From jmeehan@cc.utas.edu.au Tue Jun 7 00:23:56 1994 Received: from corinna.its.utas.edu.au for jmeehan@cc.utas.edu.au by www.ccl.net (8.6.4/930601.1506) id AAA16435; Tue, 7 Jun 1994 00:20:36 -0400 Received: from tasman.cc.utas.edu.au by corinna.its.utas.edu.au with SMTP id AA28076 (5.67a/IDA-1.5 for ); Tue, 7 Jun 1994 14:19:06 +1000 Date: Tue, 7 Jun 1994 14:16:58 +1000 (EST) From: John Meehan Subject: Re: CCL:polymer chemistr list To: ipcakc@vigyan.iisc.ernet.in Cc: CHEMISTRY@ccl.net In-Reply-To: <9406062156.AA09772@vigyan.iisc.ernet.in> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII G'day > > Is there anything like "Ploymer Chemistry List" as we have > computational chemistry list? > There is a newsgroup -- sci.chem.polymers -- (I thinkthat's it!) that maight be able to help you. Cheers ---------------------------------------------- John Meehan O CH2-COOH Department of Biochemistry, " / University of Tasmania, HO-P-C-COOH Australia | \ HO CH2-COOH PHOSPHOCITRIC ACID ---- A powerful, natural inhibitor of Pathological Biomineralization ---------------------------------------------- From tylera@agric.nsw.gov.au Tue Jun 7 04:24:01 1994 Received: from quord.agric.nsw.gov.au for tylera@agric.nsw.gov.au by www.ccl.net (8.6.4/930601.1506) id DAA17288; Tue, 7 Jun 1994 03:27:10 -0400 Received: from wolsun.noname (wolsun.agric.NSW.GOV.AU) by quord.agric.nsw.gov.au (4.1/SMI-4.1) id AA13934; Tue, 7 Jun 94 17:23:47 EST Received: by wolsun.noname (4.1/SMI-4.1) id AA02727; Tue, 7 Jun 94 17:22:35 EST Date: Tue, 7 Jun 1994 17:11:07 +1000 (EST) From: Tony Tyler Subject: Re: CCL:Real-Time Conference To: "Dr. Tom Pierce" Cc: Henry Rzepa , Chemistry@ccl.net In-Reply-To: <9405311259.AA19544@monte.br.RohmHaas.Com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 31 May 1994, Dr. Tom Pierce wrote: > Previously, Henry Rzepa wrote: > > > > As for www94, the consensus was that we all needed > > to meet in person for precisely the > > feedback. The most successful aspect were the > > workshops with round table discussions. > > Of course this format may not be needed for > > a purely chemical discussion! Perhaps the model > > of the chemistry www94 workshop could be used. > > About 8 people contributed papers, but did > > not actually attend. The discusion amongst > > the physically present participants revolved around > > issues raised in part by these papers. > > > > We hope to arrange a "prototype" conference before the fall. If this works, > > we could try a larger scale experiment? > > Dear Prof. Rzepa and potential participants, > > I propose that a 'larger scale' experiment be run at a ACS symposia. > I was *volunteered* to help organize a "Chemistry on the Infobahn" > Symposia for the Computers and Chemistry Division of the American > Chemical Society. My hope is that much of this can be electronic. > The symposia is scheduled for Fall 1995 (Aug 27th-Sept 1.) and > will physically be in Chicago, Illnois USA. > > This is too long from now for a "prototype test", but it is > soon enough to plan for a larger implementation. > > If Prof. Rzepa is willing, perhaps we could jointly make this work? > -- > Sincerely, Thomas Pierce - THPierce@RohmHaas.Com - Computational Chemist > "These opinions are those of the writer and not the Rohm and Haas Company." > I consider that it is a great idea. It is difficult to get to conferences, especially if you are not working in that speciality. Many people could "attend" and enter the discussion at will. The main benefits are the minimal cost and being able to remotely present questions to the presenters of the papers. Best wishes Tony Tyler tylera@agric.nsw.gov.au From eloranta@kala.jyu.fi Tue Jun 7 04:32:13 1994 Received: from kala.cc.jyu.fi for eloranta@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@kala.jyu.fi (Jussi Eloranta) Subject: gaussian 92 and GEN basis sets To: chemistry@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 sanja@indigo.irb.hr Tue Jun 7 05:24:00 1994 Received: from indigo.irb.hr for sanja@indigo.irb.hr by www.ccl.net (8.6.4/930601.1506) id EAA17625; Tue, 7 Jun 1994 04:59:36 -0400 From: Received: by indigo.irb.hr (920330.SGI/920502.SGI) for CHEMISTRY@ccl.net id AA10771; Tue, 7 Jun 94 11:02:12 +0200 Date: Tue, 7 Jun 94 11:02:12 +0200 Message-Id: <9406070902.AA10771@indigo.irb.hr> To: CHEMISTRY@ccl.net Subject: Help on ChemX This is the message of my colleague: Hi netters! Recently, I have done some statistics using CHEM-X program, October 93' update and I have run into several problems. DBS database has a restriction of 100 variables-the problems arise if I define them all and want to change the names of the variables or make a new database with some selected variables. Furthermore, the PLS method, when used within the created database (segments and variables) doesn't provide me enough statistical information. I wonder if anyone has the experience using CHEM-X statistics package and could help me with some information. I will summarize the answers to the list if there is enough interest. Zeljka Zeljka Medven Institute R. Boskovic Zagreb, Croatia e-mail:MEDVEN@OLIMP.IRB.HR From mullier@jh01sg.demon.co.uk Tue Jun 7 06:24:00 1994 Received: from gate.demon.co.uk for mullier@jh01sg.demon.co.uk by www.ccl.net (8.6.4/930601.1506) id FAA17737; Tue, 7 Jun 1994 05:28:45 -0400 Received: from post.demon.co.uk by gate.demon.co.uk id aa07134; 7 Jun 94 10:23 GMT-60:00 Received: from jh01sg.demon.co.uk by post.demon.co.uk id ab15882; 7 Jun 94 10:19 GMT-60:00 Received: by JH01SG (920330.SGI/zeneca.jf.30Nov93) for @gate.demon.co.uk:CHEMISTRY@ccl.net id AA10499; Tue, 7 Jun 94 10:18:24 +0100 From: "Graham W. Mullier" Message-Id: <9406070918.AA10499@JH01SG> Subject: Indys with 8-bit graphics - summary To: CHEMISTRY@ccl.net Date: Tue, 7 Jun 1994 10:18:23 +0000 (BST) Cc: "Graham W. Mullier" X-Mailer: ELM [version 2.4 PL21] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 21770 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@ucmod2.che.uc.edu * * CCCCCCC Jeffrey.Nauss@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@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@dragon.pharm.utoledo.edu|For I am a cat, & College of Pharmacy | :LFindse@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@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@gac.edu | Scholar in Residence, Chemistry & Physics | Gustavus Adolphus College, St. Peter MN 56082-1498 -------------------------------------------------------------- From: Peter Shenkin Message-Id: <9405201048.ZM22695@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@still3.chem.columbia.edu; (212) 854-5143 ***************************************************************************** -------------------------------------------------------------- Date: Fri, 20 May 1994 16:59:36 +0200 From: reinert@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@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@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@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@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@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@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@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@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@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@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@jh01sg.demon.co.uk From system@alchemy.chem.utoronto.ca Tue Jun 7 11:24:12 1994 Received: from alchemy.chem.utoronto.ca for system@alchemy.chem.utoronto.ca by www.ccl.net (8.6.4/930601.1506) id KAA21329; Tue, 7 Jun 1994 10:29:28 -0400 Received: from localhost (system@localhost) by alchemy.chem.utoronto.ca (8.6.4/8.6.4) id KAA15673 for chemistry@ccl.net; Tue, 7 Jun 1994 10:28:51 -0400 Date: Tue, 7 Jun 1994 10:28:51 -0400 From: System Admin (Mike Peterson) Message-Id: <199406071428.KAA15673@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: Re: gaussian 92 and GEN basis sets Your problem is that G92 defaults to UHF when it finds an open shell calculation, and you need ROHF to reproduce the calculation. Forcing ROHF will not work either, since it occupies the P orbitals with 2, 2 and 1 electrons respectively, not the 5/6 per P orbital that the F(2P) state requires. I'm not sure you can reproduce this calculation with Gaussian even with alteration of the initial guess since you have to force the 5/6 occupation all through the SCF as well. This is normally done using Coulomb and Exchange coupling constants that are specific to each state and occupation scheme (here 5 electrons in a triple degenerate level), and I don't see anywhere that G92 lets you put them in. I'd like to know how it can be done too. You will get H atom right because UHF=ROHF for the 1 electron case, but I'm surprised you get Li atom right - UHF should give 2 alpha spin eigenvalues, and 1 beta spin eigenvalue which wouldn't match the first alpha eigenvalue except by accident (or if the 1s AO describes exactly the lowest MO, which it might if this basis set was energy optimized on the atom, so that none of the 2s AO gets mixed in?). The ROHF option will give the right answer for Li since the open shell is singly degenerate - ROHF will get all cases right where the open shell is exactly half occupied with alpha spin electrons (the "high spin" cases), provided the proper initial guess orbitals are occupied. The (obsolete) MONSTERGAUSS program will do this type of ROHF with explicit control over the orbital occupation (and computes the correct coupling constants for most real-life cases except some excited pi states of linear molecules), but it can't handle contraction schemes involving more than 10 primitives. Mike Peterson, U/Toronto Department of Chemistry E-mail: system@alchemy.chem.utoronto.ca From bennett@guru.unibas.ch Tue Jun 7 13:24:05 1994 Received: from ki1.chemie.fu-berlin.de for bennett@guru.unibas.ch by www.ccl.net (8.6.4/930601.1506) id MAA24708; Tue, 7 Jun 1994 12:44:36 -0400 Received: by ki1.chemie.fu-berlin.de (Smail3.1.28.1) from leibniz.math.fu-berlin.de (130.133.4.10) with smtp id ; Tue, 7 Jun 94 18:44 MEST Received: by leibniz.math.fu-berlin.de (/\=-/\ Smail3.1.18.1 #18.14) id ; Tue, 7 Jun 94 18:44 MET DST Received: by gibb.math.fu-berlin.de (/\=-/\ Smail3.1.18.1 #18.14) id ; Tue, 7 Jun 94 18:43 MET DST Message-ID: Date: Tue, 7 Jun 94 17:53:10 +0200 From: "Frederick Bennett" Subject: MOLPRO To: chemistry@ccl.net X-Mailer: VersaTerm Link v1.1 Hi everyone, I am trying to calculate some excited state CASSCF wavefunctions and am having a bit of difficulty. I am using Knowles and Werners MULTI program as implemented in GAMESS-UK. MULTI is the choice mcscf program as I am dealing with rather large ci expansions in the CAS. The problem is that when I optimise only one root (ie ground state for a given spin/symm) there is no problem at all. When I choice for a higher root I get the problem below in the first internal optimisation. non zero p-space gradient; istate,j,jj,sigma: 1 1453 -0.7242E-01 I am afraid that I can't figure a solution. I tried to not carry out the internal optimisation and just diagonalise the ci before the newton-raphson optimisation. It seems however, that the implementation of multi in GAMESS-UK does not allow this choice. You have no choice but to run the internal optimisation in each step. I am not sure but I think that a straight davidsons diagonalisation would do the trick and solve the problem. Does anybody have any clues??? Thanks Fred ====================================================== Papernet Address : Frederick R. Bennett Institute for Physical Chemistry Klingelbergstrasse 80 CH-4056 Basel Switzerland Mouthnet Address : [41]-(61)-267-3821 Internet Address : bennett@guru.urz.unibas.ch ====================================================== From ghislain@jupiter.sun.csd.unb.ca Tue Jun 7 15:24:40 1994 Received: from unb.ca for ghislain@jupiter.sun.csd.unb.ca by www.ccl.net (8.6.4/930601.1506) id OAA27209; Tue, 7 Jun 1994 14:41:54 -0400 Received: from jupiter.sun.csd.unb.ca by unb.ca (4.1/SMI-4.1-940224-08:05) id AA17247; Tue, 7 Jun 94 15:41:48 ADT Received: from [131.202.47.1] by jupiter.sun.csd.unb.ca (4.1/SMI-4.1-940126-11:10) id AA26159; Tue, 7 Jun 94 15:41:46 ADT Date: Tue, 7 Jun 94 15:41:45 ADT Message-Id: <9406071841.AA26159@jupiter.sun.csd.unb.ca> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@ccl.net From: ghislain@jupiter.sun.csd.unb.ca (Ghislain Deslongchamps) Subject: Sun SCSI disk on an Indigo Dear Netters, please forgive me for posting this here as it is a hardware related question. I don't have an address for a more appropriate listserver. We are upgrading our Indigo XS24 to handle Quanta 4.0 and MacroModel 4.5 and need to add a 1 Gb external hard drive to the system. We have access to a new Sun 1.05 Gb SCSI disk and want to try to use it on the Indigo. After finding the proper SCSI adaptor cable and connecting the disk to the Indigo we find that the Indigo recognizes the disk when the "hinv" command is typed (we set the disk on SCSI address 5). However, the System Manager's "Disk & File" window does not see the unmounted disk resource. We also tried the "Add_Disk 5" command but were told that it was "unable to create a filesystem on SCSI disk 5". Is it possible to use that Sun disk, if so how? If not, what are our options, Parity Inc.? Thank you for your help Ghis +++++++++++++++++++++++++++++++++++++++++++++++++++++ + Ghislain Deslongchamps, Assistant Professor + + Department of Chemistry + + University of New Brunswick + + Fredericton, N.B. CANADA E3B 5A3 + + e-mail: GHISLAIN@UNB.CA + + phone: 506-453-4795 (or 453-4792) + + FAX: 506-453-4599 + +++++++++++++++++++++++++++++++++++++++++++++++++++++