From raman@bioc01.uthscsa.edu Fri Nov 12 00:25:56 1993 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.1/930601.1506) id AAA10401; Fri, 12 Nov 1993 00:16:09 -0500 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Thu, 11 Nov 1993 23:16:55 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA27645; Thu, 11 Nov 93 23:16:37 CST From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9311120516.AA27645@bioc01.uthscsa.edu> Subject: Re:Misfolded Protein Structures.... To: PATTABIR@FCRFV1.NCIFCRF.GOV (N. Pattabiraman) Date: Thu, 11 Nov 1993 23:16:37 -0600 (CST) Cc: chemistry@ccl.net X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 2839 Dear Pattabi: Although I don't have any misfolded structures to provide you at the moment, the following might be the next best thing I would suggest. It should get you started. Database of deliberately misfolded protein models ------------------------------------------------- reference: Holm, L., Sander, C. (1992) Evaluation of protein models by atomic solvation preference. J. Mol. Biol. 225, 93-105. The models were generated by selecting pairs of known structures which have an equal number of residues. The backbone conformation of the crystallo- graphic structure was kept, but the sequences were swapped and side chains optimized using a fast Monte Carlo algorithm with a simple energy function. The misfolded models were then subjected to 500 steps of steepest descents energy minimization using the GROMOS program. The models are named AAAAonBBBB, where AAAA is the Protein Data Bank (PDB) identifier for the sequence and BBBB is the PDB identifier of the backbone coordinates. 1bp2on2paz.brk 1cbhon1ppt.brk 1fdxon5rxn.brk 1hipon2b5c.brk 1lh1on2i1b.brk 1p2pon1rn3.brk 1ppton1cbh.brk 1reion5pad.brk 1rhdon2cyp.brk 1rn3on1p2p.brk 1sn3on2ci2.brk 1sn3on2cro.brk 2b5con1hip.brk 2cdvon2ssi.brk 2ci2on1sn3.brk 2ci2on2cro.brk 2croon1sn3.brk 2croon2ci2.brk 2cypon1rhd.brk 2i1bon1lh1.brk 2pazon1bp2.brk 2ssion2cdv.brk 2tmnon2ts1.brk 2ts1on2tmn.brk 5padon1rei.brk 5rxnon1fdx.brk ............................................................................. The best way to get these structures is via gopher. Follow the procedure given below to accomplish the same: 1. gopher ftp.embl-heidelberg.de 2. choose #3 on the menu 3. #2 databases 4. #24 protein-extras 5. #4 misfolded 6. This directory has a README file (excerpted above) as its last entry and the others are the misfolded structures in the pdb format. If you have trouble downloading via gopher, then, ftp to the same site to get the files you want. Good luck and let me know if you have difficulty in downloading the files. Regards -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From fares@host11.lctn.u-nancy.fr Fri Nov 12 04:25:58 1993 Received: from arcturus.ciril.fr for fares@host11.lctn.u-nancy.fr by www.ccl.net (8.6.1/930601.1506) id DAA10872; Fri, 12 Nov 1993 03:34:35 -0500 Received: from host11.lctn.u-nancy.fr by arcturus.ciril.fr with SMTP (1.37.109.4/16.2) id AA10110; Fri, 12 Nov 93 09:34:59 +0100 Received: by host11.lctn.u-nancy.fr (AIX 3.2/UCB 5.64/4.03) id AA15283; Fri, 12 Nov 1993 09:21:58 +0100 Date: Fri, 12 Nov 1993 09:21:58 +0100 From: fares@host11.lctn.u-nancy.fr (Mohamed Fares) Message-Id: <9311120821.AA15283@host11.lctn.u-nancy.fr> To: chemistry@ccl.net Subject: Second Quantization Cc: fares@host11.lctn.u-nancy.fr Dear Netters, I have posted the question : I would like to know about some books and articles dealing with second quantization in quantum chemistry. Here is the summary, I would like to thank everyone who gave me a useful suggestions and references. M. Fares ============================================================================= From: Frank Jensen Try "second quantization-based methods in quantum chemistry' by Poul Jorgensen and Jacs Simons, Academic Press 1981. Frank ============================================================================= From: "Cory C. Pye" You may wish to consider: P. Surjan, I. Mayer, R. Poirier, {\em J. Mol. Struct (Theochem)}, {\bf 170}, (1988) 1 ` " Second Quantization and the Hellman-Feynmann Theorem: A Unifie View on Energy Derivatives" P. Surjan has also written a book on second quantization, but I don't have the reference handy. You may be interested to know that he is in France at th -Cory Pye ============================================================================= From: Diane Lynch Hello, You might try "Second Quantization-Bases Methods in Quantum CHemistry" by Poul Jorgensen and Jack Simons. Academic Press (1981). There must be newer literature but its a start - enjoy. D. Lynch ============================================================================= From: jtgolab@amoco.com VERY good books on the subject of second quantization are: a) J. Linderberg and U. Ohrn, "Propagators in Quantum Chemistry", Academic Press, New York (1993). Known as the "The Little Yellow Book". b) P. Jorgensen and J. Simons, Second Quantization-Based Methods in Quantum Chemistry, Academic Press, New York (1981). :Joe jtgolab@amoco.com ============================================================================= From: Youling Wang M. Fares, As I know, there is a book written by P.R.Surjan which deals with many basic problems in quantum chemistry. The name is " Second Quantization ...". Good lucky Y. Wang ============================================================================= From: gerardo@houston.cray.com (Gerardo Cisneros) Mohamed, I can recommend John Avery's book, "Creation and Annihilation Operators", (New York: McGraw-Hill, 1976) ISBN 0-07-002504-5 You're welcome. Saludos, Gerardo Dr. Gerardo Cisneros |Cray Research de M'exico, S.A. de C.V. Applications Scientist |Tuxpan 10-403, Col. Roma Sur gerardo@cray.com |06760 M'exico, D.F. (+52+5)622-8584 |MEXICO ============================================================================= From: rittby@dirac.phys.tcu.edu (C. Magnus L. Rittby) Dr. Fares, Two books come to mind: Jorgensen & Simons: Second Quantized-Based Methods in Quantum Chemistry (Academic Press 1981). (Not a 'first read' book but still a 'classic') Harris, Monkhorst, and Freeman: Algebraic and Diagrammatic Methods in Many-Fe methods) Mags C. Magnus L. Rittby Internet: rittby@dirac.phys.tcu.edu Department of Physics BITNET: RITTBY@TCUCVMS Texas Christian University FAX: (817) 921-7110 or 926-7477 Box 32915 Phone: (817) 921-7131 or 921-7375 Fort Worth, TX 76129 USA ============================================================================= From: shepard@dirac.tcg.anl.gov (Ron Shepard) Look at chapter 2.4 of Szabo and Ostlund "Modern Quantum Chemistry". Also, if your library has it, "A guide to Feynman diagrams in the many-body problem" by R. D. Mattuck has the most entertaining discussion you're likely to find. Regards, -Ron Shepard ============================================================================= From: "100012.1163@compuserve.com" <100012.1163@CompuServe.COM> Dear Dr. Fares, We have published three books with reference to second quantization. The first is totally devoted to the subject: ------------------------------------------------------ P.R. Surjan, Budapest Second Quantized Approach to Quantum Chemistry - An Elementary Introduction 1989. Approx. 200 pp. 11 figs. 1 tab. Hardcover ISBN 3-540- 51137-7 Contents: Introduction.- Concept of Creation and Annihilation Operators.- Particle Number Operators.- Second Quantized Representation of Quantum Mechanical Operators.- Evaluation of Matrix Elements.- Advantages of Second Quantization: Illustrative Examples.- Density Matrices.- Connection to "bra and ket" Formalism.- Using Spatial Orbitals.- Some Model Hamiltonians in Second Quantized Form.- The Brillouin Theorem.- Many-Body Perturbation Theory.- Second Quantization for Nonorthogonal Orbitals.- Second Quantization and Hellmann- Feynman Theorem.- Intermolecular Interactions.- Quasiparticle Transformations. A Theory of the Localized Chemical Bond.- Miscellaneous Topics Related to Second Quantization.- Problem Solutions.- References.- Index. The subject of this book is the application of the second quantized approach to quantum chemistry. Second quantization is an alternative tool for dealing with many-electron theory. The vast majority of quantum chemical problems are more easily treated using second quantization as a language. This book offers a simple and pedagogical presentation of the theory and some applications. The reader is not supposed to be trained in higher mathematics, though familiarity with elementary quantum mechanics and quantum chemistry is assumed. Besides the basic formalism and standard illustrative applications, some recent topics of quantum chemistry are reviewed in some detail. This book bridges the gap between sophisticated quantum theory and practical quantum chemistry. ------------------------------------------------------- Lecture Notes in Quantum Chemistry European Summer School in Quantum Chemistry B.O. Roos, University of Lund, Sweden (Ed.) (Lecture Notes in Chemistry Vol. 58) 1992. VII, 421 pp. 13 figs. 23 tabs. Softcover ISBN 3-540- 55371-1 Quantum Chemistry is the course material of a European Summer School in Quantum Chemistry, organized by Bjrn O. Roos. It consists of lectures by outstanding scientists who participate in the education of students and young scientists. The book has a wider appeal as additional reading for University courses. Contents: P.-A. Malmquist, Lund, Sweden: Mathematical Tools in Quantum Chemistry.- J. Olsen, Lund, Sweden: The Method of Second Quantization.- P.R. Taylor, Moffet Field, CA: Molecular Symmetry and Quantum Chemistry.- B.O. Roos, Lund, Sweden: The Multiconfigurational (MC) Self-Consistent Field (SCF) Theory.- P.E.M. Siegbahn, Stockholm, Sweden: The Configuration Interaction Method.- T. Helgaker, Oslo, Norway: Optimization of Minima and Saddle Points.- P.R. Taylor, Moffet Field, CA: Accurate Calculations and Calibration.- U. Wahlgren, Stockholm, Sweden: Effective Core Potential Method. Computational chemistry has today reached a status where available methods and program systems are also used by scientists who are not specialists in the field. As a result there is a growing need to acquire the background knowledge necessary for a skilful use of these methods. This book will be useful as a textbook for students and researchers interested in learning more about modern methodology in quantum chemistry. ------------------------------------------------------ A. Bencini, D. Gatteschi, Florence, Italy Electron Paramagnetic Resonance of Exchange Coupled Systems 1989. Approx. 320 pp. 177 figs. 38 tabs. 519 ref. Hardcover ISBN 3-540-50944-5 >From the Contents: Exchange and Superexchange.- Spin Hamiltonians.- Spectra of Pairs.- Spectra of Clusters.- Relaxation in Oligonuclear Species.- Spectra in Extended Lattices.- Selected Examples of Spectra of Pairs.- Coupled Transition Metal Ions-Organic Radicals.- Biological Systems.- Low Dimensional Materials.- Excitons.- Appendix A: Second Quantization.- Appendix B: Properties of Angular Momentum Operators and Elements of Irreducible Tensor Algebra. The subject of this book is EPR Spectroscopy of systems in which two or more spins are magnetically coupled. These systems are relevant to many different scientific areas, ranging from chemistry to solid state physics and to biology. The book is based on the spin hamiltonian approach and extensive use is made of irreducible tensor techniques. The most novel feature is that for the first time the whole field is brought together including pairs, oligonuclear species and infinite species, in an attempt to provide a unitary approach. The book collects in one place information which up to now has been scattered in many different original papers, reviews and books. Quantum Chemistry, Quantum Theory, Chemical Bonding, Electron Correlation, Valence Bond Theory, Physical Chemistry, Theoretical Chemistry Hope it helps! Dr. Rainer Stumpe Springer-Verlag Chemistry Editorial Tiergartenstr. 17 D-69121 Heidelberg INTERNET:STUMPE@SPINT.COMPUSERVE.COM ============================================================================= From: gil@aluminum.nersc.gov (Tomasz J Gil) Hello, I would advise you to read the papers and the book by Linderberg and Ohrn. To begin see J. Chem. Phys. vol. 86, 4523 (1985). I think there is a whole volume of Int. Jour. Q. Chem. devoted to this problem. Tomasz Gil ============================================================================= From: casida@CHIMCN.UMontreal.CA (Casida Mark) Bonjour! [good morning] Je peux recommender deux livres aux quelles je refere assez souvent : [I recommend to you two books to which I refer very often] 1) Alexander L. Fetter et John Dirk Walecka, "Quantum Theory of Many-Particle Systems" (McGraw-Hill, 1971). Je trouve ce livre bien ecrit mais c'est sur que c'est un livre pour physiciens. Les titres des chapitres sont : 1] Second quantization 2] Statistical mechanics 3] Green's functions and field theory (fermions) 4] Fermi systems 5] Linear response and collective modes 6] Bose systems 7] Field theory at finite temperatures 8] Physical systems at finite temperature 9] Real-time Green's functions and linear response 10] Canonical transformations 11] Nuclear matter 12] Phonons and electrons 13] Superconductivity 14] Superfluid helium 15] Applications to finite systems: The atomic nucleus 2) Poul Joergensen et Jack Simons, "Second Quantization-Based Methods in Quantum Chemistry" (Academic Press, 1981). Ce livre est specifique a chimie quantique, mais l'approache est un peu original. Les titres des chapitres sont : 1] Introduction to Second-Quantization Methods 2] Energy and Wavefunction Optimization Methods 3] Perturbation Theory 4] The Coupled-Cluster Method 5] Physical Properties 6] Green's functions ... Mark Casida Note : text between brackets was added by M. Fares ============================================================================= From ferenc@rchsg8.chemie.uni-regensburg.de Fri Nov 12 04:35:56 1993 Received: from rrzs1.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.6.1/930601.1506) id DAA10877; Fri, 12 Nov 1993 03:46:27 -0500 Received: from rchsg8.chemie.uni-regensburg.de by rrzs1.rz.uni-regensburg.de (4.1/URRZ-relay (1.4)) id AA05541; Fri, 12 Nov 93 09:46:12 +0100 Received: by rchsg8.chemie.uni-regensburg.de (920330.SGI/BelWue-1.0SG(subsidiary)) (for CHEMISTRY@ccl.net) id AA18771; Fri, 12 Nov 93 09:46:52 +0100 Date: Fri, 12 Nov 93 09:46:52 +0100 From: ferenc@rchsg8.chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9311120846.AA18771@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: constraints in molecular dynamics Dear Netters, a few days ago I asked a question about an efficient algorithm for the handling of constrained molecules in molecular dynamics simulations. I got a lot of response and I would like to thank those people who wrote me. The information can be summarized as follows: 1) read the book of Allen and Tildesley 2) use "rattle" or "shake" I read this book before and I knew about those algorithms. In fact I was looking for something more efficient... I want to add two references which describe another possibility (maybe an alternative also to quaternions). a) Ciccotti, G. et al. (1982), Mol.Phys., 47, 1253-1264. b) Ciccotti, G., and Ryckaert, J. P. (1986), Comput.Phys.Rep., 4, 345-392. (Review) The rest of the answers is appended to this letter. Now again I have a question and a request. Can anybody tell me where I can get the GROMOS package referenced in one of the letters? Can someone send me a code of rattle and/or shake for arbitrarily chosen molecules and constraints or tell me where I can find one? I will report to the net. Thank you very much in advance, Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): ferenc@rchsg8.chemie.uni-regensburg.de c5071@rchs1.chemie.uni-regensburg.de ferenc@rchnw2.ngate.uni-regensburg.de --------------------------------------------------------------------------- :-) There is more to live than increasing its speed. -- Ghandi ;-) --------------------------------------------------------------------------- P.S.: (answers to the request) From gl@coil.mdy.univie.ac.at Mon Nov 8 14:33:07 1993 Received: from coil.mdy.univie.ac.at by rchsg8.chemie.uni-regensburg.de via SMTP (920330.SGI/BelWue-1.0SG(subsidiary)) (for ferenc) id AA10875; Mon, 8 Nov 93 14:33:07 +0100 Received: by coil.mdy.univie.ac.at (930416.SGI/930416.SGI) for ferenc@rchsg8.chemie.uni-regensburg.de id AA09959; Mon, 8 Nov 93 14:28:43 +0100 From: "Gerald Loeffler" Message-Id: <9311081428.ZM9957@coil.mdy.univie.ac.at> Date: Mon, 8 Nov 1993 14:28:41 +0100 In-Reply-To: ferenc@rchsg8.chemie.uni-regensburg.de (Ferenc Molnar) "constraints im molecular dynamics" (Nov 8, 12:12pm) References: <9311081112.AA10681@rchsg8.chemie.uni-regensburg.de> X-Mailer: Z-Mail (3.0B.0 25aug93 MediaMail) To: ferenc (Ferenc Molnar) Subject: Re: constraints im molecular dynamics Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Status: RO On Nov 8, 12:12pm, Ferenc Molnar wrote: > Subject: constraints im molecular dynamics > Dear Netters! > > I am looking for information on methods to impose constraints > on molecules (constant bond-length etc.) in molecular > dynamics simulations. > > Does anybody know about a fast constraints-algorithm in connection > with Gear's (predictor-corrector) or Verlet's (velocity verlet) > algorithm. > > the algorithm that does constraining on either distances or angels is called shake: 1) Ryckaert, Ciccotti, Berendsen, J. Comp. Phys., 23, 327 (1977) 2) van Gunsteren, Berendsen, Mol. Phys. 34, 1311 (1977) -- Gerald Loeffler gl@coil.mdy.univie.ac.at Theoretical Biochemistry Group Department of Theoretical Chemistry University of Vienna A-1090 Vienna, Austria Institut fuer Theoretische Chemie und Strahlenchemie der Universitaet Wien Arbeitsschwerpunkt Theoretische Biochemie Waehringerstrasse 17/Parterre A-1090 Wien, Austria From ravishan@swan.wcc.wesleyan.edu Mon Nov 8 14:51:51 1993 Received: from swan.wcc.wesleyan.edu by rchsg8.chemie.uni-regensburg.de via SMTP (920330.SGI/BelWue-1.0SG(subsidiary)) (for ferenc) id AA10898; Mon, 8 Nov 93 14:51:51 +0100 Received: by swan.wcc.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA16022; Mon, 8 Nov 1993 08:46:46 -0500 Date: Mon, 8 Nov 1993 08:46:46 -0500 Message-Id: <9311081346.AA16022@swan.wcc.wesleyan.edu> From: G. Ravishanker Sender: ravishan@swan.wcc.wesleyan.edu To: ferenc In-Reply-To: <9311081112.AA10681@rchsg8.chemie.uni-regensburg.de> (ferenc@rchsg8.chemie.uni-regensburg.de) Subject: Re: constraints im molecular dynamics Status: RO Ferenc SHAKE proposed by Ryckaert and implemented by van Gunsteren's work and RATTLE from Andersen are the most commonly used. For references and example code can be found in the book by M.P. Allen and D.J. Tildesley on Computer simulation of liquids published by Oxford Science publications. Hope this helps. Ravi **************************************************************************** * Ganesan Ravishanker Ph: (203) 344-8544 Ext. 3110 * * Coordinator of Scientific Computing, Fax:(203) 344-7960 * * Adjunct Associate Professor(Dept. of Chem.) * * Wesleyan University e-mail:ravishan@swan.wcc.wesleyan.edu * * Middletown, CT 06457. * **************************************************************************** From csoares@iris1.Fki.UU.SE Mon Nov 8 15:47:13 1993 Received: from iris1.FKI.UU.SE by rchsg8.chemie.uni-regensburg.de via SMTP (920330.SGI/BelWue-1.0SG(subsidiary)) (for ferenc) id AA10996; Mon, 8 Nov 93 15:47:13 +0100 Received: from [130.238.69.55] (Mac55.FKI.UU.SE) by iris1.Fki.UU.SE with SMTP id AA14492 (5.67a8/IDA-1.5 for ); Mon, 8 Nov 1993 15:22:16 GMT Date: Mon, 8 Nov 1993 15:22:16 GMT Message-Id: <199311081522.AA14492@iris1.Fki.UU.SE> To: ferenc From: csoares@iris1.fki.uu.se Subject: Re: constraints im molecular dynamics Cc: csoares@iris1.fki.uu.se Status: RO >Dear Netters! > >I am looking for information on methods to impose constraints >on molecules (constant bond-length etc.) in molecular >dynamics simulations. > >Does anybody know about a fast constraints-algorithm in connection >with Gear's (predictor-corrector) or Verlet's (velocity verlet) >algorithm. > > >Thanks in advance. > >Ferenc > >Ferenc Molnar The most widely use algorithm for bond length constraints is the SHAKE algorithm which was initially applied in the framework of the Verlet algorithm (1) but it can also be incorporated in predictor-corrector methods (2). The same formulation can be used to other types of constraints. The GROMOS package has a subroutine to do this (with Verlet's). Hope it helps, Claudio (1) Ryckaert, J.-P., Ciccotti, G., Berendsen, H.J.C. (1977) "Numerical integration of the cartesian equations of motion of a system with constrains: Molecular dynamics of n-Alkanes",J.Comp.Phys., 23, 327-341 (2) van Gunsteren, W.F., Berendsen, H.J.C.(1977) "Algorithms for macromolecular dynamics and constraint dynamics", Mol.Phys., 34, 1311-1327 ----------------------------------------------------------------- I Claudio Soares I MOLECULAR MODELLING I I Uppsala University I GROUP I I Dep.Physical Chemistry I I I Box 532 I : I I S-751 21 Uppsala I l I I SWEDEN I C=O I I I l I I Pho: +46 18 183631 I H-N I I Fax: +46 18 508542 I l I I Email:CSOARES@IRIS1.FKI.UU.SE I : I ----------------------------------------------------------------- From chemistry-request@ccl.net Mon Nov 8 16:08:46 1993 Received: from www.ccl.net by rchsg8.chemie.uni-regensburg.de via SMTP (920330.SGI/BelWue-1.0SG(subsidiary)) (for ferenc) id AA11016; Mon, 8 Nov 93 16:08:46 +0100 Received: from localhost for chemistry-request@ccl.net by www.ccl.net (8.6.1/930601.1506) id IAA21897; Mon, 8 Nov 1993 08:59:45 -0500 Received: from ben.britain.eu.net for JEREMYW@num-alg-grp.co.uk by www.ccl.net (8.6.1/930601.1506) id IAA21756; Mon, 8 Nov 1993 08:44:11 -0500 Received: from num-alg-grp.co.uk by ben.britain.eu.net via JANET with NIFTP (PP) id ; Mon, 8 Nov 1993 13:43:59 +0000 Message-Id: <6950.9311081343@nags2.nag.co.uk> Received: from vax.nag.co.uk (nagvax) by nags2.nag.co.uk (4.1/UK-2.1) id AA06950; Mon, 8 Nov 93 13:43:08 GMT Date: 8 Nov 93 13:40:00 WET From: JEREMY WALTON Subject: Re: constraints in MD To: CHEMISTRY Sender: chemistry-request@ccl.net Errors-To: jkl@ccl.net Precedence: bulk Status: RO > Does anybody know about a fast constraints-algorithm in connection > with Gear's (predictor-corrector) or Verlet's (velocity verlet) > algorithm. It's been a while since I looked at this, but something like van Gunsteren's and Berendsen's SHAKE algorithm has been useful in implementing bond constraints. It's available in the GROMOS, the complete MD package. References to other methods (I think) would perhaps be found in M.P. Allen & D.J. Tildesley, "Computer Simulation of Liquids", Oxford University Press, Oxford, 1987. -------------------------------------------------------------------------------- | Jeremy Walton nagjpw@vax.oxford.ac.uk | | The Numerical Algorithms Group Ltd, Oxford, UK jeremyw@nag.co.uk | | Tel: +44 865 511245 | | Fax: +44 865 310139 | -------------------------------------------------------------------------------- ---Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net (coming soon) Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search From epw@ppco.com Tue Nov 9 17:31:02 1993 Received: from newton.ncsa.uiuc.edu by rchsg8.chemie.uni-regensburg.de via SMTP (920330.SGI/BelWue-1.0SG(subsidiary)) (for ferenc) id AA12970; Tue, 9 Nov 93 17:31:02 +0100 Received: from ppco.com by newton.ncsa.uiuc.edu with SMTP id AA17007 (5.65a/IDA-1.4.2 for ferenc@rchsg8.chemie.uni-regensburg.de); Tue, 9 Nov 93 10:30:08 -0600 Received: from [0.0.0.0] ([138.32.132.50]) by ppco.com (4.1/SMI-4.1) id AA08525; Tue, 9 Nov 93 10:30:39 CST From: "Eric P. Wallis" Date: Tue, 9 Nov 93 10:30:28 CST Message-Id: <2563.epw@charon_POPMail/PC_3.2.3_Beta_2> Reply-To: X-Popmail-Charset: English To: ferenc Subject: Re: constraints im molecular dynamics Status: RO There are two programs that work well with verlet algorithm to constrain internal coordinates. The Shake algorithm (by Ryckaert, Ciccotti, and Berendsen; J. Comput. Phys., 23, 327 (1977)) and Rattle (Anderson, J. Comput. Phys., 52, 24 (1983)). They are discussed in Allen and Tildesley book "Computer Simulations of Liquids". >Dear Netters! > >I am looking for information on methods to impose constraints >on molecules (constant bond-length etc.) in molecular >dynamics simulations. > >Does anybody know about a fast constraints-algorithm in connection >with Gear's (predictor-corrector) or Verlet's (velocity verlet) >algorithm. > > >Thanks in advance. > >Ferenc > >Ferenc Molnar >--------------------------------------------------------------------------- >Institut fuer Physikalische und Theoretische Chemie >- Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 >Universitaet Regensburg Fax.: (+49) 941 943-4488 >Universitaetsstrasse 31 >D-93053 Regensburg >Deutschland / Germany >--------------------------------------------------------------------------- >EMail (SMTP): ferenc@rchsg8.chemie.uni-regensburg.de > c5071@rchs1.chemie.uni-regensburg.de > ferenc@rchnw2.ngate.uni-regensburg.de >--------------------------------------------------------------------------- >:-) There is more to live than increasing its speed. > -- Ghandi ;-) >--------------------------------------------------------------------------- > > >---Administrivia: This message is automatically appended by the mail exploder: >CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator >MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net (coming soon) >Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search ***************************************************** Dr. Eric P. Wallis Computational Chemistry Phillips Petroleum Co. (918) 661-7956 Voice 331A PL (918) 662-1097 FAX Bartlesville, OK 74004 epw@ppco.com e-mail ***************************************************** From ackerman@theochem.tu-muenchen.de Fri Nov 12 07:26:09 1993 Received: from theo1.theochem.tu-muenchen.de for ackerman@theochem.tu-muenchen.de by www.ccl.net (8.6.1/930601.1506) id HAA11222; Fri, 12 Nov 1993 07:18:26 -0500 Received: from theo80.theochem.tu-muenchen.de by theo1.theochem.tu-muenchen.de (5.64/1.34) id AA13670; Fri, 12 Nov 93 12:59:21 +0100 Received: by theo80.theochem.tu-muenchen.de (4.1/SMI-4.1) id AA16285; Fri, 12 Nov 93 12:59:19 +0100 Date: Fri, 12 Nov 93 12:59:19 +0100 From: ackerman@theochem.tu-muenchen.de (Lutz Ackermann) Message-Id: <9311121159.AA16285@theo80.theochem.tu-muenchen.de> To: CHEMISTRY@ccl.net Subject: Wanted:material for Comp. Chem. course Dear Colleagues, We are currently elaborating on a curriculum for a Lab Course in Computational Chemistry (two quarters, fourth year chemistry students). We have started this project only recently by evaluating different computational methods we employ ourselfs for their usefulness in this contents. At the same time conceptual work has to be done. We want to design our own course, but not necessarily all "from scratch". Indeed, as I started my search for material of that kind, I found the description of "Chemistry 8003" by C. J. Cramer (University of Minnesota) via anonymous ftp at www.ccl.net. This was very inspiring and has a structure quite similar to what we are envisioning (the emphasis being somewhat different, though). This strenghthened my conviction, that there must be some more material around someplace. So if you know ***any*** textbook, curriculum, collection of material (slides, handouts, tests, problem sets) printed or electronic please let me know. Also, if you have personal experience in teaching Computaional Chemistry to Chemistry students I would appreciate to learn from you. References to literature would be helpfull, too (J. Chem. Educ. seems to cover some stuff of that sort, but it will be tedious work to find it without any hint). Thanks a lot (in advance) for any contribution L. Ackermann ***************************************************** * * * Dr. Lutz Ackermann * * * * Lehrstuhl fuer Theoretische Chemie (TU Munich) * * Lichtenbergstr. 4 * * 85747 Garching * * Germany * * * * room Nr. 63103 * * Tel. (+49 +89) 3209 3602 * * Fax (+49 +89) 3209 3622 * * e-mail ackerman@theo1.theochem.tu-muenchen.de * * * ***************************************************** From fh@oberon.zipc.wtza-berlin.de Fri Nov 12 07:31:48 1993 Received: from oberon.zipc.wtza-berlin.de for fh@oberon.zipc.wtza-berlin.de by www.ccl.net (8.6.1/930601.1506) id GAA11133; Fri, 12 Nov 1993 06:54:38 -0500 Received: by oberon.zipc.wtza-berlin.de (AIX 3.2/UCB 5.64/4.03) id AA14564; Fri, 12 Nov 1993 12:52:54 +0100 From: fh@oberon.zipc.wtza-berlin.de (Frank Haase) Message-Id: <9311121152.AA14564@oberon.zipc.wtza-berlin.de> Subject: satellite meeting on QC aspects of catalysis To: chemistry@ccl.net Date: Fri, 12 Nov 93 12:52:49 NFT X-Mailer: ELM [version 2.3 PL2] ------------------------------------------------------------------------- Quantumchemical Aspects of Heterogeneous Catalysis Humboldt University, Berlin/Germany, June 26 - 28,1994 ------------------------------------------------------------------------- 8th International Congress on Quantum Chemistry, Prague, 1994 ******************************************************************** A Post-Conference Satellite Meeting on Quantumchemical Aspects of Heterogeneous Catalysis will be held at Humboldt University, Berlin/Germany, June 26 - 28, 1994 ******************************************************************** Honorary Presidents: Gerhard Ertl (Berlin) and Hans-Georg von Schnering (Stuttgart) Organizers: Klaus Hermann and Joachim Sauer Topics: Acidic catalysts and catalysis (zeolites etc.); Metal oxides in catalytic systems; Reactions on metal surfaces and clusters; Chemisorption on metals: bonding and energies; Theoretical concepts and computational methods Further information: Prof. Joachim Sauer Max-Planck-Gesellschaft Arbeitsgruppe Quantenchemie an der Humboldt-Universitaet Jaegerstrasse 10/11 D-10117 Berlin Tel. +49-30-20192-300 FAX +49-30-20192-302 E-mail: js@uranos.zipc.wtza-berlin.de Prof. Klaus Hermann Max-Planck-Gesellschaft Abteilung Theorie des Fritz-Haber-Institutes Faradayweg 4-6 D-14195 Berlin Tel. +49-30-8305 526 FAX +49-30-8305 531 E-mail: hermann@fhi-berlin.mpg.de Invited Speaker: E.J. Baerends (Amsterdam), P.S. Bagus (San Jose), B. Bigot (Lyon), A.M. Bradshaw (Berlin), A.W. Castleman, Jr. (University Park/Pennsylvania), H.-J. Freund (Bochum), A.C. Hess (Washington), M.P. Irion (Darmstadt), H. Kobayashi (Kyoto), G.J. Kramer (Amsterdam), K. Morokuma (Atlanta), L. Pettersson (Stockholm), D.R. Salahub (Montreal), H. Schwarz (Berlin), P.E.M. Siegbahn (Stockholm), V. Staemmler (Bochum), P. Ugliengo (Torino), R.A. van Santen (Eindhoven), J.L. Whitten (Raleigh), M. Witko (Krakow), T. Ziegler (Calgary) Theoretical contributions will be supplemented by talks of experimentalists highlighting cross-links between theory and experiment. ------------------------------------------------------------------------------ Quantumchemical Aspects of Heterogeneous Catalysis Preregistration Form Please check where appropriate and return this form at your earliest convenience but ****************** not later than 30/11/1993. ************************ We encourage reply by FAX or E-mail. I plan to participate I would like to make a contribution I prefer to present a poster I prefer an oral presentation Tentative titel: Address: E-mail FAX Tel. ------------------------------------------------------------------------------ -- ------------------------------------------------------------------------------ Dr. Frank Haase Max-Planck-Society Quantum Chemistry Group at the Humboldt University Berlin Jaeger Str. 10/11 D-10117 Berlin Germany ------------------------------------------------------------------------------ Phone: +(49) 30 20192 308 FAX : +(49) 30 20192 302 E-mail: fh@oberon.zipc.wtza-berlin.de ------------------------------------------------------------------------------ No RISC, no fun ! ------------------------------------------------------------------------------ From PA144188%UTKVM1.BITNET@phem3.acs.ohio-state.edu Fri Nov 12 09:27:24 1993 Received: from phem3 for PA144188%UTKVM1.BITNET@phem3.acs.ohio-state.edu by www.ccl.net (8.6.1/930601.1506) id IAA11930; Fri, 12 Nov 1993 08:48:18 -0500 Received: from UTKVM1.BITNET (MAILER@UTKVM1) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #3557) id <01H5809WQCLC8XD10Y@phem3.acs.ohio-state.edu>; Fri, 12 Nov 1993 08:48:11 EST Received: from UTKVM1 (PA144188) by UTKVM1.BITNET (Mailer R2.10 ptf000) with BSMTP id 7451; Fri, 12 Nov 93 08:47:55 LCL Date: Fri, 12 Nov 93 08:39:14 LCL From: Ron Peterson Subject: Finding force constants for C2v molecules on Hondo To: "chemistry@ccl.net" Message-id: <01H5809WQCLE8XD10Y@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT I'm working on 5 atom molecules that are C2v, of the type MX2Y2 like CH2F2 on Hondo v8.2. My problem is that I'm not getting full resonable force constants. To save on band width, I won't go into full detail here, but if you think you can help me, please email me, and I'll send a full description of the problem and what I have done. Thanks in advance, Ron Peterson pa144188@utkvm1 (bitnet) ronp@neon.chem.utk.edu (internet) From srp@ZGI.COM Fri Nov 12 11:26:03 1993 Received: from m5.ZGI.COM for srp@ZGI.COM by www.ccl.net (8.6.1/930601.1506) id LAA12933; Fri, 12 Nov 1993 11:14:06 -0500 Received: from zgi.com (stella.ZGI.COM) by m5.ZGI.COM (4.1/SMI-4.1) id AA02743; Fri, 12 Nov 93 08:13:26 PST Received: from blaster.ZGI.COM by zgi.com (4.1/SMI-4.1) id AA01853; Fri, 12 Nov 93 08:13:22 PST Received: by blaster.ZGI.COM (920330.SGI/920502.SGI) for @stella.ZGI.COM:CHEMISTRY@ccl.net id AA06361; Fri, 12 Nov 93 08:13:21 -0800 Date: Fri, 12 Nov 93 08:13:21 -0800 From: srp@ZGI.COM (Scott Presnell) Message-Id: <9311121613.AA06361@blaster.ZGI.COM> To: CHEMISTRY@ccl.net Subject: Inventory/Bioassay Database Hi Folks, We about to start the process of creating a structure database, and are considering implementing links/xrefs to other databases (such as bioassay, inventory). In specific, we will almost certainly use MACCS for structural information, and are considering Oracle or INGRESS for bioassay/textual information. However, not being database experts, we'd be interested in hearing the experiences and recommendations of others. What sort of database systems have other people set up for keeping track of compound structure and activity? Do folks try to do it all in MACCS, or use xrefs that cross databases. Thanks for any recommendations. - Scott Presnell (srp@zgi.com) From leoh@maple.lemoyne.edu Fri Nov 12 12:26:04 1993 Received: from MAPLE for leoh@maple.lemoyne.edu by www.ccl.net (8.6.1/930601.1506) id MAA13419; Fri, 12 Nov 1993 12:16:10 -0500 Received: by maple.lemoyne.edu (MX V3.3 VAX) id 26357; Fri, 12 Nov 1993 12:15:07 EDT Date: Fri, 12 Nov 1993 12:15:05 EDT From: "Leo, Howard" To: CHEMISTRY@ccl.net Message-ID: <009756DE.0579B5E0.26357@maple.lemoyne.edu> Subject: LUMO energy summary Many thanks to everyone who responded to my question regarding the difference between semi-empirical and ab initio LUMO energies. -------------------------------------------------------------------- From: MX%"jstewart@fai.com" 8-NOV-1993 12:21:46.10 Because semiempirical methods use a very restricted basis set, they are not good at predicting LUMO energies. Jimmy Stewart -------------------------------------------------------------------- From: MX%"slee@hyper.uucp" 8-NOV-1993 13:53:06.68 I believe that this is a conseequence of the minimal basis set employed by semi-empirical methods. The extra orbitals in the extended basis set of the ab initio calculation make little difference for the occupied levels, including the HOMO, as the semi-empirical methods are parametrized to reproduce proper behaviour for the ground state properties. The semi-empirical methods (AM1 and PM3 anyway) are not parameterized to reproduce excited state properties. In the SCF procedure, the unoccupied orbitals are, to some extent, simply the left-overs of the calculation. The SCF optimizes the occupied orbitals to obtain the lowest energy state, and the unoccupied orbitals are set by orthogonality requirements. The antibonding overlaps in the minimal basis set are large because the basis set has little flxibility, and the LUMO energies are high. When you have the d orbitals as in the 6-31G* set, the d orbitals mix in to produce less drastically antibonding orbitals, with significantly lower energy. You should notice that the HOMO-LUMO gap is always quite a bit bigger than the UV absoprtion frequency anyway, for other reasons. Hope this is of use. Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 ------------------------------------------------------------------- From: MX%"lou@scripps.edu" 8-NOV-1993 14:27:40.25 Although I don't know the codes that you are using specifically, I think that most likely your problem is that in the Hartree-Fock method empty orbitals see a full N electron potential instead of the proper N-1 electron potential seen by the occupied orbitals. This means that in a neutral system like yours, the LUMO energies are actually estimates of the electron affinity (and probably not very good estimates either), i.e. the LUMO energy is the Koopman's energy of the anion. To improve this, you would need to use improved virtual orbitals, or to do CI (or both). Improved virtual orbitals (IVO's) have been described by Davidson and others. While the physical process you are trying to evaluate is optical excitation, you have instead a poor approximation to the electron affinity. Alternatively, you could try Density Functional methods which do not suffer from this problem, using either DELTA SCF or the Slater transition state. I hope this is helpful. Lou Noodleman Molecular Biology MB1 The Scripps Research Institute La Jolla CA 92037 lou@scripps.edu --------------------------------------------------------------------- From: MX%"milan@helix.nih.gov" 8-NOV-1993 15:48:08.27 Do you have also STO-3G numbers for these cases? It would be interesting to see if they are more like 6-31G or more like AM1. Milan Hodoscek (milan@helix.nih.gov) --------------------------------------------------------------------- From: MX%"john@cv1.chem.purdue.edu" 9-NOV-1993 07:52:24.67 Is it possible that the LUMO's of the molecules you are studying are falling onto "continuum functions"? We have had this same trouble with chlorides (LUMO's) and the problem stems from the diffuseness of the chlorine orbitals (which might be expected to be a problem considering the relatively diffuse basis sets you are using). A couple of references I can give you that describe this problem (as well as what needs to be done to solve it) are the following: Falcetta, M. F.; Jordan, K. D., J. Phys. Chem., 1990, 94, 5666 Falcetta, M. F.; Jordan, K. D., J. Am. Chem. Soc., 1991, 113, 2903 Hope this helps! Sincerely, John Nash -------------------------------------------------------------------------- From: MX%"PA13808@UTKVM1.BITNET" (John E. Bloor) 9-NOV-1993 13:10:25.31 If you look at the elements of the Fock matrix you will see that the charge density is only over the occupied MOS. Thus the unoccupied MOs change only because they are forced to be orthogonal to the occupied MOs and to the Ot otherunoccupied MOs. Since AM1 does not include overlap and has a very diffe rent Hamiltonian one should not expect any relationship with the ab initio results on an absolute scale. With respect to the difference in the ab initio results. When you add the * you add sets of High lying D orbitals. These by orthogonality repel the LUMO and it goes down! In order to get results which have any relationship to reality you have to add an electron into the LUMO. The accurate calc of electron aff inities though is a very difficult task. (PA13808 at UTKVM1)(John E. Bloor) -------------------------------------------------------------------------- From: MX%"sjackels@ac.wfunet.wfu.edu" 11-NOV-1993 10:58:49.80 I have noticed the same effect. In general I find that the semiempirical methods can predict geometries OK but the energies are not good. For a discussion of ab initio versus semiempirical energies in classical organic ring systems, see J. Comp. Chem. 13:525-532 (1992). I hope this helps. Susan C. Jackels Department of Chemistry Wake Forest University Winston-Salem, NC 27109 Phone: (919)759-5514 FAX: (919)759-4656 Internet: sjackels@ac.wfunet.wfu.edu On sabbatical for 1993-1994 at: Department of Medicinal Chemistry 308 Harvard Street S.E. University of Minnesota Minneapolis, MN 55455 Phone: (612)626-4429 --------------------------------------------------------------------- There was one other response which I accidently lost. I apologize to that person. Howard Leo