From feng@lisboa.ks.uiuc.edu Wed Jul 27 00:02:27 1994 Received: from lisboa.ks.uiuc.edu for feng@lisboa.ks.uiuc.edu by www.ccl.net (8.6.9/930601.1506) id XAA24780; Tue, 26 Jul 1994 23:48:35 -0400 Received: from glasgow by lisboa.ks.uiuc.edu (NX5.67d/NX3.0M) id AA23941; Tue, 26 Jul 94 22:49:07 -0500 From: Zhou Feng Message-Id: <9407270349.AA23941@lisboa.ks.uiuc.edu> Received: by glasgow.ks.uiuc.edu (NX5.67d/NX3.0X) id AA16214; Tue, 26 Jul 94 22:49:07 -0500 Date: Tue, 26 Jul 94 22:49:07 -0500 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: chemistry@ccl.net Subject: ACS annual meeting Reply-To: feng@lisboa.ks.uiuc.edu Does anybody know where is this year's chemical society meeting and how can I obtain application forms? I am a graduate student and not an ACS member. Please reply directly to me. Thanx. --- Feng Zhou +-------------------------------------------------------------------- |Theoretical Biophysics feng@lisboa.ks.uiuc.edu |University of Illinois Tel: (217)-244-1612 |3121 Beckman Institute Fax: (217)-244-6078 |405 N Mathews, Urbana, IL61801 NeXTmail Ok +-------------------------------------------------------------------- From RCMAH@bunyip.ph.rmit.edu.au Wed Jul 27 00:56:45 1994 Received: from peladon.rmit.EDU.AU for RCMAH@bunyip.ph.rmit.edu.au by www.ccl.net (8.6.9/930601.1506) id AAA25094; Wed, 27 Jul 1994 00:41:17 -0400 Received: from thal.xx.rmit.EDU.AU by peladon.rmit.EDU.AU with SMTP id AA18575 (5.65c/IDA-1.4.4 for ); Wed, 27 Jul 1994 14:40:39 +1000 Received: From RMITCC/WORKQUEUE2 by thal.xx.rmit.EDU.AU via Charon-4.0-VROOM with IPX id 100.940727144025.480; 27 Jul 94 14:42:43 -1000 Message-Id: To: "STEPHEN R. HELLER" From: "BERT HOVELING" Organization: rmit applied physics Date: Wed, 27 Jul 1994 14:40:23 EST-10 Subject: Re: CCL:More Software/Databases for Review Cc: "chminf-l" , "chemistry" , "orgchem" X-Pmrqc: 1 Return-Receipt-To: "BERT HOVELING" Priority: normal X-Mailer: WinPMail v1.0 (R1) Date: 26 Jul 94 09:19:00 EDT From: "STEPHEN R. HELLER" Subject: CCL:More Software/Databases for Review To: "chemed-l" Cc: "chminf-l" , "chemistry" , "orgchem" 26 July, 1994 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. Since I sent a note out yesterday two additional packages have arrived. I am looking for someone who is willing to review these software/databases products. In return for the review you get to keep the software. The review should be completed in 1-3 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. Please try to give me some (short) reason to choose you over another person. DO NOT SAY YOU WILL REVIEW ANYTHING I HAVE AVAILABLE. Messages with such replies are trashed! I have tried this approach for about the past three years and it is working reasonably well. (REMINDER: For those who haven't finished your reviews of software sent months and months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e- mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within a few days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 27 July, 1994 (Wednesday), as I am sure the software will be gone by then. I can be reached on Internet (SRHELLER@ASRR.ARSUSDA.GOV). PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I send the software by Federal Express.) Without this information I WILL NOT consider your request. Steve Heller The two additional packages I now have are from Megalon: 1. ChemStructure for Windows. It is a structure drawing program. 2. Compounds for Windows. A database of about 27,000 organic compounds with some two dozen types of numeric and spectral data associated with each compound. ---Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV Hi Steve, You probably don't remember me, Bert Hoveling, from Melbourne, Australia. I did 4 months with Bill Milne at NIH in 1976. I would be interested in this project you are involve in, if i can be of any help. I am also interested in anything else of interest in Chemical Information Systems, particularly relating to the hypertext protocol on Mosaic etc. Sorry to hear you are not well, and hope you improve soon. Could you please let me know what Bill is up to, and his E-mail address, if that's O.K. All the best, and I wish you well. Regards, Bert. Dr.A.W.(Bert) Hoveling Department of Applied Chemistry, R.M.I.T. 124 La Trobe Street Melbourne, Victoria, Australia, 3001 Phone: (03) 660-2117 Facsimile: (03) 639-1321 E mail: hoveling@rmit.edu.au From Patrick.Bultinck@rug.ac.be Wed Jul 27 04:56:49 1994 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.9/930601.1506) id EAA26075; Wed, 27 Jul 1994 04:37:15 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA08422 (5.67b/IDA-1.5 for ); Wed, 27 Jul 1994 10:37:27 +0200 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA14415; Wed, 27 Jul 94 10:34:14 +0200 Date: Wed, 27 Jul 1994 10:34:13 +0200 (MET DST) From: Patrick Bultinck Sender: Patrick Bultinck Reply-To: Patrick Bultinck Subject: Summary : Z-matrices To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Length: 10708 Dear netters, Please hereby find a summary to a question on Z-matrix I posted about a week ago !!!! Thanks to those who reacted .... Original message : Dear Netters, I was wondering if anyone had some clues or ideas on how to set up a Z-matrix. The trouble is that some of my optimizations do not converge to a stationary point. However when I make another alternative Z-matrix I converge to the Stat. Point. Now my question is : how does one judge, given e.g. five different possibilities, which is the best Z-matrix. Is this a matter of "Zen" or rather a matter of "science" ? Thanks for your time, a summary will be made if useful answers get to me. Patrick, University of Ghent, Belgium Patrick.Bultinck@rug.ac.be And these are the replies ... I build up my Z-matrices buy building the structure in a molecular editor, at the moment I use the one InsightII (Biosym) but any will do. When you add an atom to the existing structure make sure it is bonded to an atom that is already described in the structure. If possible build up your structure such that each consecutive atom is connected to the existing atoms and can make proper torsion angles, not improper torsions. Once you have built the structure, what I do is run a single point calculation in the AMPAC/MOPAC module of InsightII to get z-matrix, but it build the matrix based on the atom orders. The long and the short of the process is to get a z-matrix which as only bond lengths for the distance coordinate, bond angle for the first angle coordinate and proper torsion angle for the second angle coordinate. I know I haven't explained this very well but this method seems to work for me. If you follow this method you should be able to look at the z-matrix and see that the first column of coordinates are all under 2.0 Angs, The second column has values from about 100 to 135 (note 180 deg bond angles are not good), the torsion angles of the third column of coordinates can be -180 to +180, but it is worth checking to see if aromatics etc have reasonable values. Hope this is of some help. Andy. -- ############################################################################### Structural and Computation Chemistry Group_________chp1aa@uk.ac.surrey - JANET. Department of Chemistry____________________________phone_______+44(483)-259591. University of Surrey_______________________________fax_________+44(483)-300803. Guildford, Surrey, GU2 5XH, UK_____________________ftp____________131.227.110.2 ############################################################################### In my experience, the most common cause of of a Z-matrix defined in *internal* coordinates not giving a stationary point is this: the degrees of freedom in the molecule are not independent. I have never seen or heard a proper expaination of how to *know* you are avoiding this when you define the Z-matrix. Because of these difficulties, I began defining all my structures in *cartesian* coordinates. This avoids the problem of angles being dependent on bonds and so forth. The important thing to remember when optimizing a structure in this way is to define six of the 3n coordinates to be constant, thus eliminating the rotational and translational degrees of freedom. This must be done carefully and not simply at random to avoid constraining the molecule in some way. Usually, you'll want to hold all three coords of on atom constant, two of one bonded to the first, and one of another. Make sure that the bond between the first two atoms is along one of the three axes of your coord system. This, then, does not constrain any of the bonds and so forth, since, of course, any two points define a line, and any three define a plane. Defining them as I have suggested merely specifies *which* line and plane. If you are using Gaussian92 (I don't think you specified a program...) then the Fopt keyword will check your Z-matrix and make sure all degrees of freedom are present and independent. One must also be careful here, since if the program finds some initial symmetry, say CS, then it only acknowledges the number of deg of freedom appropriate to this symmetry, and Fopt stops, believing that there are not enough. One may avoid this by pushing one atom ever so slightly out of, say, a mirror plane so that the program finds C1 symmetry initally. I hope I have been of some help. I have no doubt that you'll receive many responses, but just let me know if you have any questions about what I've suggested. Anthony Kurt Grafton Department of Chemistry and Biochemistry University of Oklahoma, Norman, USA kgrafton@aardvark.ucs.uoknor.edu Patric, There are some clear criteria for making good Z-matrices but not so clear for the "best" Z-matrix. A good article is Schlegel, in New Theoretical Concepts for Understanding Organic Reactions", Bertran and Csizmadia (ed) Kluwer Academic Press (1989). One option for automatically making Z-matrices with Gaussian is newzmat. Given a Z-matrix you can use newzmat -redoz old_zmat.in new_zmat.in Doug Fox Dear Patrick, If you have access to a relatively new GAMESS-US manual (less than six months old), read the "further information" section on internal coordinates. A new version of the manual, as well as the GAMESS-US program is available from Mike Schmidt at mike@si.fi.ameslab.gov. Best regards, Jan Jensen Dept. of Chemistry Iowa State University Patrick, one of the most important considerations is to make sure that the z matrix you specify has the required number of variables for a complete specification of the required symmetry. This can easily be ensured by using fopt instead of opt (in gaussian92 anyway). I usually simply check that the number of variables I give the z matrix is the same as gaussian tells me the particular symmetry demands. You can find this near the top of the log file around about where a print out of FRAME is. ie search for "FRAME" and you will also see the number of variables required. fopt has the advantage however of also checking for linearly dependent variables that can slow the rate of convergence down quite considerable. A good z matrix IS somewhat of an art, possibly one of the reasons that optimizations in cartesian space is becoming more commonplace now (apart from the advent of graphical interfaces). Hope this is of help. If you would like me to suggest an appropriate z matrix I would be delighted to be of assistance. Kind regards, Anthony P. Scott Research Officer Computational Chemistry Group Research School of Chemistry Australian National University Canberra, ACT, Australia Dear Patrick, No definite answers, but: 1) problem of generating the Z-matrix. I have already experienced that different programs treat differrently the third line of a Z-matrix (the line ending usually with "1 2 0"). Mathematically it's a question of two +/- signs in the algorithm. The result of this mistake depends also on the original numbering of the molecule, or when generating the Z-matrix, which atoms are choosen for the starting 3 atoms. 2) I don't dare to say loudly, but there may be problem with the program. The above problem, or for example, there are 3 collinear atoms in the molecule and the program doesn't like this in some phase. Well, what I should do, to generate 2-3 different Z-matrices from the same molecule, and to minimaze all of them with two different programs. From the result I could step forward. Best wishes Tamas E. Gunda L.Kossuth Univerity Debrecen Hungary tamasgunda@tigris.klte.hu Hi I did not do any detailed studies on the performance of different Z-matrizes, but my experience leads to the following directives: -- It is good to choose a central atom of the molecule to be the first atom in the Z-matrix. This causes the chains in the Z-matrix to be as short as possible ( The C-3 of pentane is a better starting-atom than the C-1 ). This choice is often necessary if you want to use symmetric Z-matrizes. -- The angles in the Z-matrix should be in the range of 30 to 150 . If they are close to linear, small movements cause relatively great changes in dihedral angles. Another drawback of near-linear-angles is that they more easily run out of the 0 to 180 limits of the Z-matrix angles. Stefan Fau, AK Frenking, FB Chemie der Philipps-Universitaet Marburg, Hans-Meerwein-Str. 35032 Marburg, Deutschland fau@ps1515.chemie.uni-marburg.de Hi again Here is some more information on the "chain-effect": You can write a Z-matrix in two different styles: the star-style and the chain-style. In the chain-style the position of a nucleus X is defined by the distance to the next nucleus X-1, the angle with X-1 and the second-next nucleus X-2 and the dihedral angle with X-1, X-2 and the third-next nucleusX-3. So the position of the last nucleus in a long chain is defined by the positions of the second-, the third- and the fourth-last nucleus of the chain. The positions of these nuclei depend on the positions of their predecessing nuclei. As far as I know, the new values of the optimization variables are determined without accounting for the motion of the predecessing nuclei. This means that the actual new position of X is not identical to the intended new position of that X because the nuclei X-1 .. X-3 also changed their positions. So the Atoms at the end of a chain can not reach their optimum positions until the predecessing atoms are at their optimum positions. The other style is star-style: Here the position of any nucleus is defined relative to the Positions of three central Atoms A, B and C. They should be chosen near the center of mass. So all chains have four members: A, B, C and X. The disadvantage of this style is the possibility of long distances and correspondingly poor angle resolution in the definition of the Z-matrix. In effect this should correspond to looser convergence-criteria. In short: Chain-style causes the last nuclei in the definition-chain to find their optimum places last. The angle-resolution is good. The Z-Matrix is easy to understand. Star-style Z-matrizes should converge faster because there should be less random-motion caused by the intermediate nuclei between C and X-3. The angle resolution of the outer nuclei is worse than the angle resolution of the inner nuclei. The Z-Matrix may be complicated to understand. Stefan Fau, AK Frenking, FB Chemie der Philipps-Universitaet Marburg, Hans-Meerwein-Str. 35032 Marburg, Deutschland fau@ps1515.chemie.uni-marburg.de From mn1@helix.nih.gov Wed Jul 27 11:56:55 1994 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.6.9/930601.1506) id LAA00548; Wed, 27 Jul 1994 11:31:30 -0400 Received: by helix.nih.gov (931110.SGI/1.35(big_sgi-1.0)) id AA21461; Wed, 27 Jul 94 11:32:25 -0400 Date: Wed, 27 Jul 94 11:32:25 -0400 From: mn1@helix.nih.gov (M. Nicklaus) Message-Id: <9407271532.AA21461@helix.nih.gov> To: CHEMISTRY@ccl.net Subject: Summary: Gauche effect ab initio calculations Cc: mn1@helix.nih.gov Dear Net-Workers, Some time ago I posted the following QUESTION: ========= > We are thinking about doing ab initio modeling (using Gaussian 92) > on small organic molecules which possess, apart from C, H, N, O, > a sulfur and a halogen atom (F, Cl, Br, I) in such an arrangement > that we expect interactions of the gauche-effect type to occur > between them. > We would like to ask the experts what level of theory, basis > sets, electron correlation methods etc. they would recommend for > obtaining reliable conformational energies when calculating > local energy minima for such compounds. Would different approaches > be advisable for geometry optimization vs. the final energy > calculation? Would using non-standard basis sets (which ones? > obtainable where?) be necessary especially for the higher-period > halogens? I am summarizing the answers I received below. The bottom line seems to be that the more "**" and "++" the better (and hence the more "$$", I fear). Thanks to all who responded or even sent me preprints. Marc C. Nicklaus Lab. of Medicinal Chemistry e-mail: mn1@helix.nih.gov National Cancer Institute, NIH Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 Bethesda, MD 20892 ====================================================================== ANSWERS: ======== From: RSTOLOW@PEARL.TUFTS.EDU Bob Stolow We have done ab initio computations using Gaussian for 1,2-difluoroethane to find out what level of theory was adequate to reproduce the results of published gas-phase experiments. We can confirm that it is necessary to use a level of theory approaching those reported in the following articles: Wiberg, K.B.; Murcko, M.A. J. Phys. Chem. 1987, 91, 3616. Dixon, D.A.; Smart, B.E. J. Phys. Chem. 1988, 92, 2729. For 1,2-difluoroethane, we found that MP2/6-311G**//6-311G** and lower levels of theory were unsatisfactory. Diffuse functions on all atoms gave a reasonable result at the MP2/6-311++G**//6-311G** level of theory. Electron correlation cannot be neglected. Dixon also used MP2, while Wiberg used MP3/6-311++G**//6-311G*. This should give you some idea of the minimum level required for your calculations to yield reasonable results. Of course, the current state-of-the-art would use even higher levels of theory. --------------------------------------------------------------------- From: Patrick Bultinck I am just finishing some work on ethylene glycol, ethylenediamine and ethane-dithiol.... My results can be trusted now, contrary to some of my early findings which were not so good. My calculations contain : 3-21 G optimizations, 6-31++G** optimizations (full) and MP2 calculations... ----------------------------------------------------------------------- From: TOPOL@FCRFV1.NCIFCRF.GOV Igor Topol Many recepies how to calculate accurately different conformational minima including problems with gauche effects you can find in our recently published paper: T. Oie, I.A.Topol, S.K.Burt "Ab Initio and Density Functional Calculations on Ethylene Glycol", J.Phys.Chem., 98 (1994) 1121-1128. ------------------------------------------------------------------------ From: friedman@tammy.harvard.edu (Dawn Friedman) Use the best basis set you can, with plenty of polarization functions, and diffuse functions (+) would be good too, as you will be looking at systems whose resonance structures would include lots of lone pairs and possibly anions; 3-21G*+ at the minimum, but preferably 6-31G**++. Use the best basis set you can muster for the geometry optimization; energies calculated at that geometry but at a higher basis set probably won't give you much more information than you already have. If you don't reoptimize the geometry at each dihedral angle you try, your results will be deceptive, but everyone knows that by now, right? You'll want to do some post-Hartree-Fock, perhaps CISD; if you really need to try for the absolute geometry changes between conformations, you'll have to try optimizing with post-HF, but HF will give you the trends in geometry changes. If you're using Gaussian, which has it available as a keyword, the Reed-Weinhold Natural Bond Orbitals are custom-made for this sort of thing. They'll tell you which orbitals are interacting and how much (relative to other systems in the set you're looking at.) --------------------------------------------------------------------------- From: Patrick Bultinck Have a look at the following : 1/ Wiberg and Murcko, J. Phys. Chem., 1987, Vol. 91, 3616-3620 Title : Rotational barriers, 1. 1,2-Dihaloethanes 2/ Hirano et al., J; Chem. Soc. Chem. Comm., 1986 An NMR study that has as aim the study of the gauche effect among others. 3/ Wolfe, Acc. Chem. Res., Vol. 5, 1972 Must reading ... 4/ Siam et al., J. Mol. Struct., 236 (1991), 1-13 Maybe less interesting !!!! 5/ Radom et al., JACS, 95 (3), 1973, 693 Albeit a little low level calculus (but then again this is 1994, not 1973 !!) it gives a good comparison between different molecules. I think nr 1 would have to be very interesting for you, since it gives a flavour of different results with different HF-basissets, and MPx results. If you would be interested, I have some results for 6-31++G** optimizations on FCH2CH2F... in which one clearly sees that the reason for stabilisation of the G-conformer in the XCH2CH2X is governed by the relative size of the 1-el energy lowering in the G-conformer resp. to the increase of the N-N energy. -------------------------------------------------------------------------------- From: billys@chmboy.srl.ford.com (Bill Schneider) We have recently submitted a paper to JACS in which we have looked at (essentially) the gauche effect in halogenated methanols. I will drop a preprint of the paper in the mail to you. Perhaps it will be of help. [Thanks for the preprint. M.N.] ------------------------------------------------------------------------------- From: RSTOLOW@PEARL.TUFTS.EDU Bob Stolow Since the time we completed our own calculations on 1,2-difluoroethane, the following pertinent papers have appeared: Wiberg, K.B.; Murcko, M.A.; Laidig, K.E.; MacDougall, P.J. J. Amer. Chem. Soc. 1990, 94, 6956-6959. Durig, J.R.; Liu, J.; Little, T.S.; Kalasinsky, V.F. J. Phys. Chem. 1992, 96, 8224-8233. -------------------------------------------------------------------------------- From sling@euclid.chem.washington.edu Wed Jul 27 14:57:12 1994 Received: from euclid.chem.washington.edu for sling@euclid.chem.washington.edu by www.ccl.net (8.6.9/930601.1506) id OAA03356; Wed, 27 Jul 1994 14:55:07 -0400 Received: by euclid.chem.washington.edu (AIX 3.2/UCB 5.64/4.03) id AA40670; Wed, 27 Jul 1994 11:57:12 -0700 Date: Wed, 27 Jul 1994 11:57:12 -0700 From: sling@euclid.chem.washington.edu (Song Ling) Message-Id: <9407271857.AA40670@euclid.chem.washington.edu> To: CHEMISTRY@ccl.net Subject: American Physical Society Council election Please allow me to interrupt the net for a moment, for those of you who are members of APS, I urge you to vote Jen Cohen for the Council, she has been most effective in helping young scientists obtain employment in their trained fields. Thanks. From dyang@acs.ucalgary.ca Wed Jul 27 15:56:59 1994 Received: from acs7.acs.ucalgary.ca for dyang@acs.ucalgary.ca by www.ccl.net (8.6.9/930601.1506) id OAA03249; Wed, 27 Jul 1994 14:45:50 -0400 Received: from acs2.acs.ucalgary.ca by acs7.acs.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA62172; Wed, 27 Jul 1994 12:50:06 -0600 Received: by acs2.acs.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA26553; Wed, 27 Jul 1994 12:50:06 -0600 Message-Id: <9407271850.AA26553@acs2.acs.ucalgary.ca> Subject: Geometric packing on surfaces, any software available? To: chemistry@ccl.net Date: Wed, 27 Jul 94 12:50:05 MDT From: "Danya Yang" Cc: dyang@acs.ucalgary.ca (Danya Yang) X-Mailer: ELM [version 2.3 PL11x] Hello Netters, Can any one tell me where I can find a public domain or commercial software that, with visualization capability (better in 3D), models molecules packing on a solid or solvent surface. It would be even better if it can deal with curved surfaces. Thanks in advance for any suggestions. Danya From sgsrini@u.washington.edu Wed Jul 27 16:09:58 1994 Received: from hardy.u.washington.edu for sgsrini@u.washington.edu by www.ccl.net (8.6.9/930601.1506) id OAA03002; Wed, 27 Jul 1994 14:23:44 -0400 Received: by hardy.u.washington.edu (5.65+UW94.4/UW-NDC Revision: 2.30 ) id AA08010; Wed, 27 Jul 94 11:24:41 -0700 X-Sender: sgsrini@hardy.u.washington.edu Date: Wed, 27 Jul 1994 11:24:39 -0700 (PDT) From: Srinivasan Srivilliputhur Subject: Software to CALCULATE Free-Energies of Silicates. To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters- I would appreciate if any of you could give me pointers to softwares that calculate (NOT MINIMIZE) the Free-Energies of Silicates. I would like to compare the energies of 2 different structures having the same stoichiometry. Please reply to sgsrini@u.washington.edu. If there is sufficient interest, I will summarize the replies for the benefit of all the netters. Thanks a lot for your time. -Srini ------------------------------------------------------------------------------- S. G. Srinivasan email : sgsrini@u.washington.edu Graduate Student Dept. Of Mater. Sci. & Engg. University Of Washington Phone : (206)-633-1757 (H) Seattle, WA 98195 (206)-685-3851 (W) ------------------------------------------------------------------------------- From pacahil@somnet.sandia.gov Wed Jul 27 18:56:58 1994 Received: from somnet.sandia.gov for pacahil@somnet.sandia.gov by www.ccl.net (8.6.9/930601.1506) id SAA05731; Wed, 27 Jul 1994 18:04:25 -0400 Received: (from pacahil@localhost) by somnet.sandia.gov (8.6.7/8.6.6) id QAA28915 for CHEMISTRY@ccl.net; Wed, 27 Jul 1994 16:06:10 -0600 Date: Wed, 27 Jul 1994 16:06:10 -0600 From: Paul A Cahill Message-Id: <199407272206.QAA28915@somnet.sandia.gov> To: CHEMISTRY@ccl.net Subject: Pentium vs. PowerPC speeds for quantum chemistry? I'm trying to compare the capability of a 32 MB/2GB pentium system that costs about $5600 to a PowerPC based IBM RS/6000 that costs more than twice as much for the same configuration. Given that similar codes are now available for both, does anyone have *real* tests of computational chemistry codes (speed, ease of use). Will the PowerPC as implemented by IBM really provide twice the performance (both are 66 MHz). Thanks for your help. Paul Cahill MS 0368 Sandia National Laboratories Albuquerque, NM 87185-0368 pacahil@somnet.sandia.gov From raman@bioc01.uthscsa.edu Wed Jul 27 19:56:59 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.9/930601.1506) id TAA06267; Wed, 27 Jul 1994 19:39:35 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Wed, 27 Jul 1994 18:43:19 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA24918; Wed, 27 Jul 94 18:40:47 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9407272340.AA24918@bioc01.uthscsa.edu> Subject: Re: CCL:Geometric packing on surfaces, any software available? To: dyang@acs.ucalgary.ca (Danya Yang) Date: Wed, 27 Jul 1994 18:40:46 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <9407271850.AA26553@acs2.acs.ucalgary.ca> from "Danya Yang" at Jul 27, 94 12:50:05 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1253 Danya: > Can any one tell me where I can find a public domain or commercial software > that, with visualization capability (better in 3D), models molecules packing > on a solid or solvent surface. It would be even better if it can deal with > curved surfaces. May I suggest that you contact Mike Connolly (connolly@netcom.com) who distributes the Molecular Surface Package (MSP). I believe that MSP can be customized to do what you are asking for. I am unable to suggest other packages without knowing additional details. Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From jxh@ibm12.biosym.com Wed Jul 27 19:59:48 1994 Received: from bioc1.biosym.com for jxh@ibm12.biosym.com by www.ccl.net (8.6.9/930601.1506) id TAA06258; Wed, 27 Jul 1994 19:38:28 -0400 Received: from ibm12.biosym.com by bioc1.biosym.com (5.64/0.0) id AA00725; Wed, 27 Jul 94 16:39:01 -0700 Received: by ibm12.biosym.com (AIX 3.2/UCB 5.64/4.03) id AA21345; Wed, 27 Jul 1994 16:39:00 -0700 Date: Wed, 27 Jul 1994 16:39:00 -0700 From: jxh@biosym.com (Joerg Hill) Message-Id: <9407272339.AA21345@ibm12.biosym.com> To: CHEMISTRY@ccl.net Subject: CCL: Re: Pentium vs. PowerPC speeds for quantum chemistry? > I'm trying to compare the capability of a 32 MB/2GB pentium system that > costs about $5600 to a PowerPC based IBM RS/6000 that costs more than > twice as much for the same configuration. Given that similar codes are > now available for both, does anyone have *real* tests of computational > chemistry codes (speed, ease of use). Will the PowerPC as implemented > by IBM really provide twice the performance (both are 66 MHz). I think it should first be clarified that the PowerPC and the IBM RS/6000 CPU are two similiar (binary compatible), but nevertheless different things. The IBM RS/6000 CPU is the first implementation of IBM's so-called POWER architecture (Performance Optimization With Enhanced RISC). It consists of five chips. The PowerPC (chip) is a single chip microprocessor which was developed using the existing IBM RS/6000 CPU, but squeezing it onto one chip. Naturally, this could be done only by leaving out some of the features (the PowerPC instruction set is only a subset of the RS/6000 CPU ones). So the PowerPC chip is significant slower than the IBM RS/6000 CPU. Currently, I can provide only data for a small benchmark programme, which has been proven in the past that it reflects the real performance of com- putional chemistry codes quite good. When I get an ab initio programme running on my Pentium, I can provide more information. c c Computer Time % Compiler/Option c sec VAX c------------------------------------------------------------------------------- c CRAY Y-MP2E/164 0.00641 28081 cf77 -Zv -Wf -o scalar -o vector c IBM RISC 6000/370 0.015 12000 f77 -O c CRAY 1 0.022 8182 c SG Indigo (R4000) 0.025 7200 f77 -O2 c IBM RISC 6000/350 0.026 6923 f77 -O c IBM RISC 6000/550 0.026 6923 f77 -O c IBM RISC 6000/340 0.032 5625 f77 -O c IBM RISC 6000/530 0.043 4186 f77 -O c IBM RISC 6000/320H 0.044 4091 f77 -O c IBM RISC 6000/320 0.053 3396 f77 -O c IBM 3090 0.059 3051 Optimization compiler c SG Indigo (R3000) 0.07 2571 -O3 c SG Indigo (R4000) 0.073 2466 f77 c Pentium (60 MHz) 0.08 2250 Linux f2c + gcc -O c Joerg-R. Hill -------------------------------------------------------------------------------- Dr. Joerg-Ruediger Hill | Every attempt to employ mathematical methods in the Biosym Technologies, Inc. | study of chemical questions must be considered pro- 9685 Scranton Road | foundly irrational and contrary to the spirit of San Diego, CA 92121-3752 | chemistry ... If mathematical analysis should ever USA | hold a prominent place in chemistry - an aberration | which is happily almost impossible - it would Phone (619) 546-5508 | occasion a rapid and widespread degeneration of Fax (619) 458-0136 | that science. E-mail jxh@biosym.com | A. Comte, 1830 -------------------------------------------------------------------------------- The opinions expressed in this message are my personal opinions and no offical statements of Biosym Technologies, Inc. For informations about Biosym products send mail to: rcenter@biosym.com. -------------------------------------------------------------------------------- From jle@world.std.com Wed Jul 27 20:57:00 1994 Received: from ftp.std.com for jle@world.std.com by www.ccl.net (8.6.9/930601.1506) id UAA06574; Wed, 27 Jul 1994 20:25:35 -0400 Received: from world.std.com by ftp.std.com (8.6.8.1/Spike-8-1.0) id UAA20044; Wed, 27 Jul 1994 20:26:31 -0400 Received: by world.std.com (5.65c/Spike-2.0) id AA18579; Wed, 27 Jul 1994 20:26:29 -0400 Date: Wed, 27 Jul 1994 20:26:29 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199407280026.AA18579@world.std.com> To: chemistry@ccl.net Subject: PowerPC vs. RS/6000 (RIOS1) comparison... Recently, Joerg-Ruediger Hill posted... The PowerPC (chip) is a single chip microprocessor which was developed using the existing IBM RS/6000 CPU, but squeezing it onto one chip. Naturally, this could be done only by leaving out some of the features (the PowerPC instruction set is only a subset of the RS/6000 CPU ones). So the PowerPC chip is significant slower than the IBM RS/6000 CPU. He also included some run-times which idn't seem to include PowerPC times (the RS/6000 25T workstation)... I don't think the blanket statement that the PowerPC chip is significantly slower than the RS/6000 is correct - certainly not against the older members of the family. Remember that the PowerPC chip runs at a higher MHz rating than many/most of the RIOS1 family (i.e. all but the 390/590 recently developed - the RIOS2 chipset). This has a noticeable effect on things like graphicx/X and compilations, things which aren't terribly dependent on pipelined Real*8 operations. While I don't have the exact numbers to back it up, I expect that the 25T workstation (with the PowerPC/601 chip in it) is essentially the same as an R4000 indigo (the older 50/100 chip?). This would make it about the x50 or x60 RIOS1 RS/6000 in speed. Perhaps some of the hardware folks getting this net would be so kind to publish Linpack 100x100 or SPECfp92 numbers for the pertinent IBM machines (like the 550, 370/37T, 25T, etc.).). Joe Leonard jle@world.std.com Please direct IBM/SGI comparison flames to me, not the net (or to /dev/null :-) From PHTH1@cc.newcastle.edu.au Wed Jul 27 21:57:00 1994 Received: from BROLGA.NEWCASTLE.EDU.AU for PHTH1@cc.newcastle.edu.au by www.ccl.net (8.6.9/930601.1506) id VAA06954; Wed, 27 Jul 1994 21:32:02 -0400 Received: from cc.newcastle.edu.au by cc.newcastle.edu.au (PMDF V4.3-8 #6545) id <01HF8KG8NYHS9APMX7@cc.newcastle.edu.au>; Thu, 28 Jul 1994 11:32:47 +1000 Date: Thu, 28 Jul 1994 11:29:10 +1000 From: Tony Dyson Subject: CCL: RS/6000 PowerPC To: chemistry@ccl.net Message-id: <01HF8L74AY3O9APMX7@cc.newcastle.edu.au> MIME-version: 1.0 Content-transfer-encoding: 7BIT My RS/6k 250 has the 601 cpu in it as far as I know! So the question re comparing PowerPC RS/6k to pentium is fair, the 250 has a single-chip cpu running at 66MHz like the pentium systems. However it is important to ask what operating system you plan to use for the pentium system. Any benchmark will be dependent on this, as far as I understand it. If you have the pentium system available, we could probably compare timings for, say, one of the standard Gaussian-92 test jobs. Tony --------------------------------------------------------------------- Anthony J. Dyson Surface Theory Group Dept. of Physics, University of Newcastle Australia phth1@cc.newcastle.edu.au ---------------------------------------------------------------------