From chemistry-request@ccl.net Sat Apr 4 04:02:12 1992 Date: Sat, 4 Apr 92 02:12:02 EST From: states@ncbi.nlm.nih.GOV (David States) Subject: Re:The wind is changing To: chemistry@ccl.net Status: R >> On the hardware side the workstations and the parallel machines will slowly >> push the supercomputers against the wall. Before we used crays because >> they where the only machines to be fast enough and they had memory enough. I would not count on the supercomputer centers going away anytime soon. Supercomputer CPU time used to be the most expensive cycles money could buy, but there is a dramatic shift about to occur in the relative cost of workstation and supercomputer cycles. When you build a massively parallel processor out of generic workstation technology, the cost per cpu may actually be lower than the cost of the workstation. First, you avoid the cost of putting a display on each CPU (1/2 the cost of many workstations), and second, you amortize power supply, cooling, and hardware costs over all the processors. The second factor likely to drive the prices down will be competition. Current RISC based massively parallel projects/products include: Thinking Machines CM-5 Sparc Intel Touchstone i860 Kendall Square proprietary RISC chip DEC/Cray alpha chip HP/Convex HP-PA IBM RS/6000 Lab and departmental parallel processors will, of course, continue to get more powerful, but remember that economics have favored the small local solution since the pdp-11 went up against the mainframes. The economics are changing and high speed reliable networks are proliferating. Why should a department bother with the hassles of administering a local server if cost competitive performance is easily accessible on the net? Supercomputer centers have survived to date in the face of grossly unfavorable economics. With the costs of serving cycles shifting in their favor, the big guys are likely to be around for quite awhile. David States National Center for Biotechnology Information / National Library of Medicine From chemistry-request@ccl.net Sat Apr 4 04:54:20 1992 Date: Sat, 4 Apr 1992 02:50 CST From: "JORGE M. SEMINARIO" Subject: G90, Td symmetry To: chemistry@ccl.net Status: R We have run several calculations for Td systems of the form AB4 including MgBr4(-2) and have never had any problem. The Z-matrix used was: A B,1,d B,1,d,2,109.471221 B,1,d,2,109.471221,3,120.,0 B,1,d,2,109.471221,3,-120.,0 Of ocurse, problems will arise if the tetrahedral angle is not precisly defined. Hope this help. Jorge M Seminario From chemistry-request@ccl.net Sat Apr 4 12:12:23 1992 Date: Sat, 4 Apr 92 10:34:10 EST From: m10!frisch@uunet.UU.NET (Michael Frisch) Subject: Re: g90 opt bug To: chemistry@ccl.net Status: R Steve Williams and other G90 users, I ran into this problem a long time ago with tetrahedral systems. You described it well...after the first gradient, the opimization gives up because of a supposed change in symmetry. I never bothered the "help" line for G90 users (help@gaussian.com) because I figured my quick solution to the problem was the one that they would probabley give me. The solution is to just disable symmetry altogether with the keyword "nosymm" on the route card. Your molecule will remain in the symmetry dictated by the z-matrix while G90 crunches through the numbers without taking advantage of this symmetry. Maybe Mike Frisch has a word or two on this subject. If it is a true bug, I wonder if it has been fixed in the brand-spanking new release of Gaussian 92? I just got my brochure today in the mail, and let me tell you, this new release has so many new capabilities to explore that I may have to start working 16 hour days to satisfy my interests, 8^). (No, I already work on the weekends!) Kerwin Dobbs 99% of the "point group change" bug reports which we get are the result of a z-matrix which does not, in fact, constrain the desired symmetry. These problems can be avoided by following the standard advice for avoiding such cases -- different initial values for different variables and using FOPT rather than OPT so that the program checks for correct constraints. However, the description of the current situation -- a simple tetrahedral molecule -- doesn't sound like the typical z-matrix problem. I've certainly optimized lots of tetrahedral molecules without difficulties, so I can't say offhand what is different about the cases that Steve and Kerwin have encountered. In general, we would like people to "bother" the help system at Gaussian about problems like this (i.e., which seem to be bugs). It is true that we'd probably suggest using NOSYMM to get around the problem for the moment, but unless we are made aware of such problems, they can't be fixed in future versions. So if Steve and/or Kerwin will send some input and output for the failing cases to help@gaussian.com, we'll a) see if the problem persists in G92, and b) if so, start to look into a fix for a future minor revision of G92. Mike Frisch Gaussian, Inc. ------- From chemistry-request@ccl.net Sat Apr 4 17:47:44 1992 Date: Sat, 4 Apr 1992 11:50 CST From: C1790@slvaxa.umsl.EDU Subject: MEETING ANNOUNCEMENT To: CHEMISTRY@ccl.net Status: R INC CAMD92.DOC ************** THIS IS A MEETING ANNOUNCEMENT **************** SCIENTISTS INTERESTED IN COMPUTER-AIDED MOLECULAR DESIGN, YOU ARE INVITED TO ATTEND "THE 2ND ST. LOUIS REGION GATHERING ON COMPUTER-AIDED MOLECULAR DESIGN". THE "GATHERING" WILL BE HELD SATURDAY, JUNE 13, 1992, AT THE UNIVERSITY OF MISSOURI-ST. LOUIS. REGISTRATION FEES ARE $25 BEFORE MAY 11 (STUDENTS $15) AND $50 AFTER MAY 11 (STUDENTS $25). REGISTRATION INCLUDES ABSTRACT BOOK AND RELATED MATERIALS, LUNCH, MORNING AND AFTERNOON REFRESHMENTS, MIXER DURING POSTER SESSION, AND PARKING. FOR DETAILS AND FORMS CONTACT DR. BILL WELSH, DEPT. OF CHEMISTRY, UNIV. OF MISSOURI-ST. LOUIS, ST. LOUIS, MO 63121 (FAX: 314-553-5342; E-MAIL: C1790@UMSLVAXA). LAST YEAR'S "GATHERING" DREW AN OVERFLOW OF 150 PARTICIPANTS, SO DON'T DELAY SINCE THIS YEAR REGISTRATION IS LIMITED TO 200 PEOPLE. THE EMPHASIS IN THE "GATHERING" IS TO ADDRESS THE FUNDAMENTALS AND BASIC CONCEPTS IN APPLICATIONS OF CAMD. THIS EVENT IS COSPONSORED BY THE UNIV. OF MISSOURI-ST. LOUIS, WASHINGTON UNIVERSITY'S CENTER FOR MOLECULAR DESIGN, THE ST. LOUIS SECTION OF THE ACS, SILICON GRAPHICS COMPUTER SYSTEMS, AND TRIPOS ASSOCIATES, INC. A SUMMARY OF THE PROGRAM IS AS FOLLOWS: PRESIDING: PROFS. WILLIAM WELSH, UNIV. OF MISSOURI-ST. LOUIS AND GARLAND MARSHALL, WASHINGTON UNIV. IN ST. LOUIS "OVERVIEW OF MOLECULAR MECHANICS AND FORCE FIELDS" BY PROF. PHIL BOWEN, UNIVERSITY OF GEORGIA "OVERVIEW OF MOLECULAR DYNAMICS SIMULATIONS" BY DR. SHAWN HUSTON, WASHINGTON UNIVERSITY IN ST. LOUIS "PROTEIN HOMOLOGY MODELING" BY DR. NINA SUMMERS, MONSANTO COMPANY, ST. LOUIS LUNCH, FOLLOWED BY A "FILM FESTIVAL" OF COMPUTER-GENERATED ANIMATIONS "PATHWAYS FOR CONFORMATIONAL TRANSITIONS" BY PROF. RON ELBERS, UNIVERSITY OF ILLINOIS-CHICAGO "MOLECULAR MODELS FROM NMR SPECTRA" BY DR. DENISE BEUSEN, WASHINGTON UNIVERSITY IN ST. LOUIS "POLYMER MODELING" BY DR. LAWRENCE DEBOLT, TRIPOS ASSOCIATES, INC., ST. LOUIS "ARTIFICIAL INTELLIGENCE AND NEURAL NETWORKS" BY DR. SAMUEL TERSIGNI, UNIVERSITY OF MISSOURI-ST. LOUIS POSTER SESSION AND MIXER From chen@deakin.OZ.AU Sat Apr 4 20:00:59 1992 Date: Sun, 5 Apr 1992 11:01:10 +1000 From: chen@deakin.OZ.AU To: chemistry@ccl.net, hardy@golem.ps.uci.edu, jbrecken@uwovax.uwo.ca, Subject: SymbMath and PlotData Status: R This is news. ---------------- SymbMath 1.4: A Symbolic Calculator with Learning by Dr. Weiguang HUANG 5/6 Cara Road, Geelong, Vic. 3216, Australia SymbMath, (an abbreviation for Symbolic Mathematics), is not only a symbolic calculator but also an expert system that can solve symbolically mathematical problems. SymbMath performs symbolic formula, as well as exact numeric computation. It can manipulate complicated formulas and return answers in terms of symbols, formulas and exact numbers, not just floating-point numbers. Symbolic mathematics is also called Computer Algebra, Symbolic Manipulation, Algebraic Manipulation, Symbolic Computation, or Algebraic Computation. SymbMath is different from other software. (1) It only require 640 KBytes RAM, so it can run on small IBM PC under MS-DOS. (2) It is able to learn from human as machine learning. If users only show it one thing (e.g. one integral) without writing any line of program, it will learn many relative knowledges (e.g. many integrals) although it has no these predefined knowledges before. (3) Users easily edit the library (e.g. integral tables) in the formula format. (4) It can do something that other software cannot do. Its capabilities include facilities to provide analytical and numerical answers for: 1. Differentiation: derivatives, higher order derivatives, partial derivatives, mixed derivatives, total derivatives, implicit differentiation. 2. Integration: indefinite integration, definite integration, multiple integration, infinite integration, parametric integration, iterated integration, line integration, surface integration, discontinuous integration, implicit integration. 3. Solution of equations: polynomial equations, algebraic equations, systems of equations, differential and integral equations. 4. Manipulation of expressions: simplification, factorisation, expansion, substitution, evaluation, user-defined functions, built-in standard functions (including the error function). 5. Calculation: exact and floating-point numerical computation of integer, rational, real and complex numbers in the range from -infinity to infinity, even with different units. 6. Limits: real limits, complex limits, one-sided limits, including the indeterminate forms, (e.g. 0/0, infinity/infinity, etc.). 7. Chemical calculation: the molecular weights, atomic weights, and concentrations, by entering the symbols of the chemical elements. 8. Chemical reactions: inorganic and organic chemical reactions. 9. Others such as extrema, Taylor series, lists, arrays, vectors, matrices, sum, product, etc. Its features also include: 1. Programming as an interpreter. 2. Interface with other software (e.g. with PlotData for graph). 3. Outputting two-dimentional displays, and the BASIC format. 4. On-line help, on-line manual. 5. Syntax check and the line editor for input. Shareware version of SymbMath, SM14A.ZIP, is available from the Calculator directory in SIMTEL20 on many anonymous FTP sites (e.g. wsmr-simtel20.army.mil, garbo.uwasa.fi, rana.cc.deakin.oz.au, etc.). ---------------- PlotData 1.1: A Plotter with Analysing Data by Dr. Weiguang Huang 5/6 Cara Road, Geelong, Vic. 3216, Australia Phone: (052)443282 Plotdata is a software package of a plotter with analysing data. With PlotData, data can be plotted on the screen, viewed, edited, analysed, differentiated, integrated, calculated, and reproducted graphically. Many sets of data can be overlapped to solve systems of equations graphically. Users can zoom in and out of graph. It offers an interactive menu environment for the easy to use and on-line help. It can be interfaced with other software, e.g. SymbMath (a software package of a symbolic calculator), CurFit (a software package of a separator of overlapping peaks). PlotData can read data in these software formats without any modification, in the BAS-100 instrument format, and in many other data formats. If SymbMath is interfaced with PlotData, SymbMath produces the data table of the functions, and PlotData plots curves from the data table, as SymbMath seems to do graphics. Users can use this interface to make the pictures, to plot the function values, and to solve equations graphically. Its on-line help file is a text file, so users can edit it as they like. It runs on an IBM-PC with 100 KByte RAM under MS-DOS, the graphical monitors (CGA, EGA, or Hercules), or the dot matrix printers for the hardcopy. PlotData has three versions: Shareware, Student and Advanced versions. The shareware version (PlotD11A.ZIP) is available free from the Plot directory in SIMTEL20 on many anonymous FTP sites (e.g. wsmr-simtel20.army.mil, garbo.uwasa.fi, rana.cc.deakin.oz.au). ------------------- This file contains statistics of downloads at an anonymous FTP site of garbo.uwasa.fi in September and December 1991. ****************************************************************** The following statistics show that SM13A.ZIP is on top 14 of 2373 items. Its number of downloads is 127. The list is cut off at 100 downloads. -------------------------------------------------------- Article 758 of comp.binaries.ibm.pc.archives: >From: ts@uwasa.fi (Timo Salmi) Newsgroups: comp.binaries.ibm.pc.archives Subject: garbo download stats in Sept 1991 Date: 1 Oct 91 18:53:22 GMT Organization: University of Vaasa, Finland Here are the download statistics for garbo.uwasa.fi archives at the University of Vaasa, Finland, for the month of September 1991. This version of the download list is based on samples taken at 20 minutes intervals on the access time changes of the directories. Thus the statistics is quite approximate. The list is cut off at 25 downloads. The original list contained 2373 items. The approximate total number of downloads was 29995 files. The files with no description are either no longer on garbo.uwasa.fi lists (they were mainly old versions) or there is some technical problem with the description. This download statistics covers the /pc directories (and /unix/ts). Thus eg /mac /vms and /pc/win3 are not covered by this statistics. We also have a weekly list with a different composition, but that is not posted (available as garbo.uwasa.fi:/pc/filelist/ftplog##.lst). 380 zoo210.exe Zoo packing/unpacking facility from Rahul Dhesi 270 lha213.exe LHa v2.13 compression for .lzh files, tight, in English 224 ftpsites.lst Ftp sites for anonymous login (1 Sep 1991) 196 scanv82.zip McAfee VIRUSCAN 7.8v82; scans for all known 297 virus s 168 a1keen.lzh Commander Keen v1.31 Vol 1 (great) 162 msker311.zip MsKermit version 3.11 from Columbia (23 Aug 1991) 152 clean82.zip McAfee Clean-up virus remover 7.8v82 (run SCANV55 or gr 146 inter27b.zip Ralf Brown's interrupt list 1-Sep-91 (impressive) 144 falcon3.zip Falcon v3.0 demo (Spectrum Holobyte) 143 blast.zoo Moraff's Blast I v1.5 (HERC/CGA/EGA/VGA/SVGA) (great) 135 inter27a.zip Ralf Brown's interrupt list 1-Sep-91 (impressive) 135 0news-pd2 News about the uploads in the /pc (the MsDos) directori 134 naked100.lzh NakedEye SuperVGA Gif viewer (works?) v1.00 * 127 sm13a.zip Symbolic calculator for math and chemistry by W.Huang 123 grasp4.zoo Grasp4 display program for Grasp (.gl) files 123 bluelake.gl BlueLake .gl (good) 121 lsl5demo.zip Leisure Suit Larry 5 demo 119 amdek.gl.Z Amdek VGA Masterpieces (Van Cogh, Michelangelo etc) (go 117 fprot200.zip A Virus Protection system by Fridrik Skulason (good) 115 arj220.exe Another tight compressor; .arj v2.20 Robert Jung 111 list76b.zip Vernon Buerg's file browsing program, the definite must 108 garboidx.Z Garbo INDEX file list in Unix compressed format 105 garboidx.arc Garbo INDEX file list in archived format 103 vshld82.zip McAfee VSHIELD TSR 4.1v82; protects viri (was:SCANRES) 103 pkz110eu.exe "Legal" Euro-version of PKWARE's ZIP v1.10, no encrypti 101 balls2.gif [......] ................................................................... Prof. Timo Salmi Moderating at garbo.uwasa.fi anonymous ftp archives 128.214.87.1 School of Business Studies, University of Vaasa, SF-65101, Finland Internet: ts@chyde.uwasa.fi Funet: gado::salmi Bitnet: salmi@finfun ------------------------------------------------------------------- The following statistics show that SymbMath (sm14a.zip) is on top 14 of 2636 software on November 1991. The number of its downloads was 213. The list is cut off at 100 downloads. ----------------------------------------------------------------------- Article 1463 of comp.binaries.ibm.pc.archives: >From: ts@uwasa.fi (Timo Salmi) Newsgroups: comp.binaries.ibm.pc.archives Subject: November 1991 garbo download statistics Date: 1 Dec 91 13:51:20 GMT Organization: University of Vaasa, Finland Here are the download statistics for garbo.uwasa.fi archives at the University of Vaasa, Finland, for the month of November 1991. This version of the download list is based on samples taken at 20 minute intervals on the access time changes of the directories. Thus the statistics is quite approximate. The list is cut off at about 300 entries. The original list contained 2636 entries. The approximate total number of downloads was 50700 files. The files with no description are either no longer on garbo.uwasa.fi lists (they were mainly old versions) or there is some technical problem with the description. This download statistics covers the /pc directories (and /unix/ts). Thus eg /mac /vms and /pc/win3 are not covered by this statistics. 459 zoo210.exe Zoo packing/unpacking facility from Rahul Dhesi 320 4dos40p.zip 4dos v4.00 executables 316 4dos40d.zip 4dos v4.00 command.com replacement; docs (good) 294 lha213.exe LHa v2.13 compression for .lzh files, tight, in English 262 robotrk1.lzh RoboTruck (.fli) for aaplay (good) 250 bestprog.zip Timo's choice of 21 best MsDos SW & PD programs 2-Nov-9 247 blast.zoo Moraff's Blast I v1.5 (HERC/CGA/EGA/VGA/SVGA) (great) 246 duke.zoo Duke Nukem (good) 237 scan84.zip McAfee VIRUSCAN 7.9v84; scans for all known 301 virus s 232 arj222.exe Arj data compressor/decompressor by Robert Jung 229 a1keen.lzh Commander Keen v1.31 Vol 1 (great) 227 ftpsites.lst Ftp sites for anonymous login (1 Nov 1991) 217 naked100.zoo NakedEye SuperVGA Gif viewer (works?) v1.00 *213 sm14a.zip Symbolic calculator for math and chemistry by W.Huang 198 bench60.zip PC Mag Lab benchmarks, graphips mode + mouse interface 194 clean84.zip McAfee Clean-up virus remover 7.9v84 (run SCANV55 or gr 193 corewar.zip CoreWar game (req's EGA/VGA) 188 quadvga.lzh QUADRALIEN game (req's EGA/VGA) (good) 183 sg.zoo The Game StarGoose from the binaries (great) 173 1dark.zoo Dark Ages vol 1 v1.00 (req's 286 or better) 170 tads.zip TADS; the Text Adventure Development System v1.10 165 arc602.exe SEA's packing/unpacking system (self-extr.) 155 corwp21.zip CoreWar Pro v2.1 environment (editor, RedCode etc) 150 cw30.zip Corewars v3.0, game 148 omega11.zip Omega v1.1 (req's AT, VGA & mouse), game 146 suomi.gif Finland, 8K 640x480x16 border outline and elevation map 141 pkz110eu.exe "Legal" Euro-version of PKWARE's ZIP v1.10, no encrypti 140 bluelake.gl BlueLake .gl (good) 135 harri.gif me, myself and I ... (garbo moderator Harri Valkama) 134 sgdoc.zoo StarGoose docs 134 comic.zip Run through the scenes, game 131 bananoid.zip BANANOID game (req's VGA) (nice) 129 tsfaq24.arc Questions from UseNet and Timo's answers, 18-Oct-91. 127 hkmj.zip Honk Kong Mahjong v1.0 (good) 126 hns.zip Heart & Soul (.fli) (impressive...) 126 conqst23.zip Strategy war game on a map v2.3 (req's EGA and MS mouse 126 0news-pd2 News about the uploads in the /pc (the MsDos) directori 124 mahjg351.zip Mah Jongg rel3.51 123 head1.zip Animation file (.fli) for aaplay 122 4dosinf.zip 4dos quick information 121 aaplay.lzh PD Autodesk Animator (.fli) player v1.0 120 vshld84.zip McAfee VSHIELD TSR 4.3v84; protects viri (was:SCANRES) 120 unzip41.exe Self-extracting alternative unzippper for .zip files 119 snarf203.zoo Snarf v2.03 (EGA) arcade games (neat) 117 1ptomb.lzh Pharaoh's Tomb v3.0 116 naked100.lzh 113 grasp4.zoo Grasp4 display program for Grasp (.gl) files 112 fprot201.zip A Virus Protection system by Fridrik Skulason (good) 111 pk361.exe This packs and unpacks .arc files (self-extracting) 111 lsl5demo.zip Leisure Suit Larry 5 demo 110 vpic46.zip VPIC GIF viewer, converter (EGA,MCGA,VGA and SuperVGA) 110 entrap.zoo (AMD sponsored) Moraff's Entrap v1.11 (pretty) 109 garboidx.arc Garbo INDEX file list in archived format 107 16puzzle.zip 16 Puzzle (VGA & mouse) 106 amdek.gl.Z Amdek VGA Masterpieces (Van Cogh, Michelangelo etc) (go 104 tsrcom30.zip 104 falcon3.zip Falcon v3.0 demo (Spectrum Holobyte) 103 scram10.zip Scramble (Scrabble) crossword board game by Diana Grube 101 soviet.zip Soviet Block; tetrisish game 101 booz20.zip Zoo v2.10 extractor + sources 101 arj221a.exe 100 xbd2_exe.zoo Boulder Dash (from X Windows) (VGA) (w C) 100 ttetris.zoo Yet another Tetris 100 dtp_src.zip Desktop Paint 256 v1.2 bitmapped paint program (w SVGA) ................................................................... Prof. Timo Salmi Moderating at garbo.uwasa.fi anonymous ftp archives 128.214.87.1 School of Business Studies, University of Vaasa, SF-65101, Finland Internet: ts@chyde.uwasa.fi Funet: gado::salmi Bitnet: salmi@finfun