From dirk@rulglj.LeidenUniv.nl Fri Jul 2 05:28:16 1993 Date: Fri, 2 Jul 93 12:28:16 -0700 From: dirk@rulglj.LeidenUniv.nl (Dirk Huckriede) Message-Id: <9307021928.AA03018@rulglj.LeidenUniv.nl> To: CHEMISTRY@ccl.net Subject: Structure fitting Dear Netters, I'm looking for a program/subroutine, preferably in Fortran, with which it is possible to look for the presence of a certain sub-structure in another structure. Thanx in advance, +-------------------------------+-----------------------------------+ | Dirk Huckriede | OH O | +-------------------------------+ | / \ | | | C --- C C --- Base | | Conformational Analysis Group | | | | | Gorlaeus Laboratories | C --- C | | Leiden University | | | | | | OH OH | +-------------------------------+-----------------------------------+ | P.O. Box 9502 Phone : +31 71 274505 | | 2300 RA Leiden Fax : +31 71 274488 | | The Netherlands E-mail : dirk@rulglj.leidenuniv.nl | +-------------------------------------------------------------------+ From kudchadk@ecn.purdue.edu Fri Jul 2 01:34:17 1993 Date: Fri, 2 Jul 93 06:34:17 -0500 From: kudchadk@ecn.purdue.edu (Samir Kudchadkar) Message-Id: <9307021134.AA07298@hdpe.ecn.purdue.edu> To: CHEMISTRY@ccl.net Subject: Debye - Waller Factor Hi Netters, As part of my Ph.d work, I am reading on Mode Coupling theories of the liquid-glass transition. These theories seem to predict an anomalous behavior of the DEBYE-WALLER FACTOR ( DWF ) near the transition. Can someone out there shed some light on , or suggest a good basic text-book that will answer the foll. questions :- 1. ) What is the Debye- Waller factor ? What information does it provide about the atomic motion in the solid ? 2. ) What is the expected Temperature dependence of the DWF ? Are there any theories that explain this T-dependence ? My e-mail is kudchadk@hdpe.ecn.purdue.edu , and if anyone else is interested in these topics, I will summarize the responses. Thanx in advance . - Samir Kudchadkar. From cramer@staff.tc.umn.edu Fri Jul 2 04:29:37 1993 Message-Id: <0012c344653024198@staff.tc.umn.edu> From: "Christopher J Cramer-1" Subject: Fullerenes To: chemistry@ccl.net Date: Fri, 2 Jul 93 9:29:37 CDT Yikes!! No more C60 please -- thanks to many who responded. What I'd REALLY like is LARGER fullerenes, which seem to be somewhat less popular based on the response so far. Smaller clusters are OK too, although a fairly comprehensive list was made available to me. C. S. Raman mentioned the arizona ftp site and fullerene mailing list. These are indeed nice bibliographies, but do not contain molecular coordinates. So, I still promise to compile data upon receipt. Incidentally, I'd rather have structures which reflect the high symmetry point groups of these molecules to all significant digits, but beggars can't be choosers, I'll take what you've got and slog through the symmetry myself if necessary. Thanks, CJC -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 (612) 624-0859 From JKONG@ac.dal.ca Fri Jul 2 09:52:41 1993 Date: Fri, 02 Jul 1993 12:52:41 -0300 From: JKONG@ac.dal.ca Subject: Ask for info about modem To: chemistry@ccl.net Message-Id: <01H02FW2TCF6002EEG@AC.DAL.CA> Dear netters, I am not this is a right to place to put this but I will do it anyway. I need a modem so that I can work at home. There various kinds of modem and various prices. I would be very grateful if someone can tell me the differences between models and the street prices I can get. Thank you in advance. Jing Kong From wiedeman@altair.acs.uci.edu Fri Jul 2 04:17:32 1993 To: chemistry@ccl.net Subject: Gaussian and NFS -- Update Date: Fri, 02 Jul 93 11:17:32 -0700 Message-Id: <1083.741637052@altair.acs.uci.edu> From: Lyle Wiedeman We have received early access to Convex's latest OS, 11.0. With the NFS product in that version, we are successfully and profitably running significant G92 jobs with RWF and INT files going to NFS-mounted disk space. Lyle Wiedeman Office of Academic Computing wiedeman@uci.edu Univ. Calif. Irvine wiedeman@UCI.BITNET Irvine, CA 92717 (714) 856-8718 FAX (714) 725-2069 From ZPZCM@jazz.ucc.uno.edu Tue Jul 2 07:05:41 1993 Date: 02 Jul 1993 13:05:41 -0600 (CST) From: "ZORAN P. ZDRAVKOVSKI" Subject: Supercomputer-time grants - SUMMARY To: CHEMISTRY@ccl.net Message-Id: <01H02GHBBBFM8WY2I1@jazz.ucc.uno.edu> Hi netters, Want to thank all who responded to my posting about supercomputer time grants: Jon Erickson, Joe (jtgolab@amoco.com), Richard (richard@chroma.tc. cornell.edu), Thomas Connor Bishop, Michelle M. Francl, Thomas R. Cundari, Douglas A. Smith and Mike Whitbeck. For the benefit of all who are interested here's a summuray of the answers: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% The National Center for Supercomputing Applications (NCSA) at the University of Illinois Urbana-Champaign does grant sumpercomputer time. The number for info and application materials is (217) 244-0072. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% When I was at NCSA ('89-'91), grants like this were not easy to 'fund' because the Crays were pretty much running at capacity. At that time in fact, a popular idea was to move 'application runs', i.e. G9x, MOPAC, etc. off the Crays and onto UNIX workstations. I am not sure if that idea is still in place but it might be faster than what you have acces to now. The person to contact about this is Dr. Melanie Loots, (217) 244-2921, Manager of Applications. She can get you in touch with the grant person at NCSA now. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% There are several high-end RS6000's here at the CTC devoted to electronic structure calculations (large memory and disk space). You probably want a "serial cluster account" to access these machines. For really tough jobs, I think the ES9000 also has Gaussian etc. Daniel Sverdlik (sverdlik@tc.cornell.edu) is a good contact here. ALLOCATIONS POLICY 05/24/93 ************************************************************************* **** The upcoming deadlines for submitting proposals for research **** **** allocations are: **** **** April 9th deadline for the June committee meeting **** **** July 9th deadline for the September committee meeting **** **** October 8th deadline for the December committee meeting **** ************************************************************************* The Cornell Theory Center National Allocations Committee has adopted the following review procedures for time on the Cornell National Supercomputer Facility (CNSF). All project requests must come directly to the Theory Center, not to the National Science Foundation (NSF), and will be subject to the following procedures. Proposals will be reviewed by your discipline-specific peers. Requests by students should be submitted by the student's faculty advisor. The review process takes approximately 12 weeks. Proposals that request a large number of service units (s.u.*) will also be reviewed and subject to final approval by the Allocations Committee. All such proposals must be received by the Theory Center eight weeks prior to the Committee's meeting; the Committee meets each March, June, September, and December. For very large proposals, experts in the relevant discipline will be invited to the Committee meeting to assist in deliberations. The members of the National Allocations Committee are: David Caughey (Chair), M&AE, Cornell University Ravin Bhatt, Electrical Engineering, Princeton University Barbara T. Garrison, Chemistry, Pennsylvania State University Bruce Taggart, Materials Research, NSF Jules Moskowitz, Chemistry, New York University Anna Nagurney, General Business and Finance, University of Massachusetts at Amherst Dennis Peacock, Atmosphere Science, NSF Barry Schneider, Physics, NSF Proposals are awarded by architecture on the Cornell Theory Center's IBM ES/9000, the Parallel IBM RS/6000 Cluster, the IBM Power Visualization System (PVS) and the Kendall Square Research (KSR). One service unit (SU) is defined as the equivalent of one hour on a Cray X-MP processor, and is defined as follows on each architecture: ES/9000: 1 SU = 0.7 CPU hour RS/6000: 1 SU = 4.0 CPU hours PVS: 1 SU = 0.1 wall clock hours KSR: 1 SU = 3.0 CPU hours Exceptions to the above: Researchers associated with Smart Node institutions should contact their on-campus representatives to obtain non-renewable, non-peer-reviewed training allocations of 5 s.u. Projects requiring more than 5 s.u. must be submitted to the Theory Center for consideration through the regular review process. Strategic User projects are peer reviewed separately, after having been awarded through the regular review process; and approval as a regular project does not guarantee approval for the Strategic Users program. For an application for the SUP program, return to the Forms section of cnsfinfo. Membership in the Corporate Research Institute (CRI) includes an annual allocation of 10 s.u. on the CNSF. Requests for time by CRI researchers beyond the 10 s.u. should be sent to Linda Callahan, Director, Corporate Research Institute, 514 Engineering and Theory Center Building, Cornell Theory Center, Ithaca, NY 14853. Review of Progress Awards are generally made for a 12-month period, although multi-year proposals will be considered as well. Annual allocations of multi-year awards are based on available supercomputer time each year and review of progress reports. Short extensions for up to one year may be granted by Theory Center administration after review of a progress report. The National Allocations Committee reviews annual progress reports for large projects. Projects of one year or less in duration should conclude with a report of results to the Committee. All requests for allocations should be addressed to Theory Center Allocations Coordinator Pat Colasurdo, 518 Theory Center, Engineering and Theory Center Building, Ithaca, NY 14953-3081. For a copy of the application form, v(iew) the Forms menu of cnsfinfo. REQUEST FOR ADVANCED COMPUTING RESOURCES AT NATIONAL SCIENCE FOUNDATION SUPERCOMPUTING CENTERS * This form must be submitted in hardcopy. * * For proposal instructions, mailing addresses, and list of codes, choose * * Allocations.Request.Form.Instructions from the Forms menu of cnsfinfo * A. IDENTIFICATION Please type or print _______________________________________________________________________ |Name (last, first, middle) | Academic status | | | __ F Faculty | | | __ PD Postdoctorate | |___________________________________| __ GS Graduate Student | |Social Security Number* | __ UG Undergraduate Student | | | __ UR Univ Research Staff | | |_|_|_|-|_|_|-|_|_|_|_| | __ UN Univ Non-Research Staff | |___________________________________| __ HT High School Teacher | |Institution | __ HS High School Student | | | __ I Industrial User | | | __ O Other User | |___________________________________|___________________________________| |Department | Building Address | | | | |___________________________________|___________________________________| |Street Address | City | | | | |___________________________________|___________________________________| |State Country ZIP Code | Electronic Mail Address | | | | |___________________________________|___________________________________| |Phone Number (include area code) | FAX Number (include area code) | |( ) - | ( ) - | |___________________________________|___________________________________| |Project Title | New Project ___ Renewal ___ | | |___________________________________| | | Field of Science Codes (See List) | | | Primary Secondary | | | |_|_|_| |_|_|_| |_|_|_| |_|_|_| | |___________________________________|___________________________________| * Submission of Social Security Number (SSN) is voluntary. Failure to provide an SSN will not affect your eligibility for an award. The SSN, however, is helpful in processing your request. B. SOURCE OF FINANCIAL SUPPORT FOR THIS PROJECT (if none, state none) _______________________________________________________________________ |Sponsoring Agency/Institution (if NSF, give division and program) | | | |_______________________________________________________________________| |Award Number | Start Date (M/D/Y) | Expiration Date (M/D/Y) | | | | | |____________________|_______________________|__________________________| |Sponsoring Program's Director and Phone Number | | | |_______________________________________________________________________| |Principal Investigator's Name, Address, and Phone | |(if different from Section A.) | | | |_______________________________________________________________________| C. RESOURCE REQUIREMENTS _______________________________________________________________________ |Requested center: ___Cornell ___Illinois ___Pittsburgh ___San Diego| |_______________________________________________________________________| |Access (identify specific network, dial-up, etc.) | | | |_______________________________________________________________________| |Start Date |Completion |No. of Years |Projected Use Per Quarter | |(M/D/Y) |Date (M/D/Y) | |(First Year) | | --/--/-- | --/--/-- | | _____ _____ _____ _____ | |_____________|_____________|_____________|_____________________________| | | Service Units | Main Memory | Disk Memory | | Machine type | Needed | Needed | Needed | | |_________________|_____________|_____________| | | Total | 1st Yr | | | |1. | | | | | |2. | | | | | |3. | | | | | |_______________________________________________________________________| | FOR MASSIVELY PARALLEL SYSTEMS ONLY | |_______________________________________________| | Monthly | Monthly Code | No. of | ____| Production Hrs | Development Hrs | Processors | | 1. | | | | | 2. | | | | | 3. | | | | |____|________________|_________________|____________| D. PROJECT INFORMATION _______________________________________________________________________ |Abstract (To submit electronically, mail plain ASCII text to | | abstracts@theory.tc.cornell.edu ) | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |_______________________________________________________________________| |Suggested Key Words to Describe Research Content | | | | | |_______________________________________________________________________| |Suggested Key Words to Describe Computational Methods Used | | | | | | | |_______________________________________________________________________| E. PEER REVIEW _______________________________________________________________________ |Would you be willing to review supercomputing proposals? Yes___ No___ | | | |If yes, please list areas of expertise, including computer methodology.| | | | | | | |_______________________________________________________________________| F. SIGNATURES _______________________________________________________________________ | | | | |Applicant:_________________________________________ Date:______________| | | |Institutional | |Representative:____________________________________ Date:______________| |(Department Chair, Dean, etc.) | |_______________________________________________________________________| APPLICATION FOR ACCESS TO THE SERIAL RS/6000 CLUSTER AT THE CTC This is an application form for CNSF users who already have eagle userids and who need access to software on the serial RS/6000 cluster at the Cornell Theory Center. For access to the parallel RS/6000 cluster, users must apply for time on that platform: fill out the Allocations.Request. Form in the Forms menu of cnsfinfo. To complete this form, copy it to one of your directories (use the "c" command from the menu below). When complete, send it in a mailfile to useracct@tc.cornell.edu. (1) date: ____________________________________________________________ (2) name: ____________________________________________________________ (3) eagle userid: ____________________________________________________ (4) accounts: ________________________________________________________ (5) preferred e-mail address: ________________________________________ (where we will send you information - please use an internet style address in the form username@address) (6) surface mail address: ____________________________________________ __________________________________________________________________ __________________________________________________________________ (7) telephone number: ________________________________________________ (8) social security number: __________________________________________ (9) On the RS/6000 cluster you can have a "meaningful" userid, such as your last name. Your RS/6000 userid does not have to be the same as your eagle userid. Usernames must be 8 characters or less. Since your first choice for a userid may already be in use, please list 3 choices: preferred userid: choice 1: _________________ choice 2: _________________ choice 3: _________________ (10) Three shells are available on the RS/6000s: C shell, Bourne shell, and Korn shell. Please list the shell you would like as your default shell: preferred default shell: ____________________ (11) The serial RS/6000 cluster is intended for users with ES/9000 accounts who have software needs that cannot be met on the ES/9000. Please list your reasons for needing access to the serial RS/6000 cluster: __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ (12) software needed on the RS/6000s: __________________________________________________________________ __________________________________________________________________ %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% here' s part of a note that i recieved in regards to your request about super computer time. (our time is running out so they are kind enough to send us little reminders on what to do to get more) the allocations are broken down into several categories. applications for <100 su are taken every month for > 100 they are on a 1/4 basis then for i think >500 it's a yearly allocation. this is of course for only one of the super computer centers there are also computers at (the following aren't THE contacts necessarily but they may direct you further) san diego contact jaynek@sdsc.edu north carolina ??? don't know pittsburg contact Grants@a.psc.edu someplace else,, don't know >from NCSA at urbana champaign i recieved the following message ******************************* If additional service units (SUs) will be needed to complete the research, you may want to submit a proposal soon. The deadlines for submission and the dates of review follow: Deadline Review Month for fewer than 100 SUs January 1 February March 1 April April 1 May June 1 July July 1 August September 1 October October 1 November for 100 SUs or more February 1 March May 1 June August 1 September November 1 December If you have any questions or if you would like to receive an application packet please contact Radha Nandkumar, Allocations Coordinator 217-244-0635 allocations@ncsa.uiuc.edu %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% The National Center for Supercomputing Applications at Urbana- Champaign has regular (monthly?) reviews of grants for small amounts of time, you might try contacting them. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% As far as I know most/all of the supercomputers have the option of making unfunded (courtesy) accounts available- I have one on a cray ymp. All you have to do is basically just ask and provide a brief description of what you want to do. In general expect to have rather restrictive limits on the resources afforded a free account. You can also apply for a grant- a more formal process but many centers are underutilized so a decent proposal should get "funded". Many supercomputer centers offer on-line (via internet/e-mail) connections and applications for accounts, some are via gopher servers (or possibly XMosaic for the more up-to-the-minute types!). Your computer center types should be able to direct you to the right places to send mail/e-mail. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% What computer program are you using? The program GAMESS (Iowa State version) currently runs on the vector engines at all the NSF supercomputer centers (NCSA, PSC, SDSC and CNSF). The parallel version of GAMESS is also available on the iPSC/860 at SDSC, the parallel RS-6000 cluster at CNSF, and could be made to run on the CM-5 at NCSA. I would imagine that other programs, like Gaussian 9?, are available on the vector machines at the NSF centers. I do not know what other computational chemistry programs are on the parallel machines at the NSF centers. Grants of time are available at the NSF centers to do such research. Your sponsored research folks at UNO could probably hunt down the necessary forms and such. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Zoran Zdravkovski Department of Chemistry University of New Orleans New Orleans, LA 70148 (504) 286-7090 fax (504) 286-6860 e-mail ZPZCM@UNO.EDU From DANIELS_MICHAEL_W@Lilly.com Tue Jul 2 09:45:01 1993 Date: 02 Jul 1993 14:45:01 -0500 (EST) From: "M.W.Daniels, 317.276.1590" Subject: HyperChem/AutoDesk To: chemistry@ccl.net Message-Id: <01H02JWV31OY8WW1CC@INET.D48.LILLY.COM> Does anyone have an address, telephone #, or email address for AutoDesk. This is the company that makes HyperChem. Thanks in advance for any help you can provide. Yours, Michael From: DANIELS MICHAEL W (MCVAX0::RX65815) To: VMS MAIL ADDRESSEE (IN::"chemistry@ccl.net") From raman@bioc01.uthscsa.edu Fri Jul 2 13:29:45 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9307022329.AA02883@bioc01.uthscsa.edu> Subject: Re: Fullerenes To: cramer@staff.tc.umn.edu (Christopher J Cramer-1) Date: Fri, 2 Jul 1993 18:29:45 -0500 (CDT) Chris You might want to contact Fan Chung of Bell communication research in New Jersey for additional information on molecular coordinates for fullerenes and related species! Chung and Sternberg have a few papers out on the symmetry related aspects. Chung can be reached via email at: frkc@bellcore.com Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 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 raman@bioc01.uthscsa.edu Fri Jul 2 15:21:56 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9307030121.AA02943@bioc01.uthscsa.edu> Subject: Particle motion in Gels To: chemistry@ccl.net Date: Fri, 2 Jul 1993 20:21:56 -0500 (CDT) Dear Netters Is there anyone out there doing work on modelling particle motion in gels? By this I mean, looking at the trajectories of latex spheres in various gel concentrations? This can either be a brownian movement type study or one in which a field is involved! I am interested in modelling this random walk type phenomenon in 3 dimensions and would like to know about your experiences. Any references that can shed light in solving my problem would be highly appreciated. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 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 chiremv!andromeda!jeffb@uunet.UU.NET Fri Jul 2 17:59:16 1993 Date: Fri, 2 Jul 93 14:54:10 -0700 From: chiremv!andromeda!jeffb@uunet.UU.NET (Jeff Blaney) Message-Id: <9307022154.AA03796@andromeda> To: uunet!ccl.net!chemistry-request@uunet.UU.NET Subject: Re: Structure fitting >I'm looking for a program/subroutine, preferably in Fortran, with which >it is possible to look for the presence of a certain sub-structure in >another structure. The Daylight SMARTS and SMILES toolkits provide substructure capability (plus much more) and can be called from your own Fortran or C code on SUN, SGI, or HP workstations. You can contact Daylight for more information at (714)-476-0451. Jeff Blaney Chiron