from news.ossinc.net for jmanrique@beilstein.com by www.ccl.net (8.7.1/950822.1) id IAA29683; Mon, 25 Mar 1996 08:06:24 -0500 (EST) Received: from NULL (ad31-153.compuserve.com [199.174.134.153]) by news.ossinc.net (8.6.12/8.6.9) with SMTP id HAA09447; Mon, 25 Mar 1996 07:08:49 -0700 Date: Mon, 25 Mar 1996 07:08:49 -0700 Message-Id: <199603251408.HAA09447@news.ossinc.net> X-Sender: jmanrique@mail.beilstein.com X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Jorge Manrique Subject: Press Release For Immediate Release Editorial Contact: Jorge Manrique Beilstein Information Systems (415) 358-9091 jmanrique@beilstein.com Paul Collins Digital Equipment Corporation (508) 467-2251 paul.collins@mro.mts.dec.com Beilstein Information Systems Announces CrossFire Running on Digital's AlphaServer Family New Orleans, LA., March 25, 1996 -- Beilstein Information Systems and Digital Equipment Corporation announced today a partnership that will develop and market solutions to address the needs of the research chemist and chemical information specialist. The first development to come out of the new partnership will be Beilstein's CrossFire running across the Digital AlphaServer product family on Digital's OpenVMS and Digital UNIX platforms. The Alpha CrossFire Server, which will be available in the Summer of 1996, will deliver a new avenue for access to the Beilstein Database, the world's largest and most accurate collection of information on organic chemical compounds. ______________________________________________________ For more details, please point your browser to: http://www.beilstein.com/press.html Jorge Manrique Director of Marketing Beilstein Information Systems, Inc. jmanrique@beilstein.com Phone: 415.358.9091 Fax: 415.358.9099 From moller@sbu.ac.uk Mon Mar 25 14:19:26 1996 Received: from psb.sbu.ac.uk for moller@sbu.ac.uk by www.ccl.net (8.7.1/950822.1) id OAA05697; Mon, 25 Mar 1996 14:15:31 -0500 (EST) From: Received: from BIG (BIG::SYSTEM) by PSB (MX V4.2 VAX) with SMTP (DECnet); Mon, 25 Mar 1996 19:15:24 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Mon, 25 Mar 1996 19:12:10 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Mon, 25 Mar 1996 19:06:15 GMT Received: from PSB (PSB::SYSTEM) by BIG (MX V4.1 VAX) with SMTP (DECnet); Sat, 16 Mar 1996 04:37:20 GMT Received: from www.ccl.net by psb.sbu.ac.uk (MX V4.1 VAX) with SMTP; Sat, 16 Mar 1996 02:35:12 GMT Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.1/950822.1) id VAA01185; Fri, 15 Mar 1996 21:04:51 -0500 (EST) Received: from www.hyper.com for moller@hyper.hyper.com by www.ccl.net (8.7.1/950822.1) id LAA11156; Mon, 11 Mar 1996 11:52:47 -0500 (EST) Received: from hyper.hyper.com (hyper.hyper.com [204.50.97.9]) by www.hyper.com (8.6.12/8.6.12) with SMTP id MAA07638; Mon, 11 Mar 1996 12:07:44 -0500 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:hiroshi@U.Arizona.EDU id AA14147; Mon, 11 Mar 96 12:07:47 -0500 Date: Mon, 11 Mar 96 12:07:47 -0500 Originally-From: Message-ID: <9603111707.AA14147@hyper.hyper.com> To: Hiroshi Ogura Subject: CCL:Re: CCL:Making a crystal packing model in a computer CC: CHEMISTRY@www.ccl.net We have been having some major problems with our mail system for the last week. The backlog is now being cleared. However you may receive messages more than once. Our apologies for any inconvenience caused. =============================== Original Message follows ====================== Dear Hiroshi, The commercial product ChemPlus, from Hypercube, Inc. has a crystal builder module which allows you to create a crystal in HyperChem by defining the unit cell. For more information, send e-mail to info@hyper.com or look at our home page: http://www.hyper.com Regards, Michael ------------ Michael Moller, PhD Email to: moller@hyper.com Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 http://www.hyper.com Info: info@hyper.com Support: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com --- Administrivia: This message is automatically appended by the mail exploder: 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 polowin@sbu.ac.uk Mon Mar 25 20:18:51 1996 Received: from psb.sbu.ac.uk for polowin@sbu.ac.uk by www.ccl.net (8.7.1/950822.1) id TAA09042; Mon, 25 Mar 1996 19:59:07 -0500 (EST) From: Received: from BIG (BIG::SYSTEM) by PSB (MX V4.2 VAX) with SMTP (DECnet); Tue, 26 Mar 1996 00:59:29 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Tue, 26 Mar 1996 00:56:23 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Tue, 26 Mar 1996 00:54:37 GMT Received: from PSB (PSB::SYSTEM) by BIG (MX V4.1 VAX) with SMTP (DECnet); Sat, 16 Mar 1996 05:03:43 GMT Received: from www.ccl.net by psb.sbu.ac.uk (MX V4.1 VAX) with SMTP; Sat, 16 Mar 1996 03:40:50 GMT Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.1/950822.1) id VAA01243; Fri, 15 Mar 1996 21:06:16 -0500 (EST) Received: from www.hyper.com for polowin@hyper.com by www.ccl.net (8.7.1/950822.1) id KAA27797; Tue, 12 Mar 1996 10:02:13 -0500 (EST) Received: from joel (joel.hyper.com [204.50.97.14]) by www.hyper.com (8.6.12/8.6.12) with SMTP id KAA00401; Tue, 12 Mar 1996 10:17:01 -0500 Message-ID: <199603121517.KAA00401@www.hyper.com> Date: Tue, 12 Mar 96 09:57:59 -0500 Originally-From: To: chemistry@www.ccl.net, quant@cc.acad.md Subject: CCL:Re: ccl: C60 multiple moments We have been having some major problems with our mail system for the last week. The backlog is now being cleared. However you may receive messages more than once. Our apologies for any inconvenience caused. =============================== Original Message follows ====================== > From: quant@cc.acad.md > Date: Tue, 27 Feb 96 14:41:55 -0200 > I tried to calculate the electronic structure of this > molecule with my own CNDO program using the example from the > HyperChem. These calculations give the non zero dipole moment > for C60. Another hand on a symmetry considerations the first > non zero moment of the molecule must be of 6th order. So my > questions are: > 1. Why the dipole moment obtained with both in my CNDO > version and HyperChem CNDO for C60 is non zero? > 2. Does anybody knows any calculations of electrical moments > for C60? When I optimize C60 with CNDO with HyperChem and calculate its dipole moment, I get the expected 0 dipole. I do not know why your result differs, but it seems to me that the most likely cause is that your structure is not optimized and not symmetrical. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ --- Administrivia: This message is automatically appended by the mail exploder: 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 hinsenk@sbu.ac.uk Mon Mar 25 22:18:45 1996 Received: from psb.sbu.ac.uk for hinsenk@sbu.ac.uk by www.ccl.net (8.7.1/950822.1) id VAA09450; Mon, 25 Mar 1996 21:47:27 -0500 (EST) From: Received: from BIG (BIG::SYSTEM) by PSB (MX V4.2 VAX) with SMTP (DECnet); Tue, 26 Mar 1996 02:47:46 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Tue, 26 Mar 1996 02:45:29 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Tue, 26 Mar 1996 02:43:59 GMT Received: from PSB (PSB::SYSTEM) by BIG (MX V4.1 VAX) with SMTP (DECnet); Sat, 16 Mar 1996 05:03:07 GMT Received: from www.ccl.net by psb.sbu.ac.uk (MX V4.1 VAX) with SMTP; Fri, 15 Mar 1996 23:47:21 GMT Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.1/950822.1) id SAA00051; Fri, 15 Mar 1996 18:17:19 -0500 (EST) Received: from harfang.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.7.1/950822.1) id SAA29965; Fri, 15 Mar 1996 18:00:57 -0500 (EST) Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by harfang.CC.UMontreal.CA with ESMTP id RAA28647 (8.6.11/IDA-1.6 for ); Fri, 15 Mar 1996 17:59:56 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id RAA06688; Fri, 15 Mar 1996 17:59:56 -0500 Received: by cyclone.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id RAA13452; Fri, 15 Mar 1996 17:59:55 -0500 Date: Fri, 15 Mar 1996 17:59:55 -0500 Message-ID: <199603152259.RAA13452@cyclone.ERE.UMontreal.CA> To: CHEMISTRY@www.ccl.net Subject: CCL:File format question Originally-From: We have been having some major problems with our mail system for the last week. The backlog is now being cleared. However you may receive messages more than once. Our apologies for any inconvenience caused. =============================== Original Message follows ====================== I am trying to prepare a somewhat special picture with XMol. To do so I must be able to feed connectivity information into the program. But the only two file formats understood by XMol for which I have documentation are PDB and XYZ. XYZ does not allow connectivity data, and the PDB connectivity records seem to be ignored by XMol. Therefore I am looking for a file format that satisfies the following requirements: 1) It is understood by XMol, including connectivity information. 2) Its description is publicly available. Any help would be greatly appreciated. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: hinsenk@ERE.UMontreal.CA -- Original Sender From: Address: hinsenk@ERE.UMontreal.CA 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 gl@sbu.ac.uk Mon Mar 25 22:18:50 1996 Received: from psb.sbu.ac.uk for gl@sbu.ac.uk by www.ccl.net (8.7.1/950822.1) id VAA09488; Mon, 25 Mar 1996 21:56:19 -0500 (EST) From: Received: from BIG (BIG::SYSTEM) by PSB (MX V4.2 VAX) with SMTP (DECnet); Tue, 26 Mar 1996 02:56:51 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Tue, 26 Mar 1996 02:55:29 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Tue, 26 Mar 1996 02:53:55 GMT Received: from PSB (PSB::SYSTEM) by BIG (MX V4.1 VAX) with SMTP (DECnet); Sat, 16 Mar 1996 05:23:24 GMT Received: from www.ccl.net by psb.sbu.ac.uk (MX V4.1 VAX) with SMTP; Sat, 16 Mar 1996 02:31:02 GMT Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.1/950822.1) id VAA01096; Fri, 15 Mar 1996 21:03:06 -0500 (EST) Received: from coil.mdy.univie.ac.at for gl@coil.mdy.univie.ac.at by www.ccl.net (8.7.1/950822.1) id MAA29817; Tue, 12 Mar 1996 12:54:18 -0500 (EST) Received: by coil.mdy.univie.ac.at (940816.SGI.8.6.9/930416.SGI.AUTO) for chemistry@www.ccl.net id SAA21268; Tue, 12 Mar 1996 18:52:14 +0100 Originally-From: Message-ID: <9603121852.ZM21266@coil.mdy.univie.ac.at> Date: Tue, 12 Mar 1996 18:52:13 +0100 To: chemistry@www.ccl.net Subject: CCL:OFF Files and MD We have been having some major problems with our mail system for the last week. The backlog is now being cleared. However you may receive messages more than once. Our apologies for any inconvenience caused. =============================== Original Message follows ====================== Hi! In the manual for LEAP, a program used to setup systems for MD calculations that came with our AMBER-distribution from Oxford Molecular, I read about OFF (Object File Format). It says there: OFF is a general file format developed for LEAP... It is intention that future versions of AMBER and SPASMS will read this OFF file, rather than topology and coordinate files, for input data to molecular mechanics calculations. So OFF should contain all the information about a chemical system that is needed to start a MD simulation of that system: connectivities (topology), force-field parameters, positions and velocities of the atoms - but not the characteristics of the MD-simulation itself (as I understand it!). Before I start worrying about OFF at all, I would really like to know: 1) When will there actually be a MD-program that understands OFF? 2) Will OFF only be supported by AMBER (and SPASMS) or is there a chance that other MD-programs (CHARMM, discover) will read OFF. 3) Is there a (definitive) specification of OFF somewhere. 4) Is there any other movement towards a universal file-format for the specification of chemical systems for MD-simulations? Thanks a lot for your attention! -gerald -- Gerald Loeffler PhD student in Theoretical Biochemistry EMail: Gerald.Loeffler@mdy.univie.ac.at Phone: +43 1 40480 612 Fax: +43 1 4028525 SMail: University of Vienna Institute for Theoretical Chemistry Theoretical Biochemistry Group Waehringerstrasse 17/Parterre A-1090 Wien, Austria --- Administrivia: This message is automatically appended by the mail exploder: 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 ---