From Kurt.Hillig@um.cc.umich.edu Tue Apr 27 07:07:18 1993 Date: Tue, 27 Apr 93 11:07:18 EDT From: Kurt.Hillig@um.cc.umich.edu To: chemistry@ccl.net Message-Id: <22506386@um.cc.umich.edu> Subject: Gaussina 9x memory/disk requirements I've often seen the claim that memory (for in-core) or disk space needed by Gaussian 9x scales as N^4/4 (SCF). I expect a first-order approximation to the memory needs can be given by M = A + B N^4, where A is the "overhead" and B is a scale factor (words per integral?). I've occasionally seen some very rough estimates - for example today, the claim (paraphrased) 100 basis functions:100 MWords, 200 BF's:200 MW, 300 BF's:>1GW - but it's hard to fit this to a fourth-order polynomial with any accuracy (;-) and it doesn't match M = N^4/4 (i.e. A=0, B=.25) particularly well. Can anyone supply more accurate numbers so I can better advise my users? Dr. Kurt Hillig Dept. of Chemistry I always tell the khillig@umich.edu University of Michigan absolute truth Telephone (313)747-2867 Ann Arbor, MI 48109-1055 as I see it. hillig@chem.lsa.umich.edu From richard@TC.Cornell.EDU Tue Apr 27 06:47:17 1993 Date: Tue, 27 Apr 1993 10:47:17 -0400 From: Richard Gillilan Message-Id: <199304271447.AA20137@theory.TC.Cornell.EDU> To: chemistry@ccl.net Subject: Visualization Summer School --- Scientific Visualization of Chemical Systems --- Cornell Theory Center Summer School Offered through the Cornell School of Continuing Education and Summer Sessions Course Description Within the past ten years, the simulation and modeling of molecules has evolved from an esoteric academic subject into a international industry. Computer graphics has played a decisive role in this transformation by allowing chemists to build, visualize and interact with complex geometrical objects. While computer scientists are conversant in the language of their own discipline, they are often unfamiliar with the terminology, simulation techniques and practical needs of research chemists. Similarly, chemists are often unfamiliar with the latest paradigms and technological advances in graphical computing. This interdisciplinary course is intended to bridge the gap between computer science and chemistry and to equip chemistry researchers who wish to be more than just casual users of prepackaged graphics software. Although this is not intended to be a course in computational chemistry or drug design, data sets >from chemical research problems will be used in lab and students will be encouraged to bring data sets of their own. Lab exercises and projects will be carried out using data-flow programming (IBM Visualization Data Explorer software) and students will have access to Cornell Theory Center computing resources, including video recording equipment. Audience: researchers and students in the chemical and biological sciences interested in integrating state-of-the-art computer graphics into their research; computer scientists wishing to gain familiarity with a major application of scientific visualization. The class size will be limited to 25 participants on a first-come first-served basis. Level: Graduate/advanced undergraduate, 1 or 2 Credits. May be taken without credit as a workshop. Calculus, linear algebra and introductory chemistry required. Familiarity with Unix, X-windows and C is useful but not required. Date: June 14-25, 1993 (2 Credits) June 14-18, 1993 (1 or 0 credits) Time: Mon-Fri 9:00 am to 12:00 pm and 1:00 pm to 4:00 pm Cost: 0 or 1 credit $410 2 credits $820 Format The course will be held in the Theory Center training facility where computer workstations will be available. Daily lectures will be interspersed with laboratory exercises and ample time will be provided for project enablement and familiarization with the new computing environment. Students enrolled for one credit will be graded on the basis of their laboratory exercises and short final project. Those enrolled for a second credit will receive more advanced lectures, be given more time for project development and meet daily to share experience and discuss problems encountered. Content (may vary) Elements of computer graphics polygonal rendering, lighting models, ray tracing, volumetric rendering, stereo graphics, animation, introduction to data-flow programming (DX), interactivity. Representing the atom size, time and energy scales basic classical and quantum mechanics Important categories of molecules small molecules, biopolymers, surfaces and catalysts, miscellaneous current applications Data formats and conversions Advanced molecular graphics techniques Types of simulation and experiment electronic structure, molecular dynamics/mechanics electrostatics, X-ray crystallography, NMR, quantum dynamics and spectroscopy. Instructors The course will be taught by two instructors. Topics related to computer graphics will be handled by Dr. Bruce Land, Project Leader of Visualization, Cornell National Supercomputing Facility. Chemistry-specific aspects of the course will be handled by Dr. Richard E. Gillilan, Visualization Specialist and Research Scientist, Cornell National Supercomputing Facility TO REGISTER: mail completed form to Cornell University School of Continuing Education and Summer Sessions B20 Day Hall Ithaca, NY 14853-2801 Questions: Richard Gillilan (607) 254-8757 richard@tc.cornell.edu IMPORTANT: Acceptance will be first-come, first-served and based on a target class size of 15 full-credit and 10 single or non-credit participants. DEADLINE: May 20, 1993 ----------------------- Application Form ---------------------- Scientific Visualization of Chemical Systems Chemistry 782 Computer Science 718 U.S. Social Security number (if available) _____ - ___ - _______ Cornell ID number (if available) ________________ Name: _______________________________________________________________ Last First Middle Suffix (Jr, etc) Address: _____________________________________________________________ _____________________________________________________________ _____________________________________________________________ Home Address (where grades will be mailed): _____________________________________________________________ _____________________________________________________________ _____________________________________________________________ Local Phone ________________ Home Phone _______________ Academic Discipline _____________________________ Course number (check one): __ Chemistry __ Computer Science Credits: __.__ Status: __ Undergraduate Student __ Smart Node Consultant __ Graduate Student __ Smart Node Advisor __ Post-Doctoral __ Faculty __ Other (explain) _______________ Corporate Commercial __ Research Staff __ Other (explain) ______________ Name of Firm ___________________________________________________________ Indicate which of the following best describes you (optional): __ African American __ Alaskan Native __ Asian American __ Caucasian __ Hispanic American __ Native American List special needs (e.g. mobility impaired): ____________________________ ---------------------------------------------------------------------------- Accommodations: Blocks of rooms are available at the Sheraton. Reservations must be made no later than May 17. Be sure to tell them you are here for the "Cornell Theory Center Visualization Workshop". Sheraton Inn One Sheraton Drive, Ithaca (607) 257-2000 FAX: 607-257-398 Rates starting at $64.00 Other local motels (Make your reservation early! Our workshop coincides with other Cornell events) Econo Lodge Cayuga Mall 2303 N. Triphammer Rd. Ithaca (607) 257-1400 (800) 466-6900 FAX: (607) 257-6359 Rates from $35.10 (ask for the Cornell Rate) Dorm rooms have also been reserved participants (both credit and non-credit). Participants who are interested in dorm rooms should call (below) for registration information: Jeanne Miller (607) 254-8813 or Donna Smith (607) 254-8614 email: jeanne@tc.cornell.edu or donna@tc.cornell.edu --------------------------------------------------------------------------- From mail Tue Apr 27 12:42:46 1993 From: hyper!slee (Thomas Slee) Message-Id: <9304271623.AA12347@hyper.hyper.com> Subject: PC's and workstations To: chemistry@ccl.net Date: Tue, 27 Apr 1993 12:23:11 -0400 Dear OSC-ers, Following the "Gaussian for Windows" announcement, there has been a flurry of discussion about the relative merits or otherwise of PC's, workstations, and supercomputers. I thought I would add a couple of pieces of fairly elementary information to the pile as I haven't seen them posted yet. First, relative cpu speeds of workstations and PC's with real applications. We find that for the semi-empirical and molecular mechanics programs in HyperChem the relative speeds of a high-end, but not quite top-of-the-line, PC (486-50MHz model) and an R3000 SGI Indigo are about 1 to 2.5. An R4000 SGI Crimson is just over 2 times faster again. So, a reasonably fast PC certainly has the cpu speed to do useful calculations. The memory requirements for semi-empirical and molecular mechanics calculations are much less than those for (indirect) ab initio methods, of course: a 100-orbital AM1 calculation can be done in around 5Mb, making it quite easily within reach of standard PCs. I can make no comment on Gaussian 92 in this context. A couple of other things for those who are new to thinking about PC's for computational chemistry. Workstations have, of course, the advantage of being multi-user platforms, while PC's are single-user. Windows does not do time-slicing by itself: it will share CPU time among applications only if those programs give up the CPU. Thus, the ability to run other programs without too much interference from a big calculation depends on program implementation, rather than on the operating system. It will be interesting to see how easily Gaussian can be put "in the background". One of the big advantages of Windows is, apart of course from having lots of commercial programs available for all kinds of purposes, the ability of different programs to communicate with each other through Dynamic Data Exchange (DDE). I certainly find this one of the most attractive and powerful tools when working in Windows. Anyone know if G92 has any facility to share its results by DDE? FInally, to those who say you can't do anything worthwhile with less than a gigabyte of scratch space (or whatever): you make me feel very old. I felt like starting this posting by saying "When I were a lad, we only had 80Mb of disk space, and 4Mb of memory, TOTAL. And we STILL did ab initio calculations. Times were tough then..." And it wasn't that long ago, either. Really. Sigh... Tom Slee -- Tom Slee Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2 Internet: slee@hyper.com Tel. (519) 725-4040 From rbw@msc.edu Tue Apr 27 08:29:47 1993 Date: Tue, 27 Apr 93 13:29:47 -0500 From: rbw@msc.edu (Richard Walsh) Message-Id: <9304271829.AA25192@uh.msc.edu> To: Kurt.Hillig@um.cc.umich.edu, chemistry@ccl.net Subject: Re: Gaussina 9x memory/disk requirements Hello, I made a mistatement in my previous note .. I got my divisors mixed up and stated that closed shell systems scale as N^4/4 when this is actually the number for open shell systems. Here is the correct information: open shell incore scf memory needs scale as N^4/4 closed shell incore scf memory needs scale as N^4/8 So, for closed shell systems, explicitly: 50*50*50*50/8 = 781250 MWs 100*100*100*100/8 = 12500000 MWs 200*200*200*200/8 = 200000000 MWs 300*300*300*300/8 = 1012500000 MWs I usually give my jobs a additional 1 or 2 MWs to to be sure their is enough room for the instuctions and static data. Sorry about the mistake, Richard Walsh Minnesota Supercomputer Center From srheller@asrr.arsusda.gov Sat Apr 27 10:11:00 1993 Message-Id: <199304271814.AA14237@oscsunb.ccl.net> Date: 27 Apr 93 14:11:00 EDT From: "STEPHEN R. HELLER" Subject: Software for review To: "chemed-l" 27 April, 1993 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. I now have some packages in hand (see below) and I am looking for people who are willing to review the software. In return for the review you get to keep the software. The review should be completed in 1-2 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. I have tried this approach with some software for review in the past few months and it is working reasonably well. (For those who haven't finished your reviews of software sent a few 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 hope it continues to work. 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 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 28 April, as I am sure the software will be gone by then. I can be reached on INTERNET (SRHELLER@ASRR.ARSUSDA.GOV), or if necessary, by phone at 301-504-6055 or FAX at 301-946-2704. PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE and FAX NUMBER!!! (I send the software by Federal Express.) Steve Heller The packages I now have are: 1. LabAdvisor - IBM PC Regulatory Information database from the ACS. This is the complete LabADVISOR package with all modules. This helps you keep track of regulatory requirements for chemicals in the lab. 2. Ami-Pro 3.0 for windows. From wsonnen@rcf.usc.edu Tue Apr 27 06:42:51 1993 Date: Tue, 27 Apr 93 13:42:51 PDT From: wsonnen@alnitak.usc.edu (Wayne Sonnen) Message-Id: <9304272042.AA24285@alnitak.usc.edu> To: chemistry@ccl.net Subject: dna-ligand studies Dear computational chemists, I would appreciate any directions (references, etc.) as to where to find data on dna-ligand studies. In particular i would like to find a series of ligands (or a ligand and several of its derivatives) which bind to the same dna sequence. Any references to thermodynamic, biochemical and of course simulation studies would be most welcome. My interest is in studing the binding of these ligands via md. Regardless of the number of replies to my question, i will post a summary of the replies i receive to this network. Thank you, Wayne Sonnen wsonnen@alnitak.usc.edu