From afj@DrMemory.nuc.ucla.edu Mon Sep 26 03:00:30 1994 Received: from DrMemory.nuc.ucla.edu for afj@DrMemory.nuc.ucla.edu by www.ccl.net (8.6.9/930601.1506) id CAA08703; Mon, 26 Sep 1994 02:01:21 -0400 Received: by DrMemory.nuc.ucla.edu id AA22016 (5.65c/IDA-1.4.4 for CHEMISTRY@ccl.net); Sun, 25 Sep 1994 22:59:20 -0700 Date: Sun, 25 Sep 1994 22:59:20 -0700 From: Andy Jacobson Message-Id: <199409260559.AA22016@DrMemory.nuc.ucla.edu> To: CHEMISTRY@ccl.net Subject: RE: CCL:the first C in CCL... nash@chem.wisc.edu said: >Does anyone know if a chemistry (general) mailing list exists? There is a general purpose organic chemistry mailing list: Cheers, -A.J. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Andy Jacobson Dept. Pharmacology / Div. Nuclear Medicine and Biophysics CHS B2-086 UCLA School of Medicine Phone:310-825-8584 Los Angeles, CA 90024-6948 Fax: 310-825-4517 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From brower@myst.mbt.com Mon Sep 26 09:00:40 1994 Received: from myst.mbt.com for brower@myst.mbt.com by www.ccl.net (8.6.9/930601.1506) id IAA11482; Mon, 26 Sep 1994 08:54:38 -0400 Received: by myst.mbt.com (920330.SGI/920502.SGI.AUTO) for CHEMISTRY@ccl.net id AA09071; Mon, 26 Sep 94 08:53:47 -0400 Date: Mon, 26 Sep 1994 08:53:00 -0400 (EDT) From: "Lynn E. Brower" Subject: Re: CCL:please stop! To: The Man Cc: CHEMISTRY@ccl.net In-Reply-To: <9409231958.AA15988@luigistoaster.pds.charlotte.nc.us> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 23 Sep 1994, The Man wrote: > Dear listserv members: [part of entry deleted] > > Thank you all for reading all of my gibberish. I sincerely hope nobody > took anything that I said the wrong way. I did not mean to offend anyone's > intlligence by asking a question that was too simple. I have always been > taught that there are no stupid questions. That is why I felt comfortable > asking all of you a simple one. That is, until now. I feel that I have learned > that there ARE some stupid questions, and I just asked two of them. I am > thankful to those who mailed me responses, and I hope that those people > will agree with me (at least a little bit) that this listserv is a very > valuable learning tool. You just discouraged another young chemist from > learning what you all already know and take for granted. > > I am sorry I wasted your time. > > Dan > > mulcrone@luigistoaster.pds.charlotte.nc.us > My time was not wasted and I shall use some more bandwidth to reply to the above paragraph. You have been taught correctly, there are no stupid questions. There are questions with simple answers or difficult answers. Do not stop asking questions on the net or in class and do not be stopped by people who would imply that your questions are stupid. It is clear from your message that you understand the power of the network as a source of information and you are learning how to navigate. All of us here have to learn where the proper connection for our questions exists on the net. Remember the responses you have received and the locations for new information connections. And when the time comes share your knowledge with another newcomer and point them, gently with respect, to the right connection. Lynn replies and comments direct to brower@myst.mbt.com only. thank you From bob.zinn@chemgate.chem.lsu.edu Mon Sep 26 10:00:48 1994 Received: from chrs1.chem.lsu.edu for bob.zinn@chemgate.chem.lsu.edu by www.ccl.net (8.6.9/930601.1506) id JAA12321; Mon, 26 Sep 1994 09:29:54 -0400 Received: from chemgate.chem.lsu.edu by chrs1.chem.lsu.edu (AIX 3.2/UCB 5.64/4.03) id AA27362; Mon, 26 Sep 1994 08:27:59 -0500 Received: from cc:Mail by chemgate.chem.lsu.edu id AA780593436 Mon, 26 Sep 94 08:30:36 cst Date: Mon, 26 Sep 94 08:30:36 cst From: bob.zinn@chemgate.chem.lsu.edu (bob zinn) Encoding: 612 Text Message-Id: <9408267805.AA780593436@chemgate.chem.lsu.edu> To: CHEMISTRY@ccl.net Subject: CCL: purpose. It is not obvious There is no way that an initial posting by a first time user can be expected to comply with the purpose of the list. Adding a line to the Administrivia, giving the purpose of the list would possibly reduce the number of inappropriate postings. Something like: Please observe: list restricted to Computational Chemistry and related topics. -bz- Robert R. Zinn ("bz"), Programmer/Analyst Department of Chemistry Louisiana State University Baton Rouge, LA. 70803-1804 (504) 388-5381 audio (504) 388-3458 (FAXual) bob.zinn@chemgate.chem.lsu.edu chsec@lsumvs.sncc.lsu.edu From fant@rocketman.ncifcrf.gov Mon Sep 26 10:04:34 1994 Received: from fcs280s.ncifcrf.gov for fant@rocketman.ncifcrf.gov by www.ccl.net (8.6.9/930601.1506) id JAA12326; Mon, 26 Sep 1994 09:30:00 -0400 Received: from rocketman.ncifcrf.gov by fcs280s.ncifcrf.gov (4.1/NCIFCRF-3.0/AWF-2.0) id AA20791; Mon, 26 Sep 94 09:28:37 EDT Received: by rocketman.ncifcrf.gov (931110.SGI/930416.SGI) for @fcs280s.ncifcrf.gov:chemistry@ccl.net id AA08612; Mon, 26 Sep 94 09:31:37 -0400 From: "Andrew D. Fant" Message-Id: <9409260931.ZM8610@rocketman> Date: Mon, 26 Sep 1994 09:31:36 -0400 In-Reply-To: "Bill Laidig" "CCL:BS/MS Computational Chemists?" (Sep 23, 11:07am) References: <9409231107.ZM1179@morpheus.pg.com> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "Bill Laidig" , chemistry@ccl.net Subject: Re: CCL:BS/MS Computational Chemists? Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Sep 23, 11:07am, Bill Laidig wrote: > I was wondering if there are any resources on the Internet for locating BS/MS > chemists interested in computational chemistry? I have periodically looked > through the positions.offered and positions.wanted files on > www.ccl.net, but these are almost always by and for Ph.D.'s. I don't > know if any other readers of CCL are in the same situation, but our > computational chemists typically hire BS level scientists (chemists, physicists > or computational people) as Research Associates (BTW - I am currently looking > to hire a BS chemist). After training such people do a lot of our day to day > research: they run jobs (in my case usually G92 or CHARMm), process data > using PC/Mac software such as Excel, assist in interpreting the data, etc. > Unfortunately, the RA's we select usually know next to nothing about > computational chemistry. This means that training is a lengthy process and we > have a 6 mo. - 1 yr. minimum period where these people make little > contributions. What I would like is to be able to find individuals who have > some molecular modeling background and/or are eager to work in this area. While I can't speak to resources for specifically locating BS/MS computational chemists (except shameless self-promotion) 8-), I would like to try and egg this discussion forward, since it is on a topic near and dear to my heart. Bill Laidig mentioning that he actually used BS/MS staff in computational chemistry research raises several questions that I would like to get opionions from other researchers in the area on. First of these is "How Many research facilities actually utilize non-Ph.D. computational chemists?". Speaking from the experience of trying to find work in the field 3 years ago, I would suspect that it is not a large number. Between the job offers I have had, and the ads that I have seen in C&E News and/or on the net, I can count the number of listed positions on both hands and still have fingers to spare. Most of those that I have seen were for jobs doing something besides science, but that required a knowledge of the applications software for contractual or political reasons. This raises the question of what role a BS/MS computational chemist should fill. Is it the consensus that they should act as "force multipliers" by expanding the capacity of the senior scientist to generate and examine results, or do you assign them to systems adminstration and code development/support activities? I am torn on this one, since on one hand, I went and got my degree because I wanted to be a chemist and do science, but on the other hand, having a decent amount of unix "guru" knowledge is what has kept my employed, and I think that if you are going to practice computational chemistry, you should be as comfortable around the computer as an analytical chemist is around their particular instrument of choice. Lastly, there is the question of time availible for BS training in the field. While most departments have someone who uses computational methods in their research, few programs, that I know of, make computational chemistry a priority for their undergraduates (excepting summer programs such as at UGA that are there to encourage students into the field). In the usenet news group, sci.chem, there has been a discussion of the math skills needed to teach P-chem to chemistry majors, and the consensus seems to be that unless the major starts with a year of calculus from high-school, they will probably be missing the math background to really understand p-chem as it is taught. This rubs off on teaching computational chemistry, since most students are introduced to compuational chemistry (excepting some enlightened programs that offer some black-box exercises during organic chemistry lab) in the second semester of physical chemistry. From my, admittedly limited, experience in trying to teach undergraduates how to run mopac and/or gaussian, I also don't think most students are ready to accept the concept of defining a molecule as a set of cartesian triples or as a connected z-matrix until they have had to face the other mathematical leaps of faith that p-chem requires. ( such as the repeated question I am asked about mopac input "How do you tell the program what atoms are bonded to each other if all you give is a bunch of points?") Finally, if you expect these students to know something about computers, that adds at least one CS type course to the recommended load for the major, which is already one of the heaviest at most universities. I didn't mean to be this long winded, but I think the previous message brings up several good questions that need to be addressed. One final thing to toss into the pot: "Will chemistry departments teach real amounts of computational chemistry to their non-graduate school bound students as long as there are limited openings in the field, and there are so many other demands on the curriculum?" Anyway. I'll leave it at this, and sit back and hope that someone else is interested in this discussion. Andy FWIW: I got into computational chemistry not because of a class in it, but because I was working on a lab project, and there weren't any good ways to get a good handle on some points of stereo-specificity with the experimental tools at hand. Andrew D. Fant Applications Analyst fant@ncifcrf.gov NCI-Frederick Cancer Research Facility Biomedical Supercomuting Center (301)846-5764 Me?!? Have an official NCI or Dyncorp Opinion? HAH! "I'm just one too many mornings and a thousand miles behind" -- B. Dylan From batista@chem.bu.edu Mon Sep 26 11:00:37 1994 Received: from chem.bu.edu for batista@chem.bu.edu by www.ccl.net (8.6.9/930601.1506) id KAA13584; Mon, 26 Sep 1994 10:26:12 -0400 Received: by chem.bu.edu (8.6.9/BU_Server-1.1) id KAA08326; Mon, 26 Sep 1994 10:27:09 -0400 Date: Mon, 26 Sep 1994 10:27:09 -0400 From: batista@chem.bu.edu (Victor Batista) Message-Id: <199409261427.KAA08326@chem.bu.edu> To: chemistry@ccl.net Subject: I2 singlet excited states PES Cc: batista@chem.bu.edu Dear sir or madam, Do you know of any good reference for potential energy surfaces of the first five singlet excited states of I2 molecule ?. I've seen a set of articles by P.J. Hay and T. H. Dunning Jr (JCP 1985), where they show nice PES's (for example for Xe2+) using ECP's. Do you know of similar calculations for I2, or if there is any program in public domain for doing ECP POL-CI calculations ?. I tried to use Gaussian_92 with the same ECP but results were quite different. Thank you very much, Victor S. Batista. From brian@bert.chem.wsu.edu Fri Sep 23 00:21:56 1994 Received: from serval.net.wsu.edu for brian@bert.chem.wsu.edu by www.ccl.net (8.6.9/930601.1506) id XAA25858; Thu, 22 Sep 1994 23:36:29 -0400 Received: by serval.net.wsu.edu; id AA07607; Thu, 22 Sep 1994 20:36:26 -0700 Received: by bert.chem.wsu.edu (AIX 3.2/UCB 5.64/4.03) id AA17941; Thu, 22 Sep 1994 20:36:38 -0700 From: brian@bert.chem.wsu.edu (Brian W. Beck) Message-Id: <9409230336.AA17941@bert.chem.wsu.edu> Subject: Zeolites: Summary of Responses To: CHEMISTRY@ccl.net Date: Thu, 22 Sep 1994 20:36:37 -0800 (PDT) ================ [ --- Warning, the message was redirected to jkl@ccl.net by the script ---] [ --- as too long (> 50kB). I made it smaller by cutting "headers and ---] [ --- footers". Sorry for intruding... jkl@ccl.net ---] ================ As it now seems that the replies to my questions about zeolite modelling have died off, I thought I'd post a summary of the responses. -Brian Beck ============================= CUT HERE ====================================== >From brian Thu Sep 15 13:16:52 1994 Subject: General:Computational Work on Zeolites To: CHEMISTRY@ccl.net Date: Thu, 15 Sep 1994 13:16:52 -0800 (PDT) I have a friend who wants to do some computational work on zeolites and other Al2O3-SiO2 compounds. My experience is more biophysical, so I thought I'd query members of CCL to see if anyone has done work on such systems, and what software packages they have used. I will summarize replies. -Brian W. Beck brian@bert.chem.wsu.edu ------------------ From: "Peter Shenkin" Date: Thu, 15 Sep 1994 17:31:09 -0400 To: brian@bert.chem.wsu.edu (Brian W. Beck) Subject: Re: CCL:General:Computational Work on Zeolites I believe Biosym sells a module for just this purpose. -P. ------------------ Date: Thu, 15 Sep 1994 14:44:57 -0700 From: jxh@biosym.com (Joerg Hill) To: brian@bert.chem.wsu.edu Subject: CCL:General:Computational Work I have used Turbomole/Insight/Discover for simulations of zeolites. For details look at: Hill, J.-R. and Sauer, J.: JPC 98 (1994) 1238. Joerg-R. Hill ---------------------- Date: Fri, 16 Sep 94 08:52:52 FST From: "Sophie CREUZET ((33-1-40-01-56-39))" To: brian@bert.chem.wsu.edu Subject: Re:Computational Work on Zeolites I guess you should contact Earl Evlett, Emile Kassab or Marcel Allavena (if they don't have already sent you a message). Their e-mail address are : ev at dim.jussieu.fr, ek at dim.jussieu.fr. They've done a lot of work on Zeolites. Hope this help, Sophie Creuzet Chemistry Support IBM-France ---------------------- Date: Fri, 16 Sep 1994 11:17:12 +0100 To: brian@bert.chem.wsu.edu (Brian W. Beck) From: pgeerlin@vub.ac.be Subject: Re: CCL:General:Computational Work on Zeolites brian, We have done some work on zeolites ranging from IR to reactivity-studies using semi empirical and ab initio calculations. I propose to do a bibliography on P. Geerlings and W. Mortier (1985- ). If you need any more help or if you are interested in some reprints, feel free to contact me. Wilfried Wilfried Langenaeker - Free University of Brussels - Belgium ------------------- From: mbdtssg Subject: zeolite calculations To: brian@bert.chem.wsu.edu Date: Fri, 16 Sep 1994 11:09:43 +0100 (BST) Brian, in response to your question about zeolite calculations, it depends what your friend is trying to obtain. I cannot really comment with any great authority on MM/MD calculations as my interests are purely in the ab initio area. However, zeolite-specific force fields have been determined by Kramer et al (Phys. Rev. B, 1991, 43, 5068) and more recently by Sauer, which may be of interest. In the field of ab initio/dft studies, you can take your pick from the usual range of codes - Gaussian, Gamess (uk or us), Turbomole, Dmol, Dgauss etc. etc., all of which have been used to some degree, usually for small cluster or cluster-substrate studies. At the top end of the spectrum (cost wise), periodic Hartree-Fock studies are best performed with CRYSTAL 92, which is available from QCPE. A good place to start looking is a review by Sauer (J. Chem. Rev. 1989, 89, 199) - perhaps a little long in the tooth, but an excellent background. If you can give me more information on your friend's interests, I will be happy to supply you with further information. Steve Greatbanks ( steve.greatbanks@man.ac.uk ) ---------------------- Date: Fri, 16 Sep 1994 08:33:14 -0400 From: Fagerburg_David To: brian@bert.chem.wsu.edu Subject: zeolite question on CCL Cc: fagerbur@emn.com I am including a summary file that I compiled from responses to a zeolite modeling question I asked on the CCL net some time ago that you might find useful in deciding on Zeolite modeling. Hope this helps. Happy computing! From: Mike_Stapleton@msicam.co.uk" "Mike Stapleton" 11-JUN-1993 14:24:24.95 To: Dave Fagerburg Subj: CERIUS for ZEOLITES Date: 11 Jun 1993 15:42:03 U From: Mike Stapleton Subject: CERIUS for ZEOLITES To: Dave Fagerburg Cc: Foti Christodoulos , don gregory , PCoulter@msicam.co.uk, chris ruggles , Cathy Terwedow Dave Fagerburg, Eastman Chemical Co. Kingsport, TN Dear Dave, I have recently been forwarded an e-mail message originating from you with regard to zeolite force fields and the applicability of CERIUS. I received this message from a number of my colleagues at MSI's head office in Burlington, MA and from several CERIUS users. As Product Manager for CERIUS, I would like to take this opportunity to address the questions you originally raised and to comment on some of the points that have been made by some of the "netters". The version of CERIUS which you have installed at the moment is CERIUS 3.1. We are currently in the process of shipping CERIUS 3.2 to all customers. I think it therefore makes sense to refer to the functionality in CERIUS 3.2 in answering your questions as you will shortly have this version to work with. The first major point to make is that all the applications in CERIUS which require energy calculations take their force field information from the Open Force Field. This is a unique environment for creating and implementing force fields for any type of material, which to the best of my knowledge is only available from Molecular Simulations in CERIUS. Let me support these statements by considering the published force fields provided with CERIUS and the development environment of the Open Force Field separately. (a) There are a number of published force fields provided with CERIUS, including: Dreiding: A generic force field for molecular simulations SL Mayo, BD Olafson, WA Goddard III, J.Phys.Chem. 94(26), 8897, 1990 Universal Force Field: A full periodic table force field for molecular mechanics and molecular dynamics simulations AK Rappe, CJ Casewit, KS Colwell, WA Goddard III, WM Skiff, JACS 114, 10024, 1992 CJ Casewit, KS Colwell, AK Rappe, JACS 114, 10035, 1992 CJ Casewit, KS Colwell, AK Rappe, JACS 114, 10046, 1992 Force fields for silicas and aluminophosphates based on ab initio calculations BWH van Beest, GJ Kramer, RA van Santen, Phys.Rev.Lett. 64(16), 1955, 1990 A consistent molecular mechanics force field for all-silica zeolites E de Burchart, VA Verheij, H van Bekkum, B van de Graaf, Zeolites 12, 183, 1992 You will note that there are both general force fields (Dreiding and Universal) and specifically parameterized force fields for zeolites and aluminophosphates (van Beest and Burchart). All these force fields can be selected and applied at the press of a button. They can form the basis of Monte Carlo simulations, energy minimizations or molecular dynamics simulations of isolated or 3D periodic structures with the usual choice of long range corrections including the Ewald summation. Additionally, parameter files are provided which consist of the combined Burchart/Dreiding and the combined Burchart/Universal force fields for modeling applications of organic molecules in framework materials. (b) Developing and implementing force fields in CERIUS One of the major strengths of the Open Force Field environment within CERIUS is that it provides the user with the ability to choose from a list of functional forms for all the terms in a force field, enter parameters through the GUI and save the information to a file. In this way novel parameterizations can be performed and as new force fields appear in the literature, these can often be entered straight into CERIUS. For example, Molecular Simulations has made a significant investment over the last six months extending the work of: DM Razmus and CK Hall, J AIChE, 37(5) 769, 1991: Prediction of gas adsorption in 5A zeolites using Monte Carlo simulation. This project has resulted in a new parameterization for simple gases in zeolite structures which is provided in a force field file with CERIUS 3.2. Entering three site models from the literature for gases like nitrogen and oxygen to accurately represent the coulombic interactions was made easy with the Open Force Field GUI. A reference was made by one of the "netters" to the work of JB Nicholas, AJ Hopfinger, FR Trouw and LE Iton, J. Am. Chem. Soc. 113, 4792, 1991: Molecular modeling of zeolite structure. 2. Structure and Dynamics of Silica Sodalite and Silicate Force Field. This is a good example of a published force field which is not provided with CERIUS, but which could be applied using the Open Force Field with just a single modification. The modification is simply that the authors apply a switching function to the torsion potential when the Si-O-Si angle lies between 170 and 180 degrees. There is currently no way of doing this in CERIUS. I hope that the above information is useful to you and convinces you that there are well validated force fields for many materials including zeolites available with CERIUS. If you have any questions please do not hesitate to contact me (e-mail: mikes@msicam.co.uk) or Dr. Fotios Christodoulos (Product Development Scientist at MSI Cambridge: e-mail: foti@msicam.co.uk) who provided me with some of the references. I would appreciate it if you would forward this to the "netters" and if possible, arrange for my e-mail address to be added to the distribution list. Best regards, Dr. Mike Stapleton CERIUS Product Manager ------------------------------ From: d3g359@rahman.pnl.gov 4-JUN-1993 12:14:41.96 To: fagerbur@Kodak.COM Subj: zeolites Date: Fri, 4 Jun 93 09:04:34 -0700 From: d3g359@rahman.pnl.gov Subject: zeolites To: fagerbur@Kodak.COM Hi, I noticed that my name came up on your search for material on modeling zeolites. I have done a lot of work in this area, both classical and quantum mechanical. I have a program that does MD, energy minimizations, and normal mode calculations of zeolites with a force field I developed. If you are interested, send me your address and I will send you some papers. You can also call if you like. John Nicholas John Nicholas Pacific Northwest Lab Richland, WA 99352 (509) 375-6559 jb_nicholas@pnl.gov ------------------------ From: bobf@MSI.COM" "Bob Funchess" 4-JUN-1993 10:11:58.78 To: fagerbur@Kodak.COM CC: Subj: Re: Zeolite work From: Bob Funchess Date: Fri, 4 Jun 1993 10:11:06 -0400 Organization: Molecular Simulations Inc. Phone: (617) 229-9800 ext. 202 To: fagerbur@Kodak.COM Subject: Re: Zeolite work Dave, There's some work going on right now in the Cambridge development office to validate the force field in Cerius for zeolites; I believe there's actually a paper in the works on it. If you send me your address, I'll have them send you a copy (or you could request it by email from support@msicam.co.uk). Bob Funchess --------------------- From: ng434@sica.pnl.gov" 21-MAY-1993 09:52:41.07 To: fagerbur@Kodak.COM CC: Subj: Re: Zeolite molecular modeling Date: Fri, 21 May 93 06:50:03 PDT From: ng434@sica.pnl.gov Subject: Re: Zeolite molecular modeling To: fagerbur@Kodak.COM Dave, I noticed your request on the chemistry bulletin board and forwarded it to a colleague, John Nicholas, who shares your interest in molecular modeling of zeolites. John's program, IDEAZ, was developed for such purposes. He may already have contacted you. If not, his e-mail address is "jb_nicholas@pnl.gov". In collaboration with John, I have used density functional methods to study the properties of zeolite cluster models with a variety of different substituents (e.g., Al, B, Ga, Fe, etc.). I would also be interested in receiving a summary of the responses to your query to the net. Mark Stave Mark S. Stave, PhD Internet: ms_stave@pnl.gov ----------------- From: rao@portal.vpharm.com" "Govinda Rao" 17-MAY-1993 17:49:03.10 To: fagerbur@Kodak.COM Subj: Zeolite modeling My friend, S. Yashonath has published several papers on modeling diffusion in zeolites in J. Phys. Chem. and Nature. I hope this helps you. B. Govinda Rao rao@vpharm.com -------------- From: teppen@soilchem.uark.edu" 17-MAY-1993 16:40:30.92 To: fagerbur@Kodak.COM Date: Mon, 17 May 1993 15:41:14 -0500 From: teppen@soilchem.uark.edu To: fagerbur@Kodak.COM Subject: Zeolite modeling Dr. Fagerburg: I am a graduate student in soil chemistry who is trying to model soil clays, which are aluminosilicates rather similar to zeolites in many ways. I ran into your same problem two years ago when I tried to use MSI's Quanta/Charmm to model inorganics. Therefore my dissertation work is in development of an effective parameter set, though I have a long way to go. I have looked hard in the literature, but I have yet to find a tested "force field" that includes valence terms such as bond stretches, bends, and torsions. However, there has been a lot of work in development of zeolite force fields using nonbonded interactions, sometimes with inclusion of Si-O-Si bending terms. Some relevant citations to get you started are: 1992: J. Chem. Soc., Chem. Commun. 1992:879 J. Am. Chem. Soc. 114:7198 Chem. Phys. Lett. 188:320 1991: J. Phys. Chem. 95:4038 J. Am. Chem. Soc. 113:6435 J. Chem. Soc., Faraday Trans. 87(13):1947-1970 (three articles). Hope this helps, and I'll let you know if I find something really excellent. Also, I intend to use Cerius too, and if I achieve a decent parameter set I will tell you about it. One more thing: Quanta/CHARMm does come with Si-O and Al-O parameters. They are inadequate for clays, as Al is usually octahedrally coordinated, but they may be adequate for zeolites. They are proprietary, but perhaps your company has Quanta? Sincerely, Brian Teppen Graduate Assistant University of Arkansas teppen@soilchem.uark.edu -------------------- From: randy@pylos.cchem.Berkeley.EDU" "Randall Snurr" 17-MAY-1993 16:07:56.05 To: fagerbur@Kodak.COM CC: randy@pylos.cchem.Berkeley.EDU Subj: Zeolite modelling Dave, I'm not sure whether you are interested in simulating the zeolite itself or sorbate molecules inside a zeolite. I know much more about the latter, but I can give you some suggestions of references for both areas. "Introduction to Zeolite Science and Practice" Ed. by H. van Bekkum, E.M. Flanigen, and J.C. Jansen Chapter 9 "Introduction to Zeolite Theory and Modelling" by R.A. van Santen, D.P. De Bruyn, C.J.J. den Ouden, and B. Smit This chapter covers both areas and has lots of references. On simulations of zeolite structures (e.g. examining relative stability), I would suggest looking for papers by R.A. van Santen C.R.A. Catlow J. Sauer (quantum calculations) For simulations of sorbates inside zeolites, I could recommend the following from our group here at Berkeley: R.L. June, A.T. Bell, D.N. Theodorou "Prediction of low occupancy sorption of alkanes in silicalite," J.Phys.Chem. 1990, 94, 1508. "Molecular dynamics study of methane and xenon in silicalite" J.Phys.Chem. 1990, 94, 8232. "Transition-state studies of xenon and SF_6 diffusion in silicalite" J.Phys.Chem. 1991, 95, 8866. "Molecular dynamics studies of butane and hexane in silicalite" J.Phys.Chem. 1992, 96, 1051. R.Q. Snurr, R.J. June, A.T. Bell, D.N. Theodorou "Molecular simulations of methane adsorption in silicalite" Molec. Simulation 1991, 8, 73. I also have some work on aromatics in silicalite almost written up. These of course have references to the other work in the field of adsorption and diffusion in zeolites, so you could go from there. I've also been told that Biosym has spent a lot of time refining their potentials for their simulation software for zeolites, but I don't know any specifics. I hope this is helpful. Randy Snurr randy@pylos.cchem.berkeley.edu ----------------- From: rs0sjf@rohmhaas.com" "Dr. Susan Fitzwater" 17-MAY-1993 15:56:50.53 To: fagerbur@Kodak.COM Subj: Zeolite Stuff Hi, this is Susan Fitzwater from Rohm and Haas, I think I am rs0sjf@rohmhaas.com. I got your message via Tom Pierce, also of Rohm and Haas. I looked into zeolite modeling a couple of months ago. There is a compendium edited by C. R. A. Catlow, Modeling of Structure and Reactivity of Zeolites, which has a couple of interesting articles on what you use for charges, which for me is the big question since I figure the charge-charge interaction should swamp everything. I can't quite bring myself to do what I think of as the dumbo charge partitioning, ie oxygens -2, silicon +4, aluminum +3. There is an article in there on STO-3G charges which I think come out to around silicon +1.5 aluminum +1.3 oxygens -.8. Interestingly enough this is close to what you get if you cut out a section of a CERIUS zeolite structure and run charge equilibration on it. There is another article in the Catlow book saying that partial charges vs. dumbo charges doesn't make much difference which I find hard to believe but who knows. Also there is someone at Air Products who is running density functional calculations on zeolites which is probably the way to go to get good charges. I can't remember his name, but I'm practically sure he was doing it with someone from Cray Research so a call there might turn up some information. If you wanted to try a DFT run yourself you could probably get a copy of dMol from Biosym for a months' trial. I have this in now on trial and it seems pretty fast, ie doing zeolites with it is probably not out of the question, especially since you could take advantage of symmetry. I also tried dGauss at MSC last year, which was fast and gave interesting results but I had to pay for the Cray time, and the way they wrote the agreement I had to spend around $8K minimum. This is still cheaper than dMol but you just get runs, you don't get the program forever. On CERIUS: I presume you are using the Universal Force Field. I ran into Tony Rappe, its major developer, at the ACS meeting and according to him the CERIUS implementation is faulty. So UFF may be okay for zeolites but what's in CERIUS may not be okay for zeolites. From our experience, mostly with POLYGRAF, MSI has major quality control problems. So CERIUS may be okay but I wouldn't bet too much on it. Also, I had CERIUS in for a month trial and looked at zeolites a little and as I recall there weren't any charges in the zeolite database. Well, that's all I know. If you come up with anything else interesting I'd like to hear about it. ------------ From: doherty@msc.edu" "David C. Doherty" 17-MAY-1993 10:31:29.45 To: fagerbur@Kodak.COM Subj: Re: Zeolite molecular modeling >Hi netters! > I would like to find out who out there might be working in the area of >getting good models of zeolites. Our company has recently purchased MSI's >Cerius software which claims to do zeolites. I have, in looking into it >just a bit, however, found that apparently the force field being used has >not really been validated (MSI it turns out did not claim it was - I think >we just misunderstood). So, not wishing to reinvent the wheel, I am >interested in what is going on out there. In a cursory look, I find no >activity in the area but perhaps I have not looked in the correct spots >and/or the work is not in print yet. > I will summarize the results for the net if there seems to be >interest. Until then, thanks in advance for your replies/help. > > Dave Fagerburg > Eastman Chemical Co. > Kingsport, TN 37662 > > fagerbur@kodak.com Hello Dave, I only have pre-prints of these, but John Nicholas and Tony Hopfinger did a series of papers on this subject over the last couple of years. I don't have the actual references handy, but I they appeared in JACS. John did a *very* careful job of parameterizing a zeolite force field, and then did a series of simulations with various small organics bouncing around in cages to study diffusion. As an aside, I asked the MSI/Cerius people if their product could reproduce John's nice results, and they said something along the lines of "we are aware of John's work, and this might be a good thing to do, but we haven't done it." Seemed odd to me. I too found their pitch quite misleading. If you post a summary, please don't include the last paragraph. John Nicholas is currently at PNL, and I believe that he subscribes to this list, so you may hear from him directly. Here's his e-mail address: d3g359@rahman.pnl.gov Hope that this helps, Dave Doherty doherty@msc.edu --- David C. Doherty Minnesota Supercomputer Center, Inc. doherty@msc.edu -------------------- From: mbdtssg@hpb.ch.man.ac.uk" "Steve Greatbanks" 17-MAY-1993 10:19:00.77 To: fagerbur@Kodak.COM Subj: zeolite force fields Dave, in response to your CCL query about zeolite modelling, I assume that you are interested in Molecular Mechanics studies of zeolites. I do not know much about Cerius, and my work is to do with ab initio cluster calculations and periodic Hartree Fock calculations, but I will mention what I know about MM force fields which deal with zeolites. i) A force field for all-silica zeolites was developed by E. de vos Burchardt et al Zeolites 1992 12 183 ii) Biosym include zeolite parameters within their DISCOVER force field - used for hydrocarbon/zeolite interaction studies - Freeman et al Chem Phys Letters 1991 186 137 iii) Mabilia et al have developed parameters ( bending ) for the modelling of the sodalite cage JACS 1987 109 26 iv) Titiloye et al have produced parameters for the interaction of hydrocarbons with zeolite frameworks J Phys Chem 1991 10 4039 v) Kramer et al have a parameter set derived from ab initio data Phys Rev B 1991 43 6 5068 However, the chances are that you are interested in the interaction of host molecules within the zeolites - in which case, decent parameters are very much harder to find - these may have to be developed specifically for the study you are undertaking. A good review on ab initio calculations on zeolites ( If you are interested ) is Sauer J Chem Rev 1989 89 199. I would be interested in seeing a summary of the responses to your query. Yours sincerely, Steve Greatbanks. ----------------- From: m.sennett@ic.ac.uk" 17-MAY-1993 10:13:18.92 To: fagerbur%kodak.com@mitvma.mit.edu Subj: Zeolites, etc. In response to your recent posting to the net, I offer the following. A recent publication that you might use as a starting point.... Gubbins et al., J. Phys. Chem., 1993, vol. 97, p. 494 A book with potential relevance.... Computer Simulation and the Statistical Mechanics of Adsorption, aD. Nicholson and N.G. Parsonage, Academic Press, Oxford, 1982. A reference to MD simulations.... Sokolowski and Fischer, Mol. Phys., 1990, vol. 71, p. 393 A paper treating surface characteristics of metal oxides... Salasco et al., Mol. Phys., 1991, vol. 72, p. 267 I am interested in the subject, so if you get a lot of feedback, I'd like to see a summary. Good luck. Michael Sennett m.sennett@ic.ac.uk ---------------------- From: singer@mps.ohio-state.edu" 17-MAY-1993 10:09:40.45 To: fagerbur@Kodak.COM Subj: Re: zeolite modeling I would be particularly interested in a summary of responses on the zeolite question. A student and I are writing up some work on analysis of zeolite framework vibrations. We used the shell model potential of van Zanten and co-workers. It gives good results for some silicates, but, in our experience, does not have a minimum with the experimental crystal structure for others. We haven't attempted to improve this framework potential...yet. Iton, Hopfinger and coworkers have done some interesting stuff, also. I'd also be curious if your software gives any literature reference to how they made their potential. thanks, Sherwin --- Sherwin Singer internet: singer@mps.ohio-state.edu Department of Chemistry bitnet: singer@ohstpy Ohio State University (614)292-8909 FAX: (614)292-1685 ---------------------- From: EDELSON@EVAX12.ENG.FSU.EDU" "Dave Edelson" 17-MAY-1993 09:42:05.22 To: fagerbur@Kodak.COM Subj: zeolites Try Computers & Chemistry, the article by Leherte et al, Vol 15 p 273 (1991) and extensive references in it. David Edelson, editor Computers & Chemistry ------------------- From: jas@medinah.atc.ucarb.com" "Jack Smith" 17-MAY-1993 09:11:55.29 To: fagerbur@Kodak.COM Subj: Re: Zeolite molecular modeling You should probably check into Biosym's Catalysis and Sorption Consortium. Their main emphasis has been in zeolites and the software from the early stages of that consortium is now being made available commercially to non-members. The software has extensive solids modeling and characterization features and the mechanics/dynamics are based on METAPOCS and FUNGUS, which use a polarizable shell model. I'll let Biosym do the rest of the sales pitch. JACK A. SMITH jas@medinah.atc.ucarb.com --------------- From: r01a566@bcc9" "Adi Treasurywala" 17-MAY-1993 08:14:41.39 To: fagerbur@Kodak.COM Subj: Re: Zeolite molecular modeling Dave, Have you tried looking up the works of Bastian Van De Graff, Julianalaan 136 2628BL Delft The Netherlands I have been listening to lectures by him about this topic for about ten years now. He seems to me to be doing excellent work in this area. If he himself has not published anything (a TRUELY REMOTE possibility) then he will surely be able to put you onto the relevant literature. Good luck, Adi M Treasurywala,Sterling Winthrop Inc,1250 South Collegeville Road, PO Box 5000, Collegeville, PA 19426-0900,Voice (215)983-6610 FAX (215)983-5559, INTERNET adit@kodak.com ---------------------- From: h.rzepa@ic.ac.uk" "Henry Rzepa" 17-MAY-1993 03:28:40.84 To: fagerbur@Kodak.COM Subj: Re: Zeolite molecular modeling Richard Catlow at the Royal Institution is certainly highly active!! Using density functional code etc Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.3.1, Tel:+44 71 225 8339, Fax:+44 71 589 3869. ------------------ From: imtvi06@cc.csic.es" "Luis Montero" 17-MAY-1993 02:59:33.94 To: fagerbur@Kodak.COM (confirm) Subj: Theory on zeolites Madrid, May 17, 1993 Dear Dave: The Laboratoire de Dynamique des Interactions Moleculaires (CNRS) in the Uni- versity of Paris VI is carrying out a nice work in theoretical modeling of zeolites. We are working with them from Havana (my own Lab. of Computational and Theoretical Chemistry, in the University of Havana, and the Institute of Pedagogy there). You can follow papers from the last J. Phys. Chem. 1993, 97, 641 and references therein. I particularly recomend you to address Dr. Earl Evleth (udim018@frors31.bitnet) who is very experienced. He is now in US in vacances, but returning to Paris in one or two weeks. It would be nice to work together in the future. Yours, Luis Montero ---------------------- From: scsupham@reading.ac.uk" 16-MAY-1993 15:13:31.86 To: fagerbur@Kodak.COM CC: scsupham@reading.ac.uk Subj: Re: Zeolite molecular modeling Dave, In our group at Reading, Peter Cragg is busily validating the Cerius force field. If you have any specific queries I shall let him know. We also have a few people working on various aspects of zeolite modelling. john upham John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet) Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%reading.ac.uk@uk.ac (BITnet), scsupham@uk.ac.reading (Janet) --------------------- From: richard@TC.Cornell.EDU" "Richard Gillilan" 15-MAY-1993 17:46:59.59 To: fagerbur@Kodak.COM Subj: Zeolite summary I'm very interested in what people have to say about this and where to get common Zeolite structures. Richard --------------- Date: Fri, 16 Sep 94 10:32:04 -0400 To: brian@bert.chem.wsu.edu (Brian W. Beck) From: mfrancl@cc.brynmawr.edu Subject: Re: CCL:General:Computational Work on Zeolites A recent paper is....O'Malley, Soscun and Collins (Chem. Phys. Lett.217, 293, (1994)) Michelle M. Francl Internet: mfrancl@cc.brynmawr.edu ------------- Date: Fri, 16 Sep 1994 07:43:50 -0700 From: d3g359@rahman.pnl.gov Subject: zeolite To: brian@bert.chem.wsu.edu Brian, please have your friend contact me. I have done a lot of work in zeolites, and I'm close to your location. Thanks, John John Nicholas Office: (509) 375-6559 -------------- Date: 16 Sep 1994 15:31:24 U From: "Antony Richards" Subject: Zeolite Work To: "Brian Beck" Dear Brian, I read with interest your E-mail regarding your friend who wants to do some zeolite modelling. Without sounding too much like a salesperson I work as a support scientist for molecular simulations who sell some really very fine software for zeolite modelling. It is modular so you can just buy those bits you want. Those modules of interest might be the core visualiser, the sorption (Monte Carlo), Molecular Dynamics and Energy Minimisation. There are also modules for work on surfaces and interfaces, a quantum mechanics workbench and a whole range of analytical instruments like HRTEM, Powder Diffraction, EXAFS etc. Some of the chief users in your area are BASF, Air Products, BOC, Exxon etc. I would certainly think it is worth asking for more details especially since as an academic you get a large discount (85% I think)! The address you want is Molecular Simulations, 16 New England Executive Park, Burlington, Massachusetts USA 01803. Finally does you address have anything to do with George Pullman of Pullman carriage fame who is very popular over this side of the pond? I hope this information is of use? Don't hesitate to contact me should you want any further information. Best wishes, Antony Richards. ---------------- Date: Fri, 16 Sep 1994 23:33:06 +0600 From: newhoir@duc.auburn.edu (Irene Newhouse) To: brian@bert.chem.wsu.edu Subject: Re: CCL:General:Computational Work on Zeolites The examples that come with TurboMole (now marketed by BioSym) include Zeolites. It's a direct SCF package, & now many of the standards like G92 & GAMESS in- clude direct methods, so they can also be used. The tricky bit is *building* the zeolite: if your friend doesn't have crystal structures to start with, he/she ought to seriously consider some sort of GUI to help build them! Good luck, Irene Newhouse ------------ Date: 21 Sep 94 15:25:00 WET From: JEREMY WALTON Subject: Re: CCL:General:Computational Work on Zeolites To: brian Hi Brian, We did some work on computational modelling of adsorption and diffusion through silicalite. The reference is: "Molecular simulation of Methane and Butane in Silicalite", by S.J. Goodbody, K. Watanabe, D. MacGowan, J.P.R.B. Walton and N. Quirke, J. Chem. Soc. Faraday Trans., 1991, 87(13), 1951-1958. The same issue has some other papers on simulation of adsorption and diffusion through zeolites (it's the report of a Faraday Symposium on Molecular Transport in Confined Regions and Membranes). Hope this helps. Cheers, Jeremy | Jeremy Walton nagjpw@vax.oxford.ac.uk | -------- Date: Wed, 21 Sep 94 09:21:16 PDT From: ed@mycenae.CChem.Berkeley.EDU (Edward J. Maginn) To: brian@bert.chem.wsu.edu Subject: modeling of zeolites Reply-To: ed@mycenae.CChem.Berkeley.EDU You asked about software packages for doing computational work on zeolites. People in our group have done a lot of work modeling adsorbates inside the pores of zeolites, using locally-written software. (If your frined is interested, look for papers co-authored by A.T. Bell and D.N. Theodorou). There are also simulation packages from BioSym and Molecular Simulations Inc. that will do this kind of thing. Quantum mechanical calculations can also be done, using any of the standard packages (or again, locally-written codes). A German by the name of J. Sauer has published extensively in this area, and lists the type of algorithms he uses. Hope this helps. +---------+-------------------------------------------------------------+ |Mail | Edward Maginn, Dept. of Chem. Engr., Gilman Hall | |Internet:| ed@mycenae.cchem.berkeley.edu | |+--------+-------------------------------------------------------------+ From cmartin@rainbow.uchicago.edu Mon Sep 26 15:00:41 1994 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.9/930601.1506) id OAA19813; Mon, 26 Sep 1994 14:48:30 -0400 Received: from rainbow.uchicago.edu by midway.uchicago.edu for chemistry@ccl.net Mon, 26 Sep 94 13:48:29 CDT Received: by rainbow.uchicago.edu (920330.SGI/920502.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA11645; Mon, 26 Sep 94 14:01:19 -0500 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9409261901.AA11645@rainbow.uchicago.edu> Subject: Questions about charges To: chemistry@ccl.net Date: Mon, 26 Sep 1994 14:01:19 -0600 (CDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1503 Dear all: Recently Feng Zhou has asked: > We have performed a charge calculation using the program GAUSSIAN92 >(6-31G, AM1), the charges calculated seems somewhat larger than the charges >given in commerical packages such as CHARMm. Can anybody tell me is >that a convention to rescale the charges given by GAUSSIAN to compare >with other programs such as MOPAC? What should be the scaling factor? > I would like some of the experts out there to explain some of these charge fitting schemes to me as well. For example, are there studies which describe in detail how the charges are derived and which test the how well the choices of charges reproduce properties as compared with those computed with high level, correlated calculations and with experiment? How sensitive are the computed properties to the choice of the charges? How sensitive are HF charges to the choice of basis set? How do the charges change when using correlated densities (either from DFT or correlated ab initio calculations). With Best Regards Chuck ================================================================== Charles H. Martin email: chm6@quads.uchicago.edu US Mail: c/o Freed Group The James Franck Institute and The Department of Chemistry The University of Chicago 5640 South Ellis Avenue Chicago, Illinois 60637 Work: (312) 702-3457 Fax: (312) 702-5863 ================================================================== From lsaw00@risque.chem.rochester.edu Mon Sep 26 16:03:19 1994 Received: from risque.chem.rochester.edu for lsaw00@risque.chem.rochester.edu by www.ccl.net (8.6.9/930601.1506) id PAA20223; Mon, 26 Sep 1994 15:12:04 -0400 From: Received: by risque.chem.rochester.edu (AIX 3.1/UCB 5.61/4.03) id AA12864; Mon, 26 Sep 94 15:08:01 -0400 Date: Mon, 26 Sep 94 15:08:01 -0400 Message-Id: <9409261908.AA12864@risque.chem.rochester.edu> To: CHEMISTRY@ccl.net Subject: CCL: Matrix diagonalization Can someone give an idea about how to diagonalize the Hessian matrix in a non-cartesian coordinate system. The matrix equation is of the form HU = AUE where H is the symmetric hessian ,U the eigenvectors of H, E the eigenvalues and A the square matrix representing the space metric. When A is the identity matrix(eg. cartesian space) the problem is straight forward using the matrix diagonalization routines such as JACOBI or TRED2 and TQLI. But how do you handle this proble when A is not the identity matrix (such as for spherical coordinates). *************** Jerry Perlstein Center for Photoinduced Charge Transfer Department of Chemistry University of Rochester Rochester,NY 14627-0216 Tel: (716)275-2511 FAX: (716)473-6889 lsaw00@risque.chem.rochester.edu From ross@cgl.ucsf.EDU Mon Sep 26 17:00:42 1994 Received: from socrates.ucsf.EDU for ross@cgl.ucsf.EDU by www.ccl.net (8.6.9/930601.1506) id QAA21497; Mon, 26 Sep 1994 16:07:20 -0400 Received: (from ross@localhost) by socrates.ucsf.EDU (8.6.9/GSC4.24) id NAA15893; Mon, 26 Sep 1994 13:07:14 -0700 Date: Mon, 26 Sep 1994 13:07:14 -0700 Message-Id: <199409262007.NAA15893@socrates.ucsf.EDU> From: ross@cgl.ucsf.edu (Bill Ross ) To: chemistry@ccl.net Subject: New Amber speed record + PC timing Cc: ross@cgl.ucsf.EDU From time to time in the past I have sent my latest benchmarks for Amber (molecular mechanics) when a new machine breaks the speed record. The last 2 times it seesawed between supercomputer makers Cray and Fujitsu. Now, thanks to parallelism and the latest hot chip (SGI shared memory), we have a workstation that beats the supercomputers on raw speed. Some parallel results for Charmm on a variety of machines can also be found at http://www.ki.si/parallel.html. We are now working on MPI/PVM/TCGMSG/.. message-passing parallelism for the upcoming 4.1 release of Amber. I wouldn't be surprised if there was also a Cray shared memory version for 4.1. Apropos of questions on this list about molecular calculations on PCs - I include timings for a 486 machine running DOS, courtesy of Cezary Czaplewski of the University of Gdansk, Poland. Other benchmark news: Amber has been proposed for evaluation to be included in the SPEC benchmark suite. The writeup of the benchmarks is somewhat abbreviated, since I have sent the whole thing to the list before. See the archives or email me for all the text, and numbers for all machines covered. Bill Ross Molecular Mechanics/Dynamics Benchmarks Amber 4.0 All times are CPU seconds measured by system calls in the programs. These are single observations. Note: benchmarks supplied by manufacturers are indicated by a leading '-' in the margin. dna/Run.bench dna/Run.bench2 DNA hexamer in periodic 68 DNA base pairs in vacuum. water box, constant volume. 4282 atoms, 10A cutoff on all 7682 atoms: 274 dna, 10 nonbonded pairs. Distance- counterions, 2466 waters. dependent dielectric. All solute interactions; 8A cutoff otherwise. Constant dielectric. ______________________________ ______________________________ min min+md sander sander gibbs min md ______________________________ ______________________________ Cray C90 - /49 - /56 - /57 - /25 - /25 59 Fujitsu VP2200 52/54 62/64 63/64 26/24 26/25 92 SGI [machine.Ncpu; TFP is PowerChallenge] -TFP.1 81/85 91/96 91/96 58/58 58/57 104 -TFP.2 45/47 50/53 49/51 34/34 34/32 70 -TFP.4 26/28 29/31 28/29 19/19 19/18 52 Chall150.01 226/283 218/306 213/290 155/196 158/200 328 Chall150.02 114/153 149/165 117/162 90/110 91/114 187 Chall150.04 62/86 68/91 93/89 46/59 47/68 125 Some other (single processor) workstations for comparison HP 735 173/172 197/193 216/190 112/109 109/106 186 DEC-alpha 3000/500vms 232/275 249/294 247/286 154/191 151/191 258 rs6000 560 376/347 400/372 405/399 PC/DOS result from Cezary Czaplewski, University of Gdansk: PC486dx2.66 - /2282 - /2392 - /2328 (256Kb cache) with 16Mb RAM. NDP-Fortran-486 PROGRAM NOTES Run.bench min: 100 steps minimization minmd: 20 steps min, 80 steps md sander: 100 steps gradual warming Run.bench2 sander/min: 100 steps minimization sander/md: 100 steps gradual warming gibbs: 100 steps of dynamic windows perturbation (double-wide sampling) note: gibbs4 does not have vectorization directives note: gibbs4 is double precision Note: The minmd program contains the traditional energy minimization and molecular dynamics capabilities of Amber. Sander is essentially the same, as used here. (Both programs have significant other features which are not exercised by the benchmarks.) Gibbs is the Amber free energy perturbation program. -- From EDGECOMK@QUCDN.QUEENSU.CA Mon Sep 26 18:03:10 1994 Received: from QUCDN.QueensU.CA for EDGECOMK@QUCDN.QUEENSU.CA by www.ccl.net (8.6.9/930601.1506) id RAA24767; Mon, 26 Sep 1994 17:48:11 -0400 Message-Id: <199409262148.RAA24767@www.ccl.net> Received: from QUCDN.QUEENSU.CA by QUCDN.QueensU.CA (IBM VM SMTP V2R2) with BSMTP id 7347; Mon, 26 Sep 94 17:45:54 EDT Received: from QUCDN.QUEENSU.CA (NJE origin EDGECOMK@QUCDN) by QUCDN.QUEENSU.CA (LMail V1.1d/1.7f) with RFC822 id 3708; Mon, 26 Sep 1994 17:45:54 -0400 Date: Mon, 26 Sep 1994 17:23 EDT From: EDGECOMK@QUCDN.QueensU.CA To: chemistry@ccl.net Subject: CCL:questions about charges The waters appear to be a bit muddy in the area of 'charges'... I assume that the original question pertains to G92 output Mulliken Pop. Analysis... are these real charges? What are the charges you obtain from CHARMm or MOPAC? Why fit one to the other? In some way this is a philosophical question. What is a charge on an atom? Why would you expect a charge calculated with one program using perhaps different methods, constants (eg 1au= ? angstroms), basis sets (if any) to reproduce some other program you wish to have as a benchmark? Do each of these programs produce a 'wavefunction' you can use to calculate 'charges' using various different methods? No. G92 can produce a wavefunction file of the Bader analysis type that can be used as input into a variety of other programs for analysis. Mulliken popln. analysis is notoriously bad for a variety of reasons, however, it has proven to be very useful as within a series of molecules calculated at the same level it has on occasion reproduced 'expected' trends in atomic charges. It does not produce observables. The overlap terms are simply divided in half and there is no reason why this is any better than any other method. SO... given the variety of methods, some with a better basis in theory, why 'fit' charges ? Sorry if I have muddied the waters even further but I just glanced at a couple of papers that reported charges from certain programs without reference to the methods used. Hope this leads to some discussion on the matter as well. Ken Edgecombe From btluke@VNET.IBM.COM Mon Sep 26 19:01:14 1994 Received: from VNET.IBM.COM for btluke@VNET.IBM.COM by www.ccl.net (8.6.9/930601.1506) id SAA25986; Mon, 26 Sep 1994 18:47:41 -0400 From: Message-Id: <199409262247.SAA25986@www.ccl.net> Received: from PK705VMA by VNET.IBM.COM (IBM VM SMTP V2R2) with BSMTP id 2587; Mon, 26 Sep 94 18:47:21 EDT Date: Mon, 26 Sep 94 18:46:38 EDT To: chemistry@ccl.net Subject: Final Call: Applications of GAs SYMPOSIUM ANNOUNCEMENT and FINAL Call for Papers Application of Genetic/Evolutionary Algorithms in Computer-Aided Chemistry American Chemical Society Meeting Anaheim, CA April 2-7, 1995 Purpose: This symposium will examine the applications of Genetic Algorithms (Standard, Parallel, Adaptive Parallel, Messy and Meta), Extended Genetic Searches, and/or Evolutionary Programming to any area if Computer-Aided Chemistry. This includes, but is not limited to, substructure searching, QSAR/QSPR studies, intermolecular interactions (e.g. docking simulations), conformational searches. Sponsers: This symposium is sponsered by the Computers in Chemistry Division of the American Chemical Society. I need a 150 word abstract no later than October 28, 1994. Abstract Forms can be obtained from the ACS by calling 202-872-4396. Brian T. Luke IBM Corporation, MS 078 Neighborhood Road Kingston, NY 12401 btluke@vnet.ibm.com From rbw@msc.edu Mon Sep 26 19:05:26 1994 Received: from noc.msc.edu for rbw@msc.edu by www.ccl.net (8.6.9/930601.1506) id SAA25746; Mon, 26 Sep 1994 18:22:02 -0400 Received: from uh.msc.edu by noc.msc.edu (5.65/MSC/v3.0.1(920324)) id AA24465; Mon, 26 Sep 94 17:21:52 -0500 Received: by uh.msc.edu (5.65/MSC/v3.1r(920220)) id AA01668; Mon, 26 Sep 94 17:21:51 -0500 Date: Mon, 26 Sep 94 17:21:51 -0500 From: rbw@msc.edu (Richard Walsh) Message-Id: <9409262221.AA01668@uh.msc.edu> To: chemistry@ccl.net, ross@cgl.ucsf.EDU Subject: Re: CCL:New Amber speed record + PC timing Bill, Bill you wrote: >From time to time in the past I have sent my latest benchmarks >for Amber (molecular mechanics) when a new machine breaks the >speed record. The last 2 times it seesawed between supercomputer >makers Cray and Fujitsu. Now, thanks to parallelism and the >latest hot chip (SGI shared memory), we have a workstation that >beats the supercomputers on raw speed. Some parallel results for ... I am not sure what you mean by 'raw speed' here ... could you also report C90 parallel times or those for the T3D? It would be helpful and more complete to present these comparisons. My guess is that your benchmark would run with the most 'raw speed' on a C90 16/512 with a T3D attached. Also, these TFP timings beg the question ... when does a workstation become a supercomputer? ... when it costs $500,000.00, $1,000,000.00. The new SGI systems with multiple CPUs and functionally configured can easily exceed these numbers. Around here anyway a workstation is something that can be purchased for about $50,000. The SGI TFP performance numbers are impressive, but they should be presented here with as high a regard for completeness as for enthusiasm (excepting perhaps by those selling the hardware involved :-)). Accepting the possibility of some personal bias :-)-- | | Richard Walsh | Minnesota Supercomputer Center, Inc. <-------------