From jochen@amiga.chemie.uni-konstanz.de Thu Mar 5 09:15:53 1998 Received: from amiga.chemie.uni-konstanz.de for jochen@amiga.chemie.uni-konstanz.de by www.ccl.net (8.8.3/950822.1) id IAA18243; Thu, 5 Mar 1998 08:20:21 -0500 (EST) Received: (from jochen@localhost) by amiga.chemie.uni-konstanz.de (8.8.7/8.8.7) id OAA11450; Thu, 5 Mar 1998 14:16:51 +0100 Date: Thu, 5 Mar 1998 14:16:51 +0100 Message-Id: <199803051316.OAA11450@amiga.chemie.uni-konstanz.de> From: Jochen Buehler To: "Igor J. Barani" Cc: CHEMISTRY@www.ccl.net Subject: CCL:CCL Using Linux In-Reply-To: <34FD91FF.6C619CA3@syr.edu> References: <199711241322.NAA00205@nirvana.uncor.edu> <34FD91FF.6C619CA3@syr.edu> X-Mailer: VM 6.34 under 20.3 "Vatican City" XEmacs Lucid Mime-Version: 1.0 (generated by tm-edit 7.108) Content-Type: multipart/mixed; boundary="Multipart_Thu_Mar__5_14:16:51_1998-1" Content-Transfer-Encoding: 7bit --Multipart_Thu_Mar__5_14:16:51_1998-1 Content-Type: text/plain; charset=US-ASCII Igor J. Barani writes: > Dear CCL Readers, > > I have just recently installed Linux on a DEC Alpha and when I compile > several programs in fortran on it, they seem to compile to twice the > size and require 9 times as long to run than on DEC UNIX. Do you have > any idea why this may be so and how I may be able to speed up the > processes? Any suggestions would be greatly appreciated. Thank you. The standard gcc compiler as shipped with most Linux distributions is not optimized for Alpha chips. If you want better performance with fortran code you may want to have a look at egcs at http://www.cygnus.com/egcs . Egcs compiled binaries yield much better performance on Alphas. Regards Jochen --Multipart_Thu_Mar__5_14:16:51_1998-1 Content-Type: text/plain; charset=US-ASCII Jochen Buehler EMail: jochen@amiga.chemie.uni-konstanz.de AG Prof. Dr. Daltrozzo buehler@chemie.uni-konstanz.de Fakultaet fuer Chemie Phone: +49-7531-882094 Universitaet Konstanz Fax: +49-7531-883043 --Multipart_Thu_Mar__5_14:16:51_1998-1-- From smanian@giaspn01.vsnl.net.in Thu Mar 5 10:15:54 1998 Received: from giaspn01.vsnl.net.in for smanian@giaspn01.vsnl.net.in by www.ccl.net (8.8.3/950822.1) id JAA18741; Thu, 5 Mar 1998 09:52:52 -0500 (EST) Received: by giaspn01.vsnl.net.in; (5.65v3.2/1.1.8.2/20Feb96-0821PM) id AA05216; Thu, 5 Mar 1998 20:32:33 +0500 Date: Thu, 5 Mar 1998 20:32:33 +0500 (GMT+0500) From: Dr S K Malasubramanian To: Chemistry@www.ccl.net Subject: Guidance for internet access.Request for help. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII S. K. Balasubramanian. Ph .D., B-8, Apsara Apartments, Ph.: (0212) 620627 259,Bund Garden Road, Pune 411001. (India) e-mail address: smanian@giaspn01.vsnl.net.in 5th March 1998 8:03:37 PM To Chemsitry@www.ccl.net. Dear Sirs, I wish to place an original paper on atomic structure on the internet. The paper proposes a determinate model for atomic structure. It is a qualitiative proposal derived from structural chemistry. It explains in a rational manner the diverse chemistry of Carbon, Silicon and Boron. The structure of diborane is a compulsive consequence of the model . I am seeking your guidance on how to place the material on the internet. I have another handicap. My account with the local server is a limited one for textual material. I cannot transmit drawings or coloured photographs of which there are several in the paper. Can you help? If needed I can send the paper in full text to you with the figures and photos. I would be thankful for any help. Thanking you, Yours , S.K.Balasubramanian. From dgallis@mailbox.syr.edu Thu Mar 5 12:15:56 1998 Received: from syr.edu for dgallis@mailbox.syr.edu by www.ccl.net (8.8.3/950822.1) id LAA19550; Thu, 5 Mar 1998 11:45:58 -0500 (EST) Received: from gamera.syr.edu (dgallis@gamera.syr.edu [128.230.1.14]) by syr.edu (8.8.8/8.8.8) with SMTP id LAA29011 for ; Thu, 5 Mar 1998 11:45:58 -0500 (EST) Date: Thu, 5 Mar 1998 11:45:53 -0500 (EST) From: "Damian G. Allis" X-Sender: dgallis@gamera.syr.edu Reply-To: "Damian G. Allis" To: chemistry@www.ccl.net Subject: DeFT on Alpha's II Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all once again! I'd thank everyone individually who responded to my compliation problem, but there were just too many (ya'll know who you are, though). Of course, it turned out to be something stupid that wouldn't happen in a superior OS like Linux ;). Actually, if anyone is looking to buy a machine devoted solely to DeFT, get a Digital PW 500 and keep it using Digital Unix. It's already taken two days off of a decaborane calculation. Anyway, I've a second question for anyone. I'm trying to setup a vibrational analysis for a series of molecules, but have no idea as to how to set up the "restart" file it needs. Basically, I'm not sure if one re-does the DeFT_shell file to redirect things, where to put the restart file, etc. If anyone has a procedure for this, it'd be very cool. Thanks in advance, Damian Damian Allis dgallis@syr.edu nekid w/o a sig. From jesusmc@scripps.edu Thu Mar 5 13:15:56 1998 Received: from relay1.scripps.edu for jesusmc@scripps.edu by www.ccl.net (8.8.3/950822.1) id NAA20321; Thu, 5 Mar 1998 13:04:23 -0500 (EST) Received: from poirot.scripps.edu (poirot.scripps.edu [137.131.240.25]) by relay1.scripps.edu (8.8.8/TSRI-1.9rn) with ESMTP id KAA10604 for ; Thu, 5 Mar 1998 10:04:22 -0800 (PST) Received: (from jesusmc@localhost) by poirot.scripps.edu (8.8.5/TSRI-1.4) id KAA06221 for chemistry@www.ccl.net; Thu, 5 Mar 1998 10:03:53 -0800 (PST) Date: Thu, 5 Mar 1998 10:03:53 -0800 (PST) From: Jesus Castagnetto Message-Id: <199803051803.KAA06221@poirot.scripps.edu> To: chemistry@www.ccl.net Subject: Re: CCL:Guidance for internet access.Request for help. X-Sun-Charset: US-ASCII Sorry to all, but I tried e-mailing the originator of the email, but the address: smanian@vsnl.net.in, gave errors and the message bounced back. If someone can forward this to him, it'll be appreciated. ---- Hello, If you would like, I could get free web space in geocities or any other place like that, in your name, and give you a hand with putting your info on the web. If you already have the paper in HTML format, or a format that can be converted to HTML, it'll be even better. Greetings from San Diego. ===== Jesus M. Castagnetto Ph.D. - jesusmc@scripps.edu TSRI, Dept. of Molecular Biology |"Activation Energy: The useful 10550 N. Torrey Pines Rd. MBP326 | quantity of energy available La Jolla, CA 92037 | in one cup of coffee." Phone: 619-784-8582 Fax: 619-784-2289 E-Paper: http://www.ch.ic.ac.uk/ectoc/echet96/papers/003/ Lab: http://www.scripps.edu/research/metallo/ MetalloDB: http://mdb.scripps.edu/index.html From daizadeh@kappa.ucdavis.edu Thu Mar 5 13:19:30 1998 Received: from kappa.ucdavis.edu for daizadeh@kappa.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id MAA19993; Thu, 5 Mar 1998 12:28:28 -0500 (EST) Received: (from daizadeh@localhost) by kappa.ucdavis.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id JAA23679; Thu, 5 Mar 1998 09:34:01 -0800 From: "Iraj Daizadeh" Message-Id: <9803050934.ZM23677@kappa.ucdavis.edu> Date: Thu, 5 Mar 1998 09:34:01 -0800 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Summary:G94 -> and Cc: guo@indigo.ucdavis.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. Here is a summary of those that replied to my query (see below) concerning the printing of two electron integrals from a conventional scf calculation. In general, to print out two electron integrals into a standard G94 output file is to insert the following keywords into the input deck: extralink=l316 NORAFF (for pure integrals - optional) and make sure that the SCF keyword is set to conventional. To simply save the binary file, see the last comment below. Thank you very much. Iraj. ---------------------------------------------------------------------- -------------------------------------------------------------------------- Orginal question - Hello. In g94, how does one deal with extracting and saving the 2 electron integrals in either binary or ascii (memory) and reading them into their own programs. The g94 manuals are rather nebulous when it comes to this matter since in ``modern'' scf calculations these integrals are calculated on the fly. Thank you in advance. Iraj. -------------------------------------------------------------------- Responses. ---------------------------------------------------------------------- Dear Iraj You can read two-electrons integrals from the ouput file of gaussian.If you write on your route card extralink=l316 and iop(3/33=1) gaussian prints the list of the two-el integrals...But be carefull with the format...To obtain pure integrals you have to write also NORAFF...Now you can extract from the output file the values.If you only need the integrals you can kill te job just after they have been calculated... Bye /-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/ I Pedro Salvador Sedano I I \ Universitat de Girona I Para que necesitaran alas / I Institut de Quimica Computacional I los pajaros si la comida esta I / E-mail: perico@stark.udg.es I en el suelo...? \ I WWW :http://stark.udg.es/~perico I I \ Telf: +34 42 418358 I Anonimo / \-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\-/-\ ----------------------------------------------------------- The traditional approach is to use SCF=Conventional which will create a file with the two electron integrals. The routines for processing these are discusses with the other I/O routines, page 56 in the Programmer's Reference. Note that this limits you to s,p,d and f functions as only the direct integral routines have been updated for higher angular momentum. You can also get text printouts by turning on # ... SCF=Conventional IOP(3/33=6) EXTRALINKS=l316 which will list the integrals with labels in debug format. These will be printed in the log file. Douglas J. Fox Director of Technical Support help@gaussian.com -------------------------------------------------------------------------- Iraj, G94 integral file can be obtained with the keyword SCF=Conventional (p.149 of the user's ref. manual) Then with the Link 0 command to save the integral file %INT=filename (p. 159 of the user's ref. manual) Bill Fink --------------------------------------------------------------------------- -- Iraj Daizadeh Department of Chemistry University of California One Shields Ave. Davis, CA 95616-5295 Phone: 530.754.8695 Fax: 530.752.8995 email: daizadeh@kappa.ucdavis.edu From ra_eades@ccmail.pnl.gov Thu Mar 5 14:15:56 1998 Received: from pnl.gov for ra_eades@ccmail.pnl.gov by www.ccl.net (8.8.3/950822.1) id OAA20722; Thu, 5 Mar 1998 14:14:47 -0500 (EST) Received: from pnlmse1.pnl.gov by pnl.gov (PMDF V5.1-10 #21283) with ESMTP id <01IUB03B3WG08ZG7SX@pnl.gov> for chemistry@www.ccl.net; Thu, 5 Mar 1998 11:14:48 PST Received: from ccmail.pnl.gov ([130.20.128.23]) by pnlmse1.pnl.gov with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.1960.3) id FVG69C9J; Thu, 05 Mar 1998 11:14:41 -0800 Received: from ccMail by ccmail.pnl.gov (IMA Internet Exchange 2.12 Enterprise) id 0042C751; Thu, 05 Mar 1998 11:14:35 -0800 Date: Thu, 05 Mar 1998 11:19:09 -0800 From: ra_eades@ccmail.pnl.gov (Robert A Eades) Subject: Tutorial on NWChem & ecce' at PNNL on March 23-25 To: chemistry@www.ccl.net Message-id: <0042C751.4025@ccmail.pnl.gov> MIME-version: 1.0 Content-type: text/plain; charset=US-ASCII Content-description: cc:Mail note part Content-transfer-encoding: quoted-printable What: Tutorial on NWChem and ecce' When: March 23-25, 1998 Where: William R. Wiley Environmental Molecular Sciences Laborator= y at the Pacific Northwest National Laboratory, Richland, WA Registration Deadline: Monday, March 16, 1998 Registration Fee: None More information can be found on the web at: Tutorial - http://www.emsl.pnl.gov:2080/docs/nwchem/tutorial/train.html NWChem - http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html ecce' - http://www.emsl.pnl.gov:2080/docs/ecce/ecce.html MSCF - http://www.emsl.pnl.gov:2080/capabs/mscf.html EMSL - http://www.emsl.pnl.gov/ If you or any members of your research team are interested in attending t= his tutorial please take a few moments to fill out and return the enclosed information request form. Attendance is limited, so please return the registration form no later than March 16, 1998. Attendees MUST be regist= ered by March 16 in order to obtain a PNNL visitor badge. A block of rooms has been reserved for attendees at the Best Western Towe= r Inn in Richland, WA, (509) 946-4121 FAX (509) 946-2222. Rates are $50.00 sin= gle; $59.00 double. Please call the hotel directly before March 6, referencing= "NWChem" to make your reservations. After March 6, the rate is not guara= nteed to be available. The hotel offers shuttle service to and from the Pasco,= WA airport. PNNL has arranged additional transportation between the Lab and= the Tower Inn. = =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D = CUT HERE =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D NWChem/ecce' Tutorial Registration March 23-25, 1998 PNNL, EMSL Building Please complete (printed legibly or typed) the following and fax back to = Becky Wattenburger at (509) 375-6631 by March 16, 1998. Late submission= s will not be honored. Full name: Date of birth: Place of birth: Citizenship: Social Security number: Passport number and expiration date (if not US citizen): Business Address: = Phone: Fax: email: Select one of the Tuesday March 24 afternoon sessions: ( ) NWChem Developers training ( ) ecc=E9/NWChem Lab session ( ) Depart for home (specify your flight time: ) Will you be staying for the optional Wednesday, March 25 lab session? = = ( ) Yes ( ) No For lodging accommodations, please contact the = Best Western Tower Inn on (509) 946-4121 FAX (509) 946-2222. Rates are $= 50.00 single, $59.00 double. Please reference "NWChem" to receive the special = rates, again by March 6. Tower Inn provides a shuttle service to and from the a= irport. The specified rates are not guaranteed to be available after March 6. Transportation to and from PNNL to this hotel will be provided. Contact: Becky Wattenburger WR Wiley Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory 509-375-6450/509-375-6631 (FAX) becky.wattenburger@pnl.gov =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D CUT HERE =3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D DRAFT AGENDA: NWChem/ecce' Tutorial Sunday, March 22 5:45 PM Bus departs Tower Inn for Reception at Bookwalter Winery 6:00 PM Reception at Bookwalter Winery 8:00 PM Bus departs Bookwalter Winery for Tower Inn Monday, March 23 = 7:45am Bus departs Tower Inn to EESB building for badging 8:20 Walk to EMSL Building Training Room Users Training 8:30 NWChem Introduction (JA Nichols) functionality; targets; expectations; supported platforms; user s= upport; = WWW pages 9:10 ecce' Introduction (DK Gracio) functionality; targets; expectations; supported platforms; user s= upport; = WWW pages 9:50 NWChem input (RA Kendall) = input file structure: start, continue & restart, memory, title, p= rint & noprint, set & unset, stop, task, charge, geometry, basis & ecp 10:50 Coffee Break = 11:00 SCF & DFT (RJ Harrison & JA Nichols) 11:30 Optimization & Properties (M Dupuis) optimization; properties; esp; nbo 12:15 Lunch - EMSL Dining Room 1:15 ecce' Input (KL Schuchardt & GD Black) calc. manager; builder; calc. editor; basis set 2:15 ecce' (KL Schuchardt & DK Gracio) machine browser; launcher; calc. viewer; calc. browser = 3:15 Introduction to User Services (DR Jones) 3:30 Lab (all) 6:00 Depart EMSL for dinner at Red Robin Tuesday, March 24 = 8:00am Bus departs Tower Inn to EMSL Building 8:30 Correlated Methods (RJ Harrison) MP2, MCSCF, CI, CCSD(T) 9:00 GAPSS (AC Hess) 9:30 Molecular Dynamics (TP Straatsma) Classical MD - functionality; domain decomposition; file structur= e; = example calculations QMD - functionality QM/MM - functionality 10:30 Coffee Break 10:40 Using the IBM-SP (RA Kendall) logging on; loadl commands; NWChem job script = 11:40 Users wrap-up 12:15 Lunch - EMSL Dining Room Developers Training/Optional User Lab 1:00 NWChem architecture (RJ Harrison) code structure; distributed data; tools: ga, ma 1:30 NWChem API's (RA Kendall) task, input, module; example including new module 2:30 NWChem tools (RJ Harrison) example using tools: ga, ma, etc 3:30 NWChem build (RJ Harrison) makefile structure 4:00 NWChem future developments (JA Nichols) 4:30 Developers wrap-up Q&A session (all) 5:00 Lab (all) 6:00 Depart to Tower Inn (no dinner plans) Wednesday, March 25 9:00 - 4:00 Optional lab day =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D END OF MESSAGE =3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From kostov@rainbow.uchicago.edu Thu Mar 5 15:16:01 1998 Received: from rainbow.uchicago.edu for kostov@rainbow.uchicago.edu by www.ccl.net (8.8.3/950822.1) id PAA21122; Thu, 5 Mar 1998 15:15:00 -0500 (EST) Received: (from kostov@localhost) by rainbow.uchicago.edu (8.8.6/8.8.6) id OAA27153 for chemistry@www.ccl.net; Thu, 5 Mar 1998 14:15:02 -0600 (CST) Date: Thu, 5 Mar 1998 14:15:02 -0600 (CST) From: Konstantin Kostov Message-Id: <199803052015.OAA27153@rainbow.uchicago.edu> To: chemistry@www.ccl.net Subject: All-atom simulations of helix-coil transition without explicit solvent Dear CCLers, I would appreciate references to all-atom simulations of a helix-coil transition without explicit solvent. In particular, how is the absence of water-peptide H-bonds handled in such simulations? If solvent is present, the breaking of an intrapeptide H-bond would normally be followed by formation of a peptide-water H-bond. Since this doesn't happen in vacuo the helical state will be artificially stabilized. Any thoughts/references on how to get around this artefact? Thanks in advance, Konstantin Kostov Department of Chemistry University of Chicago From renate_griffith@uow.edu.au Thu Mar 5 20:16:00 1998 Received: from wumpus.its.uow.edu.au for renate_griffith@uow.edu.au by www.ccl.net (8.8.3/950822.1) id TAA22123; Thu, 5 Mar 1998 19:25:44 -0500 (EST) Received: from vervoid.uow.edu.au (root@vervoid.uow.edu.au [130.130.120.8]) by wumpus.its.uow.edu.au (8.8.8/8.8.7) with ESMTP id LAA24840 for ; Fri, 6 Mar 1998 11:25:35 +1100 (EST) Received: from [130.130.56.58] (sralph.sci.uow.edu.au [130.130.56.58]) by vervoid.uow.edu.au (8.8.8/8.8.6) with SMTP id LAA08407 for ; Fri, 6 Mar 1998 11:25:33 +1100 (EST) X-Sender: renate@sci-pop.uow.edu.au Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 6 Mar 1998 11:27:38 +1100 To: CHEMISTRY@www.ccl.net From: renate_griffith@uow.edu.au (Renate Griffith) Subject: Dear SIRS Dear all, I do not want to take up too much bandwidth or start a flame, so please reply to me personally rather than to the list, BUT: a plea from a female scientist: PLEASE, PLEASE, DO SEND YOUR MESSAGES TO EVERYBODY NOT JUST TO MALE SCIENTISTS. The mindset that can not even conceive of scientists being other than male (as in "Dear Sirs, ...) is extremely hurtful. Quite apart from being wrong. Regards Renate *** The FOURTH AUSTRALIAN MODELLING WORKSHOP *** is happening soon http://www.chem.mq.edu.au/MM98 *** Dr. Renate Griffith Email: renate_griffith@uow.edu.au Department of Chemistry phone: +61 42 213516 University of Wollongong fax: +61 42 214287 Northfields Ave Wollongong NSW 2522 Australia