From chemwork@sissy.crs4.it Wed Dec 2 14:26:21 1992 Date: Wed, 2 Dec 1992 13:26:21 +0100 From: chemwork@crs4.it Message-Id: <9212021226.AA14073@sissy.crs4.it> To: chemistry@ccl.net Subject: Computational Chemistry School COMPUTATIONAL CHEMISTRY AND MOLECULAR MODELLING A WORKSHOP WITH DIRECT USE OF WORKSTATIONS AND MAINFRAMES Organizing Commitee Prof. E. Clementi, Dr. G. Corongiu, Dr. D. Estrin, Dr. V. Martorana The Centre for Advanced Studies, Research and Development in Sardinia (CRS4), is organising for the summer of 1993 four one-week workshops, modularly connected, on the subjects of quantum and computational chemistry, molecular modelling and drug design. The workshop will be held in Italy, on the Mediterranean island of Sardinia, a most beautiful and well-known resort area, in the vicinity of the charming small town of Alghero, at the new research centre of CORISA. Participants will be lectured on several practical and efficient methods, techniques, and computer programs in modern computational chemistry, and will have the opportunity to get 'hands on' experience in the use of these computational tools for the solution of problems of chemical and biochemical interest. Several powerful workstations will be locally available and a large IBM mainframe in Cagliari will be accessible through a fast connection. The teaching staff will consist in a group of researchers with personal experience in the fields of computational chemistry and molecular modelling. Overall organization of the workshops : 9:00 to 13:00 The morning session is devoted either to lectures or to practical aspects related to the use of the programs. 14:30 to 17:00 Free time for discussions and/or leisure. 17:00 to 19:00 Classes will resume. -Computational facilities will be available from 9:00 to 13:00 and from 15:00 to 19:00. -Saturday afternoon is lecture free. -Participants are expected to arrive on Sunday and to leave the following Saturday. ************************************************************************** ************************************************************************** FIRST NOTICE GENERAL INFORMATION 1. Participation : Participants are requested to have a doctoral degree either in Chemistry, Physics, Chemical Engineering, or comparable knowledge. 2. Application for admission : Pre-registration forms are enclosed. 3. Language : English will be the working language of the workshop, but all staff members may also speak in Italian. 4. Accommodation : On-site accommodation is available at the CORISA centre : single rooms, and full board are available for US$ 500. Early application is recommended. In the immediate vicinity of the Centre, you will find many other hotels. 5. Registration fees : The registration fee for each one-week workshop, is US$ 1,500. It covers the cost of tuition and the use of the computers. It does not cover travel and lodging which are at the participant's expenses. Closing date for final registration is 1st April 1993, or whenever the maximum number of participants (32) for each workshop has been reached. Should less than 20 applications be received for any given workshop, the organizing committee shall retain the right to cancel it. In such event, applicants shall be notified and the full registration fee refunded. 6. Transportation : Participants should reach the CORISA site by their own means. Should you plan to rent a car, bear in mind that planning should be done well in advance since during the summer Sardinia is visited by a few hundred thousand tourists. The closest airport is Alghero-Fertilia, others are Olbia and Cagliari. Regarding sea-transportation the closest harbor is Porto Torres and others in the island are Olbia and Cagliari. Bookings for car transportation are recommended to be done as early as possible. 7 Information about the place: One nice feature of the CORISA centre is its tranquillity and the fact that marvelous sea-shores are at walking distance. Alghero (about 20Km from CORISA) is a beautiful city keeping all the charm of the old aragonese fortification remaining from the times of the Spanish Domination. Study Plan for Computational Chemistry CC-I Computational Chemistry I 23 -28 Aug '93 CC-II Computational Chemistry II 30 Aug - 4 Sep '93 Two workshops are offered, CC-I at an introductory level, CC-II more advanced and partially tuned to specific requests made by the participants at the registration time. CC-I : Introductory classes to Quantum Mechanics and to the use of computer programs in computational chemistry; Hartree-Fock and semi-empirical methods, density functional techniques for treating the exchange and correlation energies and for the correlation energy only, ab-initio post Hartree-Fock calculations either by perturbation or variational methods, choice of basis sets, basis set superposition errors effects, use of molecular graphics. Each class is followed by computational exercises, making use of several RISC 6000/560 or of the IBM ES 9000/720 mainframe located in Cagliari. Use of additional hardware is under consideration. CC-II : Classes are given assuming that participants are familiar with the content of CC-I. Focus is given in the use of computational chemistry programs : optimization of molecular geometry, computation of molecular frequencies, energy surfaces from density functionals and from ab-initio calculations, determination of reaction rates for combustion chemistry and for other chemical processes, quantum molecular dynamics a la Car-Parrinello, polymers, use of molecular graphics. The second part will make a more intensive use of our computational facilities and libraries of computational chemistry programs. If there is sufficient interest, an introduction to parallel programming and computations will be made available. All computer programs, used in CC-I and CC-II workshops will be available in MOTECC-93. Study Plan for Molecular Modelling MM-I Molecular Modelling I 6 - 11 Sep '93 MM-II Molecular Modelling II 13 - 18 Sep '93 Under the broad name of Molecular Modelling, we include quantum chemical studies for structure activity relations, drug design, molecular graphics, and use of artificial intelligence algorithms. The main techniques taken into consideration will be : quantum chemistry, computational spectroscopy, molecular dynamics and Monte Carlo methods. MM-I : Introductory classes to Statistical Mechanics, determination of the force field for Molecular Mechanics, Molecular Dynamics, and Metropolis Monte Carlo simulations. Energy minimisation for small, medium and large molecules. Molecular Dynamics simulations for macromolecules in vacuo and in solution. Analysis of the results: MSD, pair correlation functions, velocity auto correlation functions, density of states, etc. Graphical display for input preparation and output analysis, use of trajectories for animation. MM-II : Simulations of the liquid state, water in particular; solvent effects for molecules in aqueous solution, computation, from molecular dynamics trajectories, of the density of states and of the spectra for infrared, Raman, neutron, and X-rays scattering, structure determination with NOE constraints, computation of free energy differences, molecular graphics. cut here ------------------------------------------------------------------ Computational Chemistry and Molecular Modelling Workshops CORISA Centre, August-September 1993 PRELIMINARY REGISTRATION FORM I wish to receive the second circular | | Title .......... Name ............. First Name ......................... Work Affiliation ....................................................... Address ................................................................... ........................................................................... ........................................................................... Phone Number (......) ............................. Fax Number (......) ............................... Electronic mail .................................................. Do you plan to participate Yes | | No | | Maybe | | Do you plan to attend CC-I Yes | | No | | Do you plan to attend CC-II Yes | | No | | Do you plan to attend MM-I Yes | | No | | Do you plan to attend MM-II Yes | | No | | Will you come alone Yes | | No | | Number of accompanying persons ............ Do you plan to lodge at CORISA Yes | | No | | Signature ......................................................... Date ....................................... Please complete in CAPITAL LETTERS or type and return by February 28th, 1993 to : Prof. Enrico Clementi (Summer School), CRS4, POBox 488, 09100 Cagliari, Italy fax +39 70 2796-400 e-mail chemwork@crs4.it (use of e-mail and fax is preferred) For further information call +39 70 2796-402 From rsjuds@snll-arpagw.llnl.gov Wed Dec 2 02:07:11 1992 Date: Wed, 2 Dec 92 10:07:11 -0800 From: rsjuds@snll-arpagw.llnl.gov (judson richard s) Message-Id: <9212021807.AA17450@snll-arpagw.llnl.gov> To: chemistry@ccl.net Subject: Programs to predict metabolic products Dear Netters: Does anyone know of programs that take a molecule and predict the the metabolic products, based on a set of rules about bonds that are likely to be hydrolyzed, etc? ----------------------------------------------- | Richard Judson | | Center for Computational Engineering | | Sandia National Laboratories | | Livermore, CA 94551-0969 | | (510)294-1438 | | email: rsjuds@sandia.llnl.gov | | | ----------------------------------------------- From markm@portal.vpharm.com Wed Dec 2 10:08:48 1992 From: markm@portal.vpharm.com (Mark Murcko) Message-Id: <9212022008.AA03436@portal.vpharm.com> Subject: D2O parameters for MD and MC simulations To: chemistry@ccl.net Date: Wed, 2 Dec 92 15:08:48 EST Does anyone know of any parameters for D2O that have been optimized for periodic boundary simulations? In other words, a D2O model that can reproduce the heat capacity, density, heat of vaporization, etc. for heavy water. I've done some literature searching and have come up dry. Thanks! / Mark From jle@world.std.com Wed Dec 2 10:21:24 1992 Date: Wed, 2 Dec 1992 15:21:24 -0500 From: jle@world.std.com (Joe M Leonard) Message-Id: <199212022021.AA06469@world.std.com> To: chemistry@ccl.net Subject: CI in MOPAC A change of pace... I'm curious as to whether folks use the CI capabilities of MOPAC often. I'm not familiar with V6, but V5 allowed one to do a fair amount with up to 100 configs. I've not seen much mention of such calculations in the lit, but haven't been that careful/diligent. I also know that INDO/S (Or Zindo) uses CI for UV spectra work. Any thoughts on the matter would be a help - I'll summarize if there's a deluge... Joe Leonard jle@world.std.com From annick@tammy.harvard.edu Wed Dec 2 13:04:09 1992 Date: Wed, 2 Dec 92 18:04:09 -0500 From: annick@tammy.harvard.edu (Annick Dejaegere) Message-Id: <9212022304.AA25775@tammy.harvard.edu> To: chemistry@ccl.net Subject: reaction field in G92 Dear Netters, I would like to use the reaction field SCF facility of Gaussian 92 and I have a question about the input. In the manual (pp. 20 & 56) it is advised to enter the SOLVENT radius and dielectric constant as an input data. However, in the original Onsager reaction field model the solvent dielectric constant but SOLUTE radius are used as input. Is this just a typo in the manual and should one use the solvent radius? which units shoud be used (A or Bohr?). I would be interested to hear comments/tricks/ critics from persons who have experience with this option. I am interested in using water as a solvent. Thank you in advance for your help, Annick From shenkin@still3.chem.columbia.edu Wed Dec 2 16:53:36 1992 Date: Wed, 2 Dec 92 21:53:36 -0500 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9212030253.AA13988@still3.chem.columbia.edu> To: rsjuds@snll-arpagw.llnl.gov (judson richard s), chemistry@ccl.net Subject: Re: Programs to predict metabolic products > From: rsjuds@snll-arpagw.llnl.gov (judson richard s) > Does anyone know of programs that take a molecule and predict the > the metabolic products, based on a set of rules about bonds that > are likely to be hydrolyzed, etc? Such a program is given below: PROGRAM metbol CHARACTER *80 input READ( 5, *, END=900 ) input 900 CONTINUE WRITE( 6, * ) 'CO2, H20' END ;-), -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************ Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 *** In scenic New York: where the Third World is just a subway ride away ***