From raman@bioc01.uthscsa.edu Wed Dec 11 01:08:52 1996 Received: from elzip.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.8.3/950822.1) id AAA10294; Wed, 11 Dec 1996 00:40:32 -0500 (EST) Received: from bioc01.uthscsa.edu by uthscsa.edu (PMDF V5.0-5 #13300) id <01ICV2ZKGMGG00BSV0@uthscsa.edu>; Tue, 10 Dec 1996 23:40:37 -0500 (CDT) Received: from bioc01.uthscsa.edu by uthscsa.edu (PMDF V5.0-5 #13300) id <01ICV2ZERXMS00B34Q@uthscsa.edu>; Tue, 10 Dec 1996 23:40:29 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA02445; Tue, 10 Dec 1996 23:43:03 -0600 (CST) Date: Tue, 10 Dec 1996 23:43:02 -0600 (CST) From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Subject: Re: CCL:HELP: differential equation In-reply-to: <32AD7799.41C6@zeus.uncor.edu> To: jose@zeus.uncor.edu (Dr. Jose Santiago Duca) Cc: chemistry@www.ccl.net Message-id: <9612110543.AA02445@bioc01.uthscsa.edu> X-Mailer: ELM [version 2.4 PL3] Content-type: text Content-transfer-encoding: 7BIT Jose: I tried to respond directly, but it bounced back. Sorry... > I am here again to ask about *any* way to solve the following > differential equation > dP1/dt k1 (R10-P1)(k2-k21 P1-k21 P2+k21 R10+k21 R20) > -------- = ---------------------------------------------- > dP2/dt k2 (R20-P2)(k1-k12 P1-k12 P2+k12 R10+k12 R20) > P1 and P2 are functions of time (t) and also P1=f(P2) and P2=f(P1) [in > fact, THIS is the point I need to solve!!], whereas k1, k2, k12, k21, > R10 and R20 are constants. I would strongly recommend the program EASY-FIT by Prof. Klaus Schittkowski (Dept. Mathematics Uni. Bayreuth, Germany) to solve your problem. EASY-FIT is a very powerful interactive software system to identify parameters in explicit model functions, dynamical systems of equations, Laplace transforms, ODE etc. ODEs are integrated by a couple of explicit and implicit codes, also with internal numerical differentiation. Differential algebraic equations can be solved upto index 3. I suggest that you contact Prof. Schittkowski for the program. His email address is: klaus.schittkowski@uni-bayreuth.de Cheers -raman ______________________________________________________________________ C.S.Raman Tel: (210) 614-0839 Dept. of Biochemistry Fax: (210) 567-2490 University of Texas email:raman@bioc01.uthscsa.edu Health Science Center 7703 Floyd Curl Drive San Antonio, TX, 78284-7760 U.S.A. ---------------------------------------------------------------------- The real problem in speech is not precise language. The problem is clear language. --Richard Feynman ______________________________________________________________________ From alain.kessi@psi.ch Wed Dec 11 05:08:55 1996 Received: from psizi1.psi.ch for alain.kessi@psi.ch by www.ccl.net (8.8.3/950822.1) id EAA11960; Wed, 11 Dec 1996 04:44:56 -0500 (EST) Received: from localhost by psizi1.psi.ch (AIX 3.2/UCB 5.64/4.03) id AA21135; Wed, 11 Dec 1996 10:49:41 +0100 Sender: kessi@psizi1.psi.ch Message-Id: <32AE83B4.794B@psi.ch> Date: Wed, 11 Dec 1996 10:49:40 +0100 From: Alain Kessi Organization: Paul Scherrer Institut, Zuerich, Switzerland X-Mailer: Mozilla 3.0 (X11; I; AIX 2) Mime-Version: 1.0 To: CCL Computational Chemistry List Subject: Summary: molecules in strong electric fields Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netters, here's the (short) summary of the replies (actually: reply) I received to my question. It seems noone is aware of or willing to share more recent references on the subject (maybe this summary prompts one or two more replies ;-). First the original question: > I would appreciate any references to quantum chemical or DFT > calculations of molecules in large electric fields. Now the single answer (thanks to Yurii Kruglyak!): ---------------------- Subject: Re: CCL:molecules in strong electric fields Date: Tue, 3 Dec 1996 18:30:52 +0200 (EET) From: "Yurii Kruglyak" Organization: QuantumNet To: Alain.Kessi@psi.ch Dear Alain, Our publications on molecular computations in strong external electric field are listed below: 1. V.V.Lobanov, M.M.Aleksankin, Yu.A.Kruglyak Quantum-Chemical Investigation of Molecule and Ion Behaviour in an Electric Field. II. Ethanal Intern. J. Mass Spectrom. Ion Physics, v. 18, 275 - 288 (1975) 2. M.M.Aleksankin, V.V.Lobanov, Yu.A.Kruglyak Dissociation of Acetaldehyde in an Electronic Field Doklady Akademii Nauk SSSR, v. 222, No.1, 132 - 135 (1975) [In Russian] 3. M.M.Aleksankin, V.V.Lobanov, Yu.A.Kruglyak To the Theory of Hydrogen Rearrangement when Chemical Bonds are Dissociating under the Conditions of the Field Mass-Spectrometry Doklady Akademii Nauk SSSR, v. 231, No. 3, 637 - 640 (1976) [In Russian] 4. V.V.Lobanov, Yu.A.Kruglyak, M.M.Aleksankin Quantum-Chemical Study of Molecules and Ions of Acetales in Strong Electric Field Teoreticheskaya i Eksperimentalnaya Khimiya (TEK), v. 12, No. 1, 48 - 55 (1976) [in Russian] 5. M.M.Aleksankin, V.V.Lobanov, Yu.A.Kruglyak Application of the MO Method to Explain Fragmentation of Positive Molecular Ions in a Strong Electric Field Fizika Molekul (Publishing House "Naukova Dumka", Kiev) No. 4, 26 - 46 (1977) [In Russian] 6. V.V.Lobanov, M.M.Aleksankin, Yu.A.Kruglyak Field Fragmentation of Methylamine Molecular Ion TEK, v. 14, No. 3, 337 - 345 (1978) [In Russian] 7. V.V.Lobanov, M.M.Aleksankin, Yu.A.Kruglyak Conformational Analysis of Dioxane Molecule in External Electric Field Zhurnal Strukturnoi Khimii, v. 20, No. 1, 181 - 185 (1979) [In Russian] 8. V.V.Rossikhin, E.O.Voronkov, Yu.A.Kruglyak Determination of Potential Energy Surface of the Molecules in the Applied Field on the Basis of Virial Relations Intern.J.Quantum Chem., v. 17, 327 - 340 (1980) Sincerely, Yuri Kruglyak -- (\@ @/) _/_/_/_/_/_/_/_/_/_/_/_/_oOOoo_ (_) _ooOOo _/ Professor Yuri Kruglyak _/ _/ Public Association QuantumNet _/ _/ Department of Molecular Electronics _/ _/ Faculty of Chemistry _/ _/ Odessa State University _/ _/ Dvoryanskaya St. 2 _/ _/ ODESSA 270100 UKRAINE _/ _/ kruglyak@qnet.odessa.ua [off-line] _/ _/ quantum@ignet.odessa.ua [on-line] _/ _/ URL: http://194.44.93.1/friends/qnet _/ _/ FaxLine: +380-482-637785 .ooo0 _/ _/ Voice : +380-482-603314 ( ) 0ooo. _/_/_/_/_/_/_/_/_/_/_/_/_/_/_ \ ( _ _( ) \_) ) / (_/ -- Alain Kessi (alain.kessi@psi.ch), at Paul Scherrer Institut, Zurich ++++ stop the execution of Mumia Abu-Jamal ++++ ++++ if you agree copy these 3 sentences in your own sig ++++ ++++ see: http://www.xs4all.nl/~tank/spg-l/sigaction.htm ++++ From abonvin@igc.phys.chem.ethz.ch Wed Dec 11 07:08:56 1996 Received: from bernina.ethz.ch for abonvin@igc.phys.chem.ethz.ch by www.ccl.net (8.8.3/950822.1) id GAA12585; Wed, 11 Dec 1996 06:32:25 -0500 (EST) Received: from shiraz.ethz.ch by bernina.ethz.ch with SMTP inbound; Wed, 11 Dec 1996 12:31:57 +0100 Received: (abonvin@localhost) by shiraz.ethz.ch (8.6.11/8.6.11) id MAA04775 for chemistry@www.ccl.net; Wed, 11 Dec 1996 12:41:16 +0100 From: abonvin Message-Id: <199612111141.MAA04775@shiraz.ethz.ch> Subject: GROMOS96 release To: chemistry@www.ccl.net Date: Wed, 11 Dec 1996 12:41:14 +0100 (MET) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit ***************************************************************** ***************************************************************** ** ** ** A N N O U C I N G T H E R E L E A S E O F ** ** ** ** G R O M O S 9 6 ** ** ** ***************************************************************** ***************************************************************** For general information on GROMOS and information on how to get GROMOS96 visit the GROMOS home page at http://igc.ethz.ch/gromos or contact us at BIOMOS b.v Laboratory of Physical Chemistry ETH Zentrum CH-8092 Zuerich Phone : +41.1.632 5501 Fax : +41.1.632 1039 e-mail: biomos@igc.phys.chem.ethz.ch What is GROMOS ? **************** GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. Its purpose is threefold: - Simulation of arbitrary molecules in solution or crystalline state by the method of molecular dynamics (MD), stochastic dynamics (SD) or the path-integral method. - Energy minimisation of arbitrary molecules. - Analysis of conformations obtained by experiment or by computer simulation. The simulation package comes with the GROMOS force field (proteins, nucleotides, sugars, etc.) the quality of which should be judged from the scientific literature concerning its application to chemical and physical systems, ranging from glasses and liquid crystals to polymers and crystals and solutions of biomolecules. Interesting applications of GROMOS96 (the latest version of GROMOS) are: - prediction of the dependence of a molecular conformation on the type of environment (water, methanol, chloroform, DMSO, apolar solvent, crystal, etc.); - calculation of relative binding constants by evaluating free energy differences between various molecular complexes using thermodynamic integration, perturbation and extrapolation; - prediction of energetic and structural changes caused by modification of amino acids in enzymes or of base pairs in DNA; - derivation of three-dimensional (3D) molecular structure on the basis of NMR data by using restrained MD techniques including time-averaged distance- and J-value restraining; - dynamic modelling of molecular complexes by searching configuration space using MD or SD in 3- or 4-dimensions, soft-core interaction, local elevation search; - prediction of properties of materials under extreme conditions of temperature and pressure, which may be experimentally inaccessible. ========================================================================== | Dr. Alexandre Bonvin | Phone: Int+41-1-632-5504 | | Physical Chemistry, ETHZ | Fax: Int+41-1-632-1039 | | Universitatstrasse 6 | Email: abonvin@igc.phys.chem.ethz.ch | | 8092 Zurich, Switzerland | http://igc.chem.ethz.ch/abonvin | ========================================================================== From jeff@elmer.bnpi.com Wed Dec 11 13:08:59 1996 Received: from beavis.bnpi.com for jeff@elmer.bnpi.com by www.ccl.net (8.8.3/950822.1) id MAA14910; Wed, 11 Dec 1996 12:30:10 -0500 (EST) Received: from elmer.bnpi.com (elmer [198.213.32.6]) by beavis.bnpi.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id LAA04183 for <@beavis.bnpi.com:chemistry@www.ccl.net>; Wed, 11 Dec 1996 11:27:36 -0700 Received: (from jeff@localhost) by elmer.bnpi.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) id LAA04817 for chemistry@www.ccl.net; Wed, 11 Dec 1996 11:27:01 -0600 From: "Jeff D. Saxe" Message-Id: <9612111127.ZM4815@b27.bnpi.com> Date: Wed, 11 Dec 1996 11:27:01 -0600 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Need plot program for EHT MOs, including d-orbitals Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii We are looking for a program which will plot 2D MO contours from extended Huckel calculations. We need a program which can handle d-orbitals. Jeff Saxe jeff@bnpi.com -- Jeff D. Saxe jeff@bnpi.com BioNumerik Pharmaceuticals, Inc. Suite 1250 8122 Datapoint Dr. San Antonio, TX 78229 210-614-1701 (phone) 210-614-0643 (fax) From tropsha@gibbs.oit.unc.edu Wed Dec 11 23:09:03 1996 Received: from gibbs.oit.unc.edu for tropsha@gibbs.oit.unc.edu by www.ccl.net (8.8.3/950822.1) id WAA17748; Wed, 11 Dec 1996 22:24:59 -0500 (EST) Received: from localhost by gibbs.oit.unc.edu (8.6.4.3/10.1) id WAA23548; Wed, 11 Dec 1996 22:25:00 -0500 Date: Wed, 11 Dec 1996 22:24:58 -0500 From: Alex Tropsha To: chemistry@www.ccl.net Subject: UNC QSAR Web Server In-Reply-To: <9612111127.ZM4815@b27.bnpi.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear colleagues: I am pleased to anounce the availability of the QSAR Web server developed in our laboratory. Since all applications are written in JAVA, you will need to use an adequate browser. The server has the following URL: http://mmlin1.pha.unc.edu/~jin/QSAR/ Since we continue to develop this server, we would greatly appreciate your comments. Thank you very much. xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx x Alexander Tropsha, Ph.D. x x Assistant Professor, Director x x the Laboratory for Molecular Modeling x x CB # 7360, Beard Hall x x School of Pharmacy x x University of North Carolina x x Chapel Hill, NC 27599-7360 x x Tel. (919) 966-2955 x x Fax (919) 966-6919 x xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx