From vancamp@banruc60.bitnet Tue Nov 24 11:43:04 1992 Message-Id: <199211240947.AA03515@oscsunb.ccl.net> From: vancamp%banruc60.bitnet@OHSTVMA.ACS.OHIO-STATE.EDU Date: Tue, 24 Nov 92 10:43:04 +0100 To: chemistry@ccl.net Subject: Density Functional on Polymers Hi, Recently I got interested in performing DENSITY FUNCTIONAL calculations on polymers. As I am new in this field I would like to know wether anybody out there can give me information on : - the existence and availability of programs to do DF-calculations on polymers. - a recent review article covering this field or a list of important recent publications. I am familiar with density functional theory and its applications to solids. Many thanks, P.E. Van Camp University of Antwerp - RUCA Department of Physics Research Group TVS Groenenborgerlaan 171 B-2020 Antwerpen, Belgium E-mail: vancamp@banruc60.bitnet From noy@tci002.uibk.ac.at Tue Nov 24 15:19:40 1992 Date: Tue, 24 Nov 92 14:19:40 +0100 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9211241319.AA20024@tci002.uibk.ac.at> To: chemistry@ccl.net Subject: Quantum mechanically MD Dear Netters, I am interested studying in a molecular dynamics simulation which introduce quantum mechanically calculation to correct the potential surface of the solvation shell "on the fly" the simulation runs. Can anybody suggest me some literatures and some previous works ? All related topics are also welcome. Thanks in advance... yours sincerely, T.K.NOY ---------------------------------------------------------------------------- NAME : Teerakiat Kerdcharoen (NOY) ADDRESS : Instituet f. Anorganische und Analytische Chemie Innrain 52 a, A-6020, Innsbruck, Austria E-MAIL : noy@tci.uibk.ac.at,noy@tci2.uibk.ac.at,c70854@cx.uibk.ac.at FAX : (43)(512) 5073225 24 hrs HOMEPHONE: (43)(512) 2215201 21:00-07:30 OFFICE : (43)(512) 5073232 08:00-12:00 14:00-20:30 RESEARCH : Computer Simulation of Molecular Systems ----------------------------------------------------------------------------- From ravishan@swan.wesleyan.edu Tue Nov 24 04:21:12 1992 Date: Tue, 24 Nov 92 09:21:12 -0500 Message-Id: <9211241421.AA03519@swan.wesleyan.edu> From: G. Ravishanker To: chemistry@ccl.net Subject: MD simulations of DNA - literature Hi I recently did a literature search using the chemical abstracts on-line search facilities. I chose "molecular dynamics" and "DNA" as the search string and got about 160 references. I have three types of files: 1. Text file resulting from the search (very detailed). 2. BibTeX database format file (Only relevent information). 3. Postscript output file (Font - Helvetica) resulting from running LaTeX and BibTeX on the file mentioned in 2. (16 pages) If anyone is interested, please let me know and I will try to send the info by mail to you. If Jan agrees, I can send it to him and he can arrange to have it at the OSC for anonymous FTP retrieval. Since the search is so specific, I am not sure how many will benefit from this, but I thought I will give it a shot. Thank you very much. From scsupham@reading.ac.uk Tue Nov 24 14:44:39 1992 From: scsupham@reading.ac.uk Date: Tue, 24 Nov 92 14:44:39 GMT Message-Id: <13728.9211241444@scsscsc3> To: CHEMISTRY@ccl.net Subject: GAMESS working on an SGI machine ? Dear All, Does anyone use GAMESS on a SGI workstation and what experiences do they have ? john John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%susssys1.rdg.ac.uk@uk.ac (BITnet), scsupham@rdg.susssys1 (Janet)Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 From chemistry-request@ccl.net Tue Nov 24 12:20:17 1992 Message-Id: <"92-11-24-12:19:16.49*E702BS"@FRCCSC21.BITNET> Date: Tue, 24 Nov 92 12:19 FWT From: "Dr. John Irwin, Biostructure" To: chemistry@ccl.net Subject: Re: Where can I get a copy of CADPAC? --- this message was originally blocked by the mail script since --- the address e702bs@FRCCSC21.bitnet is on the exclusion list. --- However, I decided to post it, as it may be of general interest. --- I know it is controversial, but somebody has to make decisions, and --- if you make them, some people will not like them... --- Jan Labanowski, jkl@ccl.net, His Majesty Coordinator of CCL {(:-<} khillig@chem.lsa.umich.edu asked about obtaining CADPAC: You can obtain a copy of CADPAC for several types of machines direct from the author, Dr. Roger Amos at Cambridge University address: rda@theory.cambridge.ac.uk. However, if you want a really nice graphical interface to CADPAC that lets you run CADPAC jobs and display results in 3D on a SGI, RS/6000 or ESV workstation, you can contact me, John Irwin, address: e702bs@frccsc21.bitnet. John Irwin Biostructure, Strasbourg,France bitnet: e702bs@frccsc21 fax: (+33) 88.67.98.01 --- Administrivia: This message is automatically appended by the mail exploder. CHEMISTRY@ccl.net --- everyone CHEMISTRY-REQUEST@ccl.net --- coordinator OSCPOST@ccl.net send help from chemistry Anon. ftp www.ccl.net --- From jabs@chemie.uni-halle.dbp.de Tue Nov 24 20:26:03 1992 Date: Tue, 24 Nov 1992 19:26:03 +0100 From: jabs@chemie.uni-halle.dbp.de Message-Id: <921124192603*/S=jabs/OU=chemie/PRMD=UNI-HALLE/ADMD=DBP/C=DE/@MHS> To: chemistry@ccl.net Subject: hydrogen_bond Hi, Recently I got interested in performing semiempirical (PM3) calculations on alkohols and alkohol-oligomers. I am interested in calculating the vibrational spectra to show the influence of intra- and intermolecular hydrogen bonding on the OH-stretching and their comparision with experimental data. How can give me some information about the applicability of the PM3 method for this calculations and some results from literature ? Thanks Andreas Jabs M.-Luther-University Dep. of Chemistry Theoretical Chemistry Weinbergweg 16 PSF 8 O-4020 Halle/Saale E-mail: c=de;a=dbp;p=uni-halle;ou=chemie;s=jabs From ozguner@ee.eng.ohio-state.edu Tue Nov 24 10:25:25 1992 From: ozguner@ee.eng.ohio-state.edu (Dr. F Ozguner) Date: Tue, 24 Nov 92 15:25:25 EST Message-Id: <9211242025.AA00324@bambi> To: chemistry@ccl.net Subject: OAI workshop on Parallel Computing OAI Workshop Parallel and Distributed Computing (December 8, 1992, Tuesday) at the Ohio Aerospace Institute FINAL PROGRAM Opening remarks 8:45-8:55 * Fusun Ozguner, The Ohio State University Welcome 8:55-9:10 * Mike Knasel, OAI Invited lecture 9:10-9:40 * Kalpana Chawla, MCAT Institute/ NASA Ames Research Center Computing the CAS Grand Challenge Problems on Massively Parallel Computers Contributed Papers 9:40-10:30 * Jeffrey D. McDonald, MasPar Computer Corporation Data Parallel CFD on Structured and Unstructered Grids (ie the NAS BENCHMARKS and ADAPTIVE CODES on the MasPar MP-2) * Alpesh Amin, Universal Energy Systems A 3-D Metal Forming Simulation Package for MIMD Parallel Computers Break 10:30-10:45 Contributed Papers 10:45-12:00 * Eric Christensen, Air Force Institute of Technology Hierarchy of Parallelization in Simulation * James Scott, The Ohio State University A Perspective of the Growing Role of Parallel Computing in CFD * Arvind K. Bansal, Kent State University High Performance Intelligent Processing in Space Research Lunch 12:00-1:00 Invited lecture 1:00-1:45 * Joel Saltz, University of Maryland Runtime Compilation Methods for Scalable Multiprocessors Parallel Programming Languages and Environments 1:45-3:15 * Tim Mattson, Yale University and Scientific Computing Associates Portable Parallel Programming with LINDA * Adam Kolawa, Parasoft Corp. Express - A Parallel Programming Environment and its Application in Science and Industry * P. Sadayappan, The Ohio State University High Performance Fortran Break 3:15-3:30 Panel Discussion 3:30-4:30 The Impact of High Performance Computing on Engineering Design and Simulation --------------------------------------------------------------------- Pre-registration Form Name on Badge: ---------------------------------- Full name: ---------------------------------- Address: ---------------------------------- Phone: ---------------------------------- Fax: ---------------------------------- Please circle applicable fees below Student Non-student ______ Workshop 1: $12* $42* (yes/no) Interdisciplinary System Simulation and Design (Dec.7) ______ Dinner (Dec. 7, 6:30 p.m.) $18 $18 (yes/no) ______ Distinguished Lecture (free) (free) (yes/no) (Dec. 7, 7:30 p.m.) ______ Workshop 2: $12* $42* (yes/no) Parallel and Distributed Computing (Dec. 8) Total________________ Make your check payable to Ohio Aerospace Institute * Includes lunch and refreshments NASA Participants should preregister through the Office of Education at NASA Lewis Research Center. For hotel accommodation a block of rooms are set aside at Hampton Inn near OAI. This pre-registration form must be received with a check by December 3 (Thursday). Please Mail to: Ohio Aerospace Institute Attn: Vannel Hassett 22800 Cedar Point Road Brook Park, OH 44142 Phone: (216) 962-3041 Fax: (216) 962-3120 From jle@world.std.com Tue Nov 24 12:21:43 1992 Date: Tue, 24 Nov 1992 17:21:43 -0500 From: jle@world.std.com (Joe M Leonard) Message-Id: <199211242221.AA25266@world.std.com> To: chemistry@ccl.net Subject: Possible typo in Tripos' SYBYL FF V5.5 Looking at the parameters for the V5.5 FF, it seems one of the torsional angles has been messed up. In V5.2, the angle was O.2 C.2 C.3 C.3 1 0.7 -3 while in V5.5 this seems to have been replaced by C.3 C.2 C.3 O.2 1 0.7 -3 Which seems to be a transcription error, as it doesn't represent normal bonding. Has anybody seen anything on this, or am I missing something? Joe Leonard jle@world.std.com P.S. Don't get excited - we did the SYBYL V5.2 FF quite a while ago... From randy@pylos.cchem.Berkeley.EDU Tue Nov 24 10:46:19 1992 Date: Tue, 24 Nov 92 18:46:19 PST From: randy@pylos.cchem.Berkeley.EDU (Randall Snurr) Message-Id: <9211250246.AA12969@pylos.cchem.Berkeley.EDU> To: CHEMISTRY@ccl.net Subject: Potential params for xylenes Hello, I am searching for any information about molecular simulations of liquid p-xylene. If you know of any such simulations in the literature (or unpublished), please send me e-mail at the address below. I will summarize for the group if there is interest. I am interested in what potential parameters were used and how well the parameters performed in predicting experimental thermodynamic properties. The reason for wanting this information is that I am hoping to do simulations of p-xylene in zeolites and it would be best if I can start with p-xylene potential parameters from liquid phase simulations. We have already done simulations at very low sorbate loadings, but for higher loadings, we will need p-xylene/p-xylene potential parameters. For the zeolite/p-xylene interactions, we are using a combination of Lennard-Jones centers and point charges. Thanks for your help; my literature search a year ago did not turn up anything useful. Randy Snurr 201 Gilman Hall Department of Chemical Engineering University of California Berkeley, CA 94720 U.S.A. randy@pylos.cchem.berkeley.edu From jle@world.std.com Tue Nov 24 17:02:59 1992 Date: Tue, 24 Nov 1992 22:02:59 -0500 From: jle@world.std.com (Joe M Leonard) Message-Id: <199211250302.AA18400@world.std.com> To: chemistry@ccl.net Subject: Question regarding H-Bonding in MM A question sort of along the lines of my other ones... In the case of Formamide, are there any hydrogen bonds? Looking at it naively, the carbonyl oxygen can "bond" with the hydrogens on the amide nitrogen. This is a rather unusual orientation for h-bonds, and they might be dropped with more thought... They are 1,4 interactions, and I'm curious as to whether they can/should be dropped from consideration on that basis along/as well. I'm interested in learning what folks think are the "correct" ways to approach this problem, as well as what algorithms code authors have used in dealing with them. The literature isn't terribly explicit on this, usually mentioning that there ARE h-bond terms, but limiting discussion to the larger terms and cross-terms. I'll summarize if there's a bunch of replies - I'll keep the flames to myself :-) Joe Leonard jle@world.std.com P.S. Pointers to literature appreciated!