From eloranta (- at -) kala.jyu.fi Tue Jun 7 04:32:13 1994 Received: from kala.cc.jyu.fi for eloranta (+ at +) kala.jyu.fi by www.ccl.net (8.6.4/930601.1506) id EAA17454; Tue, 7 Jun 1994 04:23:41 -0400 Message-Id: From: eloranta ^at^ kala.jyu.fi (Jussi Eloranta) Subject: gaussian 92 and GEN basis sets To: chemistry -x- at -x- ccl.net Date: Tue, 7 Jun 1994 10:25:55 +0300 (EET DST) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 3311 Hi, I obtained basis set for fluorine (ftp.ccl.net: basis set library). Now, I tried to use the following exponents and coefficients with g92 (user specified basis set): ############################################################################### # atomic SCF calculation of ---> F(2P) 7s4p <--- # SCF energy is -99.3462183972 a.u. (virial theorem = 2.000000000) # A. Schaefer, Jan. 92 ############################################################################### # exponents coefficients # 1s 2s # 2973.4997046 -.52590584026E-02 -.12092301431E-02 # 447.25783120 -.39233645111E-01 -.93573417113E-02 # 101.57185900 -.17619356211 -.42823390798E-01 # 28.268552755 -.45719988226 -.14052491559 # 8.7349389301 -.44730688010 -.19520721834 # 1.3841118258 -.37028368038E-01 .51799309070 # .41199921824 .89840651033E-02 .60912564518 # eigenvalue -26.3659766 -1.5632256 # occupation 2.0000000 2.0000000 # 2p # 22.658300194 .44897518573E-01 # 4.9749914492 .23575465344 # 1.3466519487 .50828613121 # .34729031582 .45821884951 # eigenvalue -.7161735 # occupation 3 * 1.6666667 ############################################################################### * Then I generate the following stream for g92: # HF/GEN Tetst run 0 2 9 -F S 14 1.0 197347.11959 -.28184163023E-04 29558.776324 -.21907068471E-03 6726.9377956 -.11500051437E-02 1905.1637291 -.48260180222E-02 621.37226145 -.17221358226E-01 224.17852083 -.53099042237E-01 87.234531917 -.13789697333 35.916025242 -.28114096672 15.415563071 -.38289777654 6.7358200331 -.24413469399 2.5569609365 -.32911334952E-01 1.1138310004 .24115272055E-02 .44549974207 -.17148852940E-02 .16466803857 .16641631481E-03 S 14 1.0 197347.11959 .63622475516E-05 29558.776324 .49409450159E-04 6726.9377956 .26000984572E-03 1905.1637291 .10919343116E-02 621.37226145 .39388403025E-02 224.17852083 .12360484265E-01 87.234531917 .33873593861E-01 35.916025242 .76642243943E-01 15.415563071 .13666725679 6.7358200331 .13332951903 2.5569609365 -.11442436559 1.1138310004 -.44921371698 .44549974207 -.46114921253 .16466803857 -.13972573436 P 11 1.0 734.58063291 .13461172732E-03 174.10266268 .11647895815E-02 56.410104865 .62228913925E-02 21.298831774 .23990521555E-01 8.8087650181 .71566280999E-01 3.8734203606 .16053699622 1.7478894590 .25856388471 .78248058089 .30564723272 .33863051221 .27306024051 .13832555824 .17291405016 .51441819864E-01 .52370788368E-01 **** 1s and 2s eigenvalues are correct (ie. as described in basis set library) but the 2p ones are not. And, of course, the total energy is greater than mentioned in the basis set library. I tried simpler atoms (like H, Li) which only had s orbitals and those worked ok. Any ideas? Regards, Jussi Eloranta . From berry Fri Sep 23 14:56:19 1994 Received: for berry &$at$& ccl.net by www.ccl.net (8.6.9/930601.1506) id KAA04162; Fri, 23 Sep 1994 10:56:17 -0400 Date: Fri, 23 Sep 1994 10:56:17 -0400 From: "Robby A. Berry" ccl.net> Message-Id: <199409231456.KAA04162()at()www.ccl.net> To: ccl -AatT- ccl.net Subject: 0 Status: O [Test message; if you can see this, please contact berry # - at - # ccl.net immediately.] This is a test of the emergency broadcast system. The broadcasters in your area, in voluntary cooperation with federal, state and local authorities, have devised this test to keep you informed in the event of an emergency. Had this been an actual emergency, you would be dead right about now. This concludes this test of the emergency broadcast system. Sincerely, Rob Berry -- berry <-at-> ccl.net http://www.mps.ohio-state.edu/cgi-bin/hpp?RAB_home.html Resume, PGP public key available via finger, or see my WWW homepage. Disclaimer: I speak for nobody but myself. From berry Fri Sep 23 14:56:19 1994 Received: for berry (- at -) ccl.net by www.ccl.net (8.6.9/930601.1506) id KAA04162; Fri, 23 Sep 1994 10:56:17 -0400 Date: Fri, 23 Sep 1994 10:56:17 -0400 From: "Robby A. Berry" Message-Id: <199409231456.KAA04162 ( ( at ) ) www.ccl.net> To: ccl \\at// ccl.net Subject: 0 Status: O [Test message; if you can see this, please contact berry.,at,.ccl.net immediately.] This is a test of the emergency broadcast system. The broadcasters in your area, in voluntary cooperation with federal, state and local authorities, have devised this test to keep you informed in the event of an emergency. Had this been an actual emergency, you would be dead right about now. This concludes this test of the emergency broadcast system. Sincerely, Rob Berry -- berry #*at*# ccl.net http://www.mps.ohio-state.edu/cgi-bin/hpp?RAB_home.html Resume, PGP public key available via finger, or see my WWW homepage. Disclaimer: I speak for nobody but myself. From berry Fri Sep 23 14:56:24 1994 Received: for berry "at@at" ccl.net by www.ccl.net (8.6.9/930601.1506) id KAA04172; Fri, 23 Sep 1994 10:56:23 -0400 Date: Fri, 23 Sep 1994 10:56:23 -0400 From: "Robby A. Berry" Message-Id: <199409231456.KAA04172 ( ( at ) ) www.ccl.net> To: ccl # - at - # ccl.net Subject: 1 Status: O PLEASE RESPOND TO THE FOLLOWING MESSAGE TO CCLSurv()at()redvax1.dgsca.unam.mx, NOT TO THE LIST!!! Survey on the impact of the Computational Chemistry List THIS IS THE REAL THING, NOT THE TEST ANY MORE. PLEASE TAKE A SHORT TIME TO READ AND ANSWER! This is a survey on the use and impact of the Computational Chemistry List. Please answer the questions below; a short introduction follows. Please respond to CCLSurv;at;redvax1.dgsca.unam.mx, or if you have a WWW reader which supports forms, you are encouraged to use the Hypertext form: http://www.ccl.net/cgi-bin/survey which makes answering survey questions much easier/faster. The Computational Chemistry List (CCL) has been for many a valuable resource and a venue for a diversity of discussions. The list has grown steadily in subscriber and recipient numbers, interesting and sometimes heated debates have taken place, and consideration has been given recently to previously unexplored issues like the perspectives for fully electronic publications and similar ones. It may be time to ask ourselves what actual impact the CCL has had, is having, and can further have on our lives, our work, the way we use bandwidth, and the like. To that purpose I have proposed to undertake a survey of the List users with the general goal of finding out facts and opinions about electronic services and their impact on our work. I have asked the List coordinator, Jan Labanowski, if this is a valid use of CCL bandwidth and we have agreed to ask a few more questions, relevant to the List's operation and its possible improvement, in order not to bother you with TWO surveys. In this respect, the added goals are to find if the List is useful as is, what and for whom is most and least useful, what should be scratched, and how some possible improvements might work out. My own interest in the results of this survey is more on the side of understanding its workings and their meaning as underpinning for the future of academic communication. The results of the survey will be carefully analyzed, which may take some time, and I intend to publish the results of the analysis (foreseeably in an ACS monograph) as well as post them and make them available for downloading. Some aspects of the survey may be flawed from the beginning, mainly as we will not (foreseeably) get response from people who have not subscribed or have dropped out, for any of a number of reasons. However, much can be learned from your answers! It is important that everybody respond to make the survey statistically sound and not biased by "aggressive minority opinion". Please let us know better just how the CCL is working, if and how much it has changed the way you work, communicate, and teach, and understand what is to be done next. I beg you to answer the questions below as objectively as possible. I will make my best efforts to keep the responses confidential (I plan to share them with Jan WITHOUT RESPONDENT NAMES AND ADDRESSES; if you wish otherwise and say so in your answer message I will oblige). I will understand that you speak for your persons and not for your organizations unless the contrary is explicitly stated. All answers are nonbinding. Now look: the list is international, legal issues may get real tangled, so let us all assume that I will keep faithfully to my best knowledge of ethical and legal standards and we all try to get information that will benefit everybody, OK? If you are impeded to respond to any of the questions because of considerations of liability etc. do tell me so! Again, please address your answers/comments/questions to me and not to the list - lest you really want everybody to hear you! Alejandro Pisanty - CCLSurv' at \`redvax1.dgsca.unam.mx . . . . . . . . . . . . . . . . . . . . . . . . Dr. Alejandro Pisanty, Secretary of the Advisory Council on Computing, UNAM, and Head of the Graduate Division, Faculty of Chemistry, UNAM Universidad Nacional Autonoma de Mexico (UNAM) Ciudad Universitaria, 04510 Mexico DF MEXICO Tel. (+52-5) 622 4181, 616 1649; Fax 550 0904, 616 2010 . . . . . . . . . . . . . . . . . . . . . . . Survey on the use of the Computational Chemistry List (CCL). Please answer with your best estimates! In the pilot run of the survey a "closed form" for answers was suggested. I have preferred to retain the open form because of the WIDE variety of answers possible from all over the world. The survey cannot be made too short because much valuable contents would be lost. If you find that you do not have time enough to answer all the questions, please concentrate on sections I (user characterization), II and III (impact), VI and VII. Section IX provides detailed suggestions for improvement on the list in order to open a discussion on that subject. I. USER CHARACTERIZATION: This part is intended to characterize the respondent. It is important to know ourselves better as a group, and so we can crossreference other responses against particular groups of subscribers. I.1) How long have you been using CCL (few months, a year, more than a year)? Mark X on this line ................................... I.2) What is the character of your organization (e.g., for- profit/commercial, academia, secondary shool, government, military, other non-profit, self-employed consultant, etc.)? I.3) Country where you receive the CCL messages (particularly if through LISTSERV and similar, which may be different from the subscription address): I.4) Type of position (e.g, undergraduate student, graduate student, postdoctoral associate, assistant professor, full professor, lecturer, reader, research scientist, senior research scientist, management, sales associate, consultant, etc.): I.5) Approximate number of employees in your entire organization and its main line of activity (e.g. 2000/college, 1000/pharmaceutical, 20000/petroleum, etc.): I.6) Your field(s) of activity (please be specific: e.g, crystallographer, molecular biologist, quantum chemist, medicinal chemist, etc.): I.7) Is your work mainly theoretical, computational or experimental? Do you develop software? I.8) What computational chemistry methods do you use frequently (ab initio, molecular graphics, molecular mechanics, kinetics simulation, etc.)? What other computational work do you do frequently?: I.9) What computer(s) do you use to read the messages, and how are you connected to the network (e.g. PC via 2400 modem, Mac via 9600 modem, RS/6000 on Ethernet, etc.). What is the range of network access available to you (e.g., e-mail only, ftp, remote logins, gopher, WWW, Usenet, etc.). I.10) What computer(s) and software do you mostly use for your work? I.11) How did you learn about the list (e.g., from a friend, my thesis advisor, a student I supervise, from archie, by searching gopherspace, etc.) I.12) Could you briefly describe your work (say 5-10 lines): II. CCL IMPACT ON YOUR RESEARCH/LEARNING/CAREER: Please be as specific as you can be in answering these questions. The answers will be used to judge if the list is a useful resource and to assess the way media like CCL are changing our ways. II.1) Please tell how, and how many times, the messages on CCL, answers to your CCL queries, or CCL archives helped you in your research. Anecdotes and specific examples are most welcome! List all instances you can remember (e.g., you acquired particular software based on CCL messages twice, you selected computer hardware based on information from CCL, on three occassions you received needed parameters/data, five times you were directed to read particular paper based on CCL information, you changed your approach/method once based on CCL messages, comments on the CCL contributed to the discussion part in two of your papers/reports, etc.): II.2) How many times did you find about a conference via CCL and attended it as a result? II.3) Have you started a collaboration with a subscriber of the list as a result of exchanges on the CCL? II.4) Did you find a position or a candidate for the position using the positions.offered file in CCL archive? Did you seek a position in particular organization/group based on messages posted to the list? II.5) Add any comments about benefits and impacts of the list in your career: III. IMPACT ON TEACHING: Answer these questions if you are teaching or if you are involved in intracompany training. Please be specific and add as many comments as you wish. III.1) What subject/course do you teach, is it an undergraduate/graduate/professional course? III.2) Has the list had any impact on the contents of your courses? (e.g., you used materials/examples/opinions from messages or CCL archives in your course, you revised/created curriculum/syllabus based on CCL material, you suggested a graduate project based on CCL postings, etc.): III.3) Do you encourage your students to subscribe to the list, or forward material from the list to them? IV. YOUR PARTICIPATION IN THE LIST: Please supply the best estimates. We understand that they are approximate. Stories and examples are most welcome! They are becoming the oral history and lore of this trade. IV.1) How many questions have you posted to the list? How many answers or opinions did you post to the whole list? How many answers did you send directly the participants? IV.2) How many answers/opinions did you receive to your personal mailbox instead of list as a result of your question/opinion? Did you ever receive a response with the restriction "for your eyes only"? IV.3) How many people have reprimanded/flamed you for your posting(s) to the list? For what? Have you reprimanded/flamed somebody? For what? IV.4) What is your estimate of the portion of suitable messages, i.e., messages which adhere to the list rules (e.g.: 3/7, 10%)? IV.5) What portion of messages on the list do you find relevant for your own research/teaching/development/administration? Do you forward on occassion messages from CCL to people who are not subscribed? Did you encourage someone to subscribe? IV.6) How do you choose messages to read? What portion of messages do you delete/skip before reading based on the Subject: field? What portion of messages do you delete/skip after reading the first few lines? IV.7) How do you receive messages (e.g., you are subscribed to the list directly, you are subscribed to a local/internal list/newsgroup which receives messages from CCL, you are not subscribed but view archived messages via gopher/WWW)? IV.8) How frequently do you scan CCL messages and when (e.g., as they arrive, more than once a day, once a day in the evening, once a week during the weekend)? How much time on average do you spend reading messages? IV.9) Have you ever searched the CCL archives, and if not why? Did you access CCL archives and in what way (e.g., e-mail, ftp, gopher/WWW)? V. USE OF OTHER RESOURCES Please share all your experiences and use of resources other than CCL. V.1 What other Internet and network resources do you use and how heavily/frequently (e-mail, library catalogues, gopher, WWW, newsgroups, commercial databases, stock prices, commercial news, listservers/electronic-lists, electronic submissions of manuscripts to journals/books/conferences, etc., etc.). How much time do you spend on using the network resources? V.2 How much time do you spend on reading CCL list and CCL archives compared to other network resources? V.3 How do you rate the CCL for usefulness, benefit/effort ratio, etc. in comparison to other online and offline resources? VI. MEMORABLE MOMENTS. VI.1 What do you remember as the most useful/most pleasant/most unpleasant/most obnoxious event on the CCL (and/or other Internet services)? VII. OTHER ISSUES. VII.1 Please comment on the international impact of the list. VII.2 Please comment on the choice of language of the list, its quality, and its level of difficulty. Do you sometimes NOT write because of language difficulties? VII.3 If you are answering you obviously use the list. Can we learn something valuable from those who donīt? VII.4 Do you think the list, WWW etc. could provide for formal scientific/technical publication? (e.g. with formal review procedures and stable archives) VII.5) How do you see a development of networks/network services in the future (say, 10 years)? VIII. PLEASE ADD WHAT WE MISSED See also section IX: how would you improve CCL? VIII.1 What questions/topics should have been included in this survey but were missed? VIII.2 Share any thoughts concerning the CCL list which were not addressed in the survey. IX. HOW WOULD YOU IMPROVE CCL? Some specific proposals have been made to improve CCL. They are listed below. Speak out on your own thoughts; the proposals below are intended as discussion openers, not as a bias. Provide your ideas assuming that resources are not an issue and everything is possible. Try to provide ideas, and methods of implementation, though you need not be too detailed/technical. Please note that some examples given here are very controversial. IX.1) How would you improve the list if it stayed unmoderated? Examples (do not be suggested by them, unless you agree with them 100%). a) Split it into smaller lists: ccl-ab-initio, ccl-semiempirical, ccl- force-fields, ccl-molecular-graphics, ccl-???. To which smaller lists would you subscribe yourself? b) Allow anonymous postings if someone chooses to do so. c) Restrict the scope of messages even further than in the rules. d) Add specific files to the archives (which?). e) Add additional services (which?). f) Each subscriber would provide a list of keywords/regular- expressions and would receive only messages which contain/satisfy the keywords/regular-expressions. g) Allow only 10 messages a day, and queue the messages which are over the limit. IX.2) How would you improve the list if it was moderated? Please, share your ideas. For example (only an example): a) 24hrs/day monitoring of the list by anonymous moderators residing in different time zones, so the messages are essentially approved/rejected in a real time. b) provide a once a day digest of subjects and a mechanism for retrieval of full messages via e-mail, ftp, gopher, www. c) the moderator(s) beside rejecting/approving messages would classify them into topics (e.g., quantum chemistry, molecular mechanics, molecular graphics, QSAR/QSPR, hardware, drug design, [what topics?] and subscribers could choose which topics they want to receive. Which topics would you subscribe to? d) Provide a rotating body of volunteers in their respective fields, who would respond to the simple/trivial questions, forwarded to them by moderators (e.g., would point to a file already residing in CCL archives, or explain that HONDO is an ab initio program). e) Split the list into "introductory" and "advanced" and moderator(s) will assign messages to the appropriate category. IX.3) Should the list be available as Usenet newsgroup? Why? IX.4) Should the list be monitored/censored? Why and by whom? Would you be willing to act as a moderator of the list, how much time you would contribute and under what conditions (remember, your answer is nonbinding, and anonymous)? ============== SURVEY END=============== THANKS FOR YOUR KIND COLLABORATION! (Again: please respond to CCLSurv;at;redvax1.dgsca.unam.mx, or WWW, NOT TO THE LIST) !!!!!! . . . . . . . . . . . . . . . . . . . . . . . . . . Dr. Alejandro Pisanty, Secretary of the Advisory Council on Computing, UNAM, and Head of the Graduate Division, Faculty of Chemistry, UNAM Universidad Nacional Autonoma de Mexico (UNAM) Ciudad Universitaria, 04510 Mexico DF MEXICO Tel. (+52-5) 622 4181, 616 1649; Fax 550 0904, 616 2010 . . . . . . . . . . . . . . . . . . . . . . . . . . From berry Fri Sep 23 14:56:33 1994 Received: for berry "-at-" ccl.net by www.ccl.net (8.6.9/930601.1506) id KAA04178; Fri, 23 Sep 1994 10:56:32 -0400 Date: Fri, 23 Sep 1994 10:56:32 -0400 From: "Robby A. Berry" Message-Id: <199409231456.KAA04178 #*at*# www.ccl.net> To: ccl "at@at" ccl.net Subject: 2 Status: O Dear CCL readers, Due to current interest to HyperChem I decided to add my 0.02c. Last year we had a chance to try HyperChem v 3.0. This programs has good graphics and very good molecular editor/builder. Unfortunately, it is very slow, at least for semiempirical calculations. For example, it takes 35 min. on 486DX2 50MHz with 16 MB of memory to do MNDO 1SCF and gradients for C60 (compare to Sibiq - 10 min.). We send to HyperChem mail list a question 'why it is slow?', and the answer was "HyperChem have not been optimized for speed". The second thing, which surprised us, was that the best geometry optimization method we could choose was conjugated gradients. This method not only 2-10 times more slow then ordinary used in semiempirical calculation qusi-newton methods, but, also, it may has a problem with convergence for a flat potential surface. If someone is looking for program to do demonstration or teaching, HyperChem is, probably, a way to go. I don't think that it is (sorry, was, I am not sure that version 3 is the last version) a right choice to do semiempirical calculations. It is, of course, my personal opinion. Dr. Andrey Bliznyuk. From berry Fri Sep 23 14:56:39 1994 Received: for berry()at()ccl.net by www.ccl.net (8.6.9/930601.1506) id KAA04183; Fri, 23 Sep 1994 10:56:38 -0400 Date: Fri, 23 Sep 1994 10:56:38 -0400 From: "Robby A. Berry" Message-Id: <199409231456.KAA04183 { *at * } www.ccl.net> To: ccl -AatT- ccl.net Subject: 3 Status: O Dear Netters, I would like to enquire if anybody has a program to calculate spin-orbit coupling elements for an avoided crossing of two potential energy curves. I would be grateful if any body could help me in this regard. Thanking you in advance. M.Krishnamrurthy, Tata Institute of Fundamental Reseach, Homi Bhabha Road, Bombay-5 e-mail: MKRISM &$at$& tifrvax.tifr.res.in From berry Fri Sep 23 14:56:47 1994 Received: for berry ( ( at ) ) ccl.net by www.ccl.net (8.6.9/930601.1506) id KAA04190; Fri, 23 Sep 1994 10:56:46 -0400 Date: Fri, 23 Sep 1994 10:56:46 -0400 From: "Robby A. Berry" Message-Id: <199409231456.KAA04190 (+ at +) www.ccl.net> To: ccl -AatT- ccl.net Subject: 4 Status: O my original query was: > Dear netters, > > We are thinking of buying an SG Indy with base-level graphics (i.e. 8-bit) > to supplement the other workstations we have. We don't think we need > blistering 3-D graphics performance with this machine because we already have > an Indigo2 Extreme to do the more complex work for us. > > We want to be able to run Sybyl, plus perhaps the CSD graphical interface, > Spartan and Oxford Molecular's Cameleon. With Sybyl we would be using it > mostly for small-molecule stuff plus some molecular spreadsheet work. > > Our problem is that we haven't been able to see a demo machine yet, and hence > we can't decide whether the 8-bit graphics will be good enough for our > purposes. > > SO: do any of you have experience of a base-level Indy? What's the minimum > specification that we should be looking at, in your opinion? and the responses seem to be in favour of using 8-bit graphics, although some people clearly believe that 8-bit is unusable. We did (finally) get a chance to compare an 8-bit Indy with a 24-bit Indy, both running Sybyl. The decision was that, for us, 8-bit graphics would be good enough. Remember that we already have high quality devices (a ps390 with stereo, plus 2 SGs at Elan/Extreme level), so the only requirement is something to replace our tired old Personal Iris 4D/20. And now, those responses in full (well, apart from some trivial editing indicated by [...]): -------------------------------------------------------------- Date: Fri, 20 May 1994 08:13:17 -0400 From: "Jeffrey L. Nauss" Subject: Re: CCL:Is anyone using 8-bit Indys for modelling? To: "Graham W. Mullier" Can't help you with your problem but I would be interested in any responses you may get. We are considering getting an Indy to run Biosym's InsightII. Thanks.... Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss "at@at" ucmod2.che.uc.edu * * CCCCCCC Jeffrey.Nauss' at \`UC.Edu * **************************************************************************** -------------------------------------------------------------- Date: Fri, 20 May 94 12:55 GMT From: "ADRIAN STEVENS, DEPT. OF CHEMISTRY, UNI. OF PORTSMOUTH" To: MULLIER Subject: 8-bit Indy Workstation - Yes! Dear Graham Mullier, I noted that you are looking at the Indy workstation with an interest to acquire. You wanted to know about whether other chemists have used this machine to do modelling. As a postgrad for the Uni. of Portsmouth, I am engaged in a modelling study of zeolites. We use an Indy workstation to perform all our molecular modelling and Monte Carlo calcs., etc. We have a 1Gig HDD together with a secondary 1Mb CPU cache. The processor used is a 100MHz R4000 chip. In addition we have set up a 128Mb swap space to compliment the 64Mb RAM. We have NOT chosen the 24bit graphics, instead we stayed with the standard 8bit supplied. This setup is used to run the Biosym software InsightII with some other extras It has remained an excellent machine throughout all the systems investigated and can quite happily model the very vast 4000+ atom systems of zeolites. The graphics speed and quality is more than adequate for the requirements and does not present any refresh slowdown. It is my personal oppinion - and treat it as thus - that the setup above is the very least that should be considered for all but the most demanding of applications. The HDD is sufficient for our purposes but will vary depending on your needs. [...] Adrian. Email: Stevensa (- at -) uk.ac.Portsmouth.csovax Adrian Stevens, Department of Chemistry, University of Portsmouth, St. Michael's building, White Swan Road, Ports., Hants., UK. -------------------------------------------------------------- Date: Fri, 20 May 1994 08:21:35 -0500 (EST) From: "LEONORE A. FINDSEN" Subject: Re: CCL:Is anyone using 8-bit Indys for modelling? To: mullier Graham Well, I haven't gotten one, but since I will be purchasing an Indy after I move to my new position, I have looked into it. This is mostly from my e-mail corresponding with Still's group (MacroModel). I have seen a demo for the 24-bit graphics and 19" screen and the resolution there is very good. What they said is that if you want reasonable looking graphics, you really need the 24-bit graphics. This is especially true if you want to get the large 19" screen. The number of pixels is the same for both machines so the large screen will give you lower resolution. However, the graphics are poor even with the 8-bit graphics and the standard 16" screen. What I have decided to get is the 24-bit graphics with the 19" screen. However, this will be my top-end graphics device that will be available on the island (see below) so I do need the better resolution. I hope this helps, Leonore new address: Department of Chemistry University of Hawaii at Hilo Hilo, Hawaii 96720 ------------------------------------------------------------------------------- Leonore A. Findsen |e-mail:Findsen' at \`dragon.pharm.utoledo.edu|For I am a cat, & College of Pharmacy | :LFindse "-at-" uoft02.utoledo.edu |since when has a University of Toledo| voice:(419) 537-2729 |cat given a Toledo, OH 43606 | FAX:(419) 537-4940 |straight answer ------------------------------------------------------------------------------- -------------------------------------------------------------- Date: Fri, 20 May 94 08:45:49 CDT From: Brad Thompson Message-Id: <9405201345.AA04004 $#at#$ gac.edu> To: mullier Subject: Re: CCL:Is anyone using 8-bit Indys for modelling? Sorry -- this is a request, not a reply. We're in a similar position, in that we're considering getting an Indy (SGI Indy 4600PC) to run Spartan 3.0 and related stuff. If you get any really worthwhile replies, would you let me know? | H. Bradford Thompson [Brad] bradt-0at0-gac.edu | Scholar in Residence, Chemistry & Physics | Gustavus Adolphus College, St. Peter MN 56082-1498 -------------------------------------------------------------- From: Peter Shenkin Message-Id: <9405201048.ZM22695;at;still3.chem.columbia.edu> Date: Fri, 20 May 1994 10:48:35 -0400 In-Reply-To: "Graham W. Mullier" "CCL:Is anyone using 8-bit Indys for modelling?" (May 20, 9:35am) To: "Graham W. Mullier" Subject: Re: CCL:Is anyone using 8-bit Indys for modelling? I have an 8-bit, low-resolution Indigo. I use it for molecular visualization, though not with Sybyl. The dithering you get with 8-bit graphics gives an ugly and annoying display, and the low resolution is annoying, too -- especially since not all applications have appropriate X resources to display reasonably to the low-res display; this is particularly true if you have the combination of low resolution and 19" monitor, which I do. I'd recommend strongly that you get high-res, 24-bit graphics, even if you get no 3D graphics acceleration hardware. If, however, you do go with low-resolution graphics, get the 16", not the 19" monitor. I have no personal experience with the combination of 8-bit with high-resolution graphics, but the dithering thing will affect this combination as well; it just makes the display much less attractive, and much less fun to use. -P. -- *********** After the revolution, everyone will have a home page. *********** Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin { *at * } still3.chem.columbia.edu; (212) 854-5143 ***************************************************************************** -------------------------------------------------------------- Date: Fri, 20 May 1994 16:59:36 +0200 From: reinert -x- at -x- vax.mpiz-koeln.mpg.d400.de To: mullier Subject: Re: 8-bit Indy I have no experience with Indies but I have tested SYBYL, INSIGHT and PROSIMULATE on an 8-bit Indigo (R3000, Irix 4.0.5.f, 32 MB Ram) for about 3 weeks and my impression was that for the applications you mentioned an 8-bit machine should work fine. Even my RNA hammerheads with 50-70 nucleotides haven't brought the machine down as long as I avoided using spacefil models or connolly surfaces. Regards, Peter Reinert -------------------------------------------------------------- Date: Fri, 20 May 94 09:18:00 -0600 From: "Darrell R. Davis" To: mullier Subject: CCL:Is anyone using 8-bit Indys for modelling? We bought 6 Indys: We were told that the 8 bit Indys would not work well for modelling. Biosym actually had a lengthy release describing the problems and we were convinced. We went with 5 24 bit PCs and 1 24 bit SC. These work well with Biosyms Insight/Discover software which is what we used to demo the machines. SGI has a real good deal on PC to SC upgrade at the moment so we will probably move all of our machines to SC level. I also have and Indigo2 XZ and it doesn't pain me that much to use the Indys. -------------------------------------------------------------- Darrell R. Davis Medicinal Chemistry University of Utah -------------------------------------------------------------- -------------------------------------------------------------- From: Csonka Gabor Message-Id: <9405201523.AA01354 (- at -) iris.inc.bme.hu> To: mullier Subject: Indy 8-bit Hello, Indy is working fine with SYBYL, Macromodel, Spartan etc. 8-bit is satisfactory. Minimum RAM is 32 MB, minimum processor is MIPS 4600, best processor is MIPS 4400SC 150 MHz. The 4000PC processor is rather slow. Hope this helps ---------------------------------------------------------- Gabor I. Csonka Budapest University of Technology Tel/FAX: (361) 18.12.177 Inorganic Chemistry Dept. Ch. Bldg csonka at.at iris.inc.bme.hu H-1111, Bp. Szent Gellert ter 4 ---------------------------------------------------------- -------------------------------------------------------------- Date: Fri, 20 May 94 11:46:58 -0400 From: George Seibel To: mullier Subject: 8-bit Indys Reply-To: seibelgl <-at-> sb.com I looked at the original 8-bit indigo as a molecular modeling machine. SGI's GL routines fake the "extra bits" by dithering the image. It works pretty well on continuous tone photographic-type images, as long as you aren't too particular. It works pretty poorly for depth-cued stick figures. However, it may be a reasonable choice for your application anyway. Small molecule stuff is not usually that demanding, graphics-wise. Spartan uses a lot of polygon-based graphics, which should work ok, aside from the fancy transparency stuff which is not that useful anyway. CSD's graphical interface is pretty rudimentary; most of it is 2D, so that would work fine. the "3D" part of it, as it were, is an open question. You have an Indigo already... my opinion is that an 8bit Indy is better than nothing, and would be useful for enough work to make it a not-ridiculous choice. The only thing that would make me say "don't do it" is if you really want to do a lot of depth-cued 3D graphics on it. George Seibel, SmithKline Beecham seibelgl (+ at +) sb.com -------------------------------------------------------------- Date: Fri, 20 May 94 09:17:48 -0700 From: Brian Karlak To: mullier Subject: Indys We just bought an Indy to supplement our Indigo2ex as well. We, however, got the 24-bit color instead of the 8-bit color. We didn't feel that the 8-bit would be adequate for any 3D rendering in Sybyl (even, say, capped sticks mode) The 24-bit seems to do just fine, except with one wierd bug: sometimes the molecules come out as Escher-like figures. When in one static position, the molecules look just fine; upon rotation, however, different parts of the molecule rotate in different directions! A phenyl may appear to be rotating into the screen, but the hydrogens on the phenyls seem to be rotating *out* of the screen! Only the shading seems to be affected, though; bond angles and torsions remain constant. It's a weird and disconcerting effect, though. One other thing you might want to take into consideration is that (as far as I am aware) the Indy is not technically supported by Tripos. Supposedly, this will change soon; Tripos is waiting to be sure that the Indy's IRIX OS is stable or some such thing. You may want to call them and ask. Other than that, the Indy works great. Brian Karlak Onyx Pharmaceuticals "For I am a cat, and since when has a cat given anyone a straight answer?" -------------------------------------------------------------- From: Slawomir Blonski Subject: Re: CCL:Is anyone using 8-bit Indys for modelling? To: "Graham W. Mullier" Date: Fri, 20 May 1994 12:35:51 -0400 (EDT) We have tested Indy with 24-bit graphics. Numerical performance of our MD code was the same on Indy and on our Indigo 2 Extreme with R4400 processor. Graphics program, which displays ball-and-stick models with hundreds of atoms, was about 3 times slower on Indy than on Indigo. But it is 24-bit, not 8-bit. Slawomir Blonski -------------------------------------------------------------- From: "Walter E. Reiher III" Subject: Re: CCL:Is anyone using 8-bit Indys for modelling? To: "Graham W. Mullier" Date: Fri, 20 May 1994 11:13:27 -0700 (PDT) Graham, [...] I would suggest that you be certain to check with your preferred software vendors (at least Tripos, Wavefunction, and Oxford Molecular) to find out the minimum configuration THEY recommend. One shouldn't assume that they support AND CHECK all possible SGI configurations. Ask them if they've TRIED the configuration you're interested in. I also do not have direct experience with a base Indy but did try a base (8-bit) Indigo when I worked at Tripos, and it doesn't look very good. It *might* be alright for small molecule work, but your nice Spartan surfaces will probably look awful. What looked bad in Sybyl on an 8-bit Indigo was depth cueing and anything rendered (e.g., capped sticks). No depth cueing means forgetting protein displays entirely. Graphics speed was OK; shading just doesn't look very good. Extra colors, as used in depth cueing, were dithered on the 8-bit Indigo, and this caused anything shaded to look like mush. Maybe the Indy is different, but I would be skeptical unless you hear otherwise. Good luck, Wally ======================================================================== Walter E. Reiher III, Ph.D. WallyR # - at - # netcom.com Consultant in Computational Chemistry P.O. Box 61056 voice 408-720-0240 Sunnyvale, CA 94088 fax 408-720-0378 -------------------------------------------------------------- Date: Fri, 20 May 1994 15:24:17 -0400 (EDT) From: CANARY -x- at -x- acfcluster.nyu.edu Subject: 8-bit SGI graphics To: mullier We run macromodel and spartan on an 8-bit Indigo Entry without any problem. In working with small molecules, I have not felt that the higher level graphics have mattered when using fancier workstations. -------------------------------------------------------------- From: Johan Landin Message-Id: <9405202359.ZM22495 \\at// medgraf.mednet.gu.se> Date: Fri, 20 May 1994 23:59:00 -0600 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: mullier Subject: RE: Indy ... Dear Dr. Mullier, I think that you should go for an Indy R4600PC which is the latest member of the Indy family. I have not tested this machine yet but I have used Sybyl on several models including Indy R4000PC, Indigo R3000 XS, Indigo R4000 Elan and Indigo^2 R4400. Based on this experience I would suggest the following minimum configuration: Indy R4600PC (62.8 SPECint92 and 49.9 SPECfp92) 32 MB memory as an absolute minimum but 48 MB if you can afford it 8-bit graphics 16 inch monitor As all the Z-buffering is done in software instead of hardware, it is very important to have enough memory. If the performance with solid models is good enough depends on what you mean with small molecules! If you choose 8-bit graphics be prepared to that all solid models in Sybyl will look very ugly due to the 24 bitplane emulation. The appearance of the other programs depends on if they are able to swith to 8 bit mode or use emulation like Sybyl. The performance with wireframe models is definitely good enough, this statement is based on my experience with the Indigo R3000 XS I am writing this letter on, this machine has lower 2D performance than the proposed Indy. I have found the Indigo OK for running Sybyl but I am missing the ability to show solid models as I do not have the Z-buffer hardware option. The ugliness of the emulated 24bit display is something one can live with if there are better displays nearby. Hope this helps Johan Landin _________________________________________________________________ Johan Landin Tel: +46 31 773 3767, 773 3762 Dept. of Structural Chemistry Fax: +46 31 41 6108 Medicinaregatan 9 S-413 90 Goteborg, Sweden Email: landin -x- at -x- mednet.gu.se -------------------------------------------------------------- Date: Sun, 22 May 1994 09:19:26 -0600 (CST) From: Andy Holder Subject: 8-bit graphics To: mullier Dear Dr. Mullier, Our program AMPAC runs quite well in the 8-bit color environment on an SGI. If you are doing small-moleculae semiempirical work, I think that AMPAC is a better choice that Spaqrtan due to our more advanced and robust algorithms. I'll send a packet. Andy p.s. I'll be happy to provide you with a demo version.. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER President, Semichem Semichem, Inc. || Internet Addr: aholder - at - vax1.umkc.edu 7128 Summit || Phone Number: (913) 268-3271 Shawnee, KS, 66216 || FAX Number: (913) 268-3445 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= -------------------------------------------------------------- Date: Mon, 23 May 94 08:11:20 -0700 From: Soaring Bear Subject: Re: CCL:Is anyone using 8-bit Indys for modelling? It didn't take us long to add graphics card to Indy to operate Insight. Good Luck, Bear * UU UU SOARING BEAR * * UU UU Molecular Modeling Services * * UU UU Pharmaceutical Sciences, New Pharm 404 * * UU UU AA University of Arizona * * UU UU AAAA Tucson, AZ 85721 * * AA AA where the sun shines * * AAAAAAAA * * AAA AAA e-mail:bear \\at// ellington.pharm.arizona.edu * * AAA AAA * -------------------------------------------------------------- Date: Mon, 23 May 1994 12:26:18 EDT From: "CBAS25 ::P_BLADON ::CBAS25" To: mullier Subject: RE: CCL:Is anyone using 8-bit Indys for modelling? Dear Graham Mullier, My only experience with SGI 8-bit machines is a session with limited access to a Demo 8-bit Indigo (i.e. the original Indigo). I was interested in porting our own INTERCHEM modelling software to it. While it coped fairly well with software written for the 24 bit systems, the rendering of images involving lighting modes left something to be desired; the dithering left rather grainy pictures. The low screen resolution (1024 x 768) was also a drawback. So when I came to consider the Indy systems I decided to go for the 24-bit system, with the 16 inch screen which has 1280 X 1024 resolution. This has proved perfectly adequate. However, with the z-buffering using the main memory animated 3-D images tend to be displayed more slowly than on the PI-4D-20. The machine has only the primary cache so I would expect a better preformance with the SC processor. When it comes to 2-D display and straight computation the machine is a great improvement on the PI-4D-20 which I previously used. Only some minor changes in software were needed when it was ported to this system. The real test is with the software that YOU want to use. I am not sure whether the commercial software has been optimised for the 8-bit systems, wou would have to check this. Yours sincerely Peter Bladon ------------------------------------------------------------------------------ Thanks to everyone who took the time to respond to my query. Sorry for the delay in producing this summary, I was too busy hill-walking in Skye. Graham Mullier, computational chemistry group, Zeneca Agrochemicals, Jealott's Hill, UK. mullier -8 at 8- jh01sg.demon.co.uk From berry Fri Sep 23 14:56:53 1994 Received: for berry \\at// ccl.net by www.ccl.net (8.6.9/930601.1506) id KAA04195; Fri, 23 Sep 1994 10:56:53 -0400 Date: Fri, 23 Sep 1994 10:56:53 -0400 From: "Robby A. Berry" Message-Id: <199409231456.KAA04195 $#at#$ www.ccl.net> To: ccl # - at - # ccl.net Subject: 5 Status: O Hi, I obtained basis set for fluorine (ftp.ccl.net: basis set library). Now, I tried to use the following exponents and coefficients with g92 (user specified basis set): ############################################################################### # atomic SCF calculation of ---> F(2P) 7s4p <--- # SCF energy is -99.3462183972 a.u. (virial theorem = 2.000000000) # A. Schaefer, Jan. 92 ############################################################################### # exponents coefficients # 1s 2s # 2973.4997046 -.52590584026E-02 -.12092301431E-02 # 447.25783120 -.39233645111E-01 -.93573417113E-02 # 101.57185900 -.17619356211 -.42823390798E-01 # 28.268552755 -.45719988226 -.14052491559 # 8.7349389301 -.44730688010 -.19520721834 # 1.3841118258 -.37028368038E-01 .51799309070 # .41199921824 .89840651033E-02 .60912564518 # eigenvalue -26.3659766 -1.5632256 # occupation 2.0000000 2.0000000 # 2p # 22.658300194 .44897518573E-01 # 4.9749914492 .23575465344 # 1.3466519487 .50828613121 # .34729031582 .45821884951 # eigenvalue -.7161735 # occupation 3 * 1.6666667 ############################################################################### * Then I generate the following stream for g92: # HF/GEN Tetst run 0 2 9 -F S 14 1.0 197347.11959 -.28184163023E-04 29558.776324 -.21907068471E-03 6726.9377956 -.11500051437E-02 1905.1637291 -.48260180222E-02 621.37226145 -.17221358226E-01 224.17852083 -.53099042237E-01 87.234531917 -.13789697333 35.916025242 -.28114096672 15.415563071 -.38289777654 6.7358200331 -.24413469399 2.5569609365 -.32911334952E-01 1.1138310004 .24115272055E-02 .44549974207 -.17148852940E-02 .16466803857 .16641631481E-03 S 14 1.0 197347.11959 .63622475516E-05 29558.776324 .49409450159E-04 6726.9377956 .26000984572E-03 1905.1637291 .10919343116E-02 621.37226145 .39388403025E-02 224.17852083 .12360484265E-01 87.234531917 .33873593861E-01 35.916025242 .76642243943E-01 15.415563071 .13666725679 6.7358200331 .13332951903 2.5569609365 -.11442436559 1.1138310004 -.44921371698 .44549974207 -.46114921253 .16466803857 -.13972573436 P 11 1.0 734.58063291 .13461172732E-03 174.10266268 .11647895815E-02 56.410104865 .62228913925E-02 21.298831774 .23990521555E-01 8.8087650181 .71566280999E-01 3.8734203606 .16053699622 1.7478894590 .25856388471 .78248058089 .30564723272 .33863051221 .27306024051 .13832555824 .17291405016 .51441819864E-01 .52370788368E-01 **** 1s and 2s eigenvalues are correct (ie. as described in basis set library) but the 2p ones are not. And, of course, the total energy is greater than mentioned in the basis set library. I tried simpler atoms (like H, Li) which only had s orbitals and those worked ok. Any ideas? Regards, Jussi Eloranta