From chemistry-request@ccl.net Fri Nov 22 11:02:36 1991 Date: Fri, 22 Nov 91 09:49:40 -0600 From: rbw@msc.edu (Richard Walsh) To: chemistry@ccl.net Subject: Theoretical Studies of Flourocarbon Atmospheric Chemistry Status: R Fellow Simulators, I am interested in any published literature on the use of first principle chemistry applications (HF, DFT, etc.) to investigate the atmospheric chemistry of flourocarbons. I am familiar with papers published by Dr. A. G. Turner of the University of Detroit in Inorganica Chimica Acta. I will circulate any responses to others that indicate their interest. Sincerely, Richard Walsh Minnesota Supercomputer Center 612-626-1510 From chemistry-request@ccl.net Fri Nov 22 14:14:12 1991 Date: Fri, 22 Nov 91 13:55:27 EST From: allan@helios.TN.CORNELL.EDU (Douglas C. Allan) To: chemistry@ccl.net Subject: AVS data file format Status: R Dear Chem list readers, I am seeking some very basic information on how to manipulate data into a form readable by Application Visualization System (AVS). After trying to read their documentation (as filtered by DEC), I do not know how to write a standard fortran code which takes e.g. charge density data on a regular three dimensional grid of points and create a "field" data input file as AVS apparently needs to render lovely pictures. Almost any user of AVS, who is also a programmer, would have to have answered this question. Would you please send a small example code or code fragment (or a big example, I don't care) to my mailing address given below. It is probably advisable NOT to respond directly to chemistry@ccl.net as there is already more than enough irrelevant traffic. My first goal is to take trivial charge density data which I can obtain on a regular orthorhombic three dimensional grid (I can get it in a cube if preferred for starters) and make three dimensional shaded solid pictures or two dimensional slices through the data. This should be the easiest thing in the world but the density of unfamiliar buzzwords in the documentation has slowed my progress. I am only considering AVS at the moment, depending on my success in making pictures easily. I welcome any comments from list readers on this subject. I wish to make the pictures on an IBM RS/6000, running motiv for X-windows, and I would like the option of making postscript files for hardcopy black and white pictures too. Again, please don't respond to chemistry@ccl.net. Thanks very much, Doug Allan Corning Incorporated, The Ohio State University, and Cornell University 607 974 3498 email: allan@helios.tn.cornell.edu From chemistry-request@ccl.net Fri Nov 22 16:25:50 1991 Date: Fri, 22 Nov 91 08:14:57 PST From: chiremv!andromeda!davids@uunet.UU.NET (David C. Spellmeyer) To: chemistry@ccl.net Subject: IBM and HP timing comparisons Status: R I am posting in response to Mark Murcko's question about relative performance of the IBM RS6000/550 and the HP-9000-730. We at Chiron used these two benchmarks to evaluate the machines: SPASMS is a general molecular dynamics package developed at UCSF as AMBER5. Spasms implements the AMBER force-fields. (Authors: D. Spellmeyer, W. Swope, E. Evensen, P. Kollman, R. Langridge) The QCPE version of DGEOM, Jeff Blaney's distance geometry package, was also tested. (QCPE #590: Authors: J.M. Blaney, G.M. Crippen, A. Dearing, J. Scott Dixon, 1984-1990.) Both benchmarks are included as validation tests in the program distributions. I have seen consistent relative speeds between the IBM 550 (or 540) and the SGI 340 for varied input choices for both programs. David Spellmeyer ============== SPASMS timings ============== Crambin (all atom ff) with 1259 waters (tip3p) in a periodic box. 100 steps at 0.001 ps timestep and 8 Ang cutoff. All times are for double precision, non-parallelized code. CPU time Relative(to SGI-340) CRAY/Y-MP 83.5 11.5 (1 processor only) IBM RS/6000 550 268.6 3.60 IBM RS/6000 540 382.4 2.52 IBM RS/6000 530 445.8 2.17 HP 9000 730 264.4 3.65 HP 9000 720 353.7 2.73 SGI 340/GTXB 967.2 1.00 (1 processor only) ============= DGEOM timings ============= Cyclosporin test case, 100 structures, fixed random seed (last column shows speed relative to a single CPU on a SGI4D/320 in double precision): sum sum funct funct #bits Errfn Dist Calls #convg cpu Calls/s prcs Rel ----- ---- ----- ------ ------ ------- ----- ----- CRAY/XMP 209 2846 98223 36 623 s 157.6 64 4.9 HP9000/730 195 2731 97949 49 1055 92.8 64 2.9 HP9000/720 195 2731 97949 49 1452 67.5 64 2.1 IBM6000/550 202 2803 100691 43 1313 76.6 64 2.4 IBM6000/540 202 2803 100691 43 1852 54.3 64 1.6 IBM6000/530 202 2803 100691 43 2418 41.6 64 1.3 IBM6000/530 203 2815 99735 34 2593 38.5 32 1.2 IBM6000/520 202 2803 100691 43 3094 32.5 64 1.0 IBM6000/520 203 2815 99735 34 3258 30.6 32 0.9 SGI4D/320* 202 2794 97097 43 3053 31.8 64 1.0 SGI4D/240* 202 2794 97097 43 3807 25.5 64 0.8 SGI4D/240* 210 2858 98731 36 2820 35.0 32 1.1 VAX/8800* 191 2723 100050 47 18040 5.5 64 0.2 VAX/8800* 215 2872 98668 32 11559 8.5 32 0.3 CRAY is an X-MP running COS; DGEOM optimized specifically for CRAY with special vectorized routine. * 1 CPU This example is included as a standard example in the QCPE release. Reference: "Calculating three-dimensional molecular structure from atom-atom distance information: cyclosporin-A", J. Lautz, H. Kessler, J.M. Blaney, R.M. Scheek, W.F. van Gunsteren, Int. J. Peptide Protein Res., 33, 1989, 281-288. ============================================================================== Neither program was tuned specially for the HP nor for the IBM. However, SPASMS was developed at least partly on IBM equipment through a joint study with the IBM Palo Alto Science Center. Info on the specific configurations for each machine listed in the tables below is not available. ============================================================================== From chemistry-request@ccl.net Fri Nov 22 17:18:54 1991 Date: Fri, 22 Nov 91 16:04:45 CST From: Jan Jensen Organization: North Dakota Higher Education Computer Network Subject: Onsager reaction field model To: chemistry@ccl.net Status: R Hi.. Lars Onsager published a reaction field model in 1936 (JACS, 1936, 58, 1486) for spherical molecules. Has anyone derived more general equations for, say, ellipsoidal molecules? Any tips, or even references would be appreciated. Jan H. Jensen Dept. of Chemistry North Dakota State University Fargo, ND 58105 e-mail: nu145752@vm1.nodak.edu nu145752@ndsuvm1 From chemistry-request@ccl.net Fri Nov 22 18:25:19 1991 Date: Fri, 22 Nov 91 23:18:29 GMT From: amm@wag.caltech.edu (Alan M. Mathiowetz) To: chemistry@ccl.net Subject: Simulations of Membranes Status: R I would like to know what the state of the art is in simulations of lipid bilayers, membranes, and/or liposomes. If any of you could send me or post references to work in this area, I would greatly appreciate it. Thanks. ----------------------------------------------------------------------------- Alan M. Mathiowetz amm@wag.caltech.edu ----------------------------------------------------------------------------- Caltech Materials and Molecular Simulation Center Mail Code 139-74 Beckman Institute Pasadena, CA 91125-0001 California Institute of Technology ----------------------------------------------------------------------------- From chemistry-request@ccl.net Fri Nov 22 20:12:14 1991 From: Dongchul Lim Subject: References and source codes for NMR simulation To: chemistry@ccl.net (Computational Chemistry) Date: Fri, 22 Nov 91 20:06:49 EST Status: R I'm interested in working on simulation of NMR spectra and I need a list of available references and sources codes developed so far. I have found some relevant books and papers, but I want to hear more about it. Books: 1. NMR Basic Principles and Progress ed. P. Diehl, E. Fluck, and R. Kosfed, "Computer Assistance in the Analysis of High-Resolution NMR Spectra, P. Diehl and H. Kellerhals, Vol 6, 1972, Springer-Verlag. 2. Ibid, "Analysis of NMR Spectra", R. A. Hoffman, S. Forsen, and B. Gestblom. Vol 5, 1971, Springer-Verlag. 3. Numerical Methods in Chemistry, K. J. Johnson, 1980, Marcel Dekker Inc. Papers: 1. Computer Simulation of NMR Spectra, A. Ellison, J. Chem. Educ. 1983, 60, 425. -dongchul ******************************************************************** * Dongchul Lim | Phone (203) 432-6288 * * Dept. of Chemistry, Yale Univ. | Email: lim@rani.chem.yale.edu * * 225 Prospect Street | (130.132.25.65) * * New Haven, CT 06511 | * ********************************************************************