From rich@censa.org Fri Aug 15 04:17:47 1997 Received: from venus.star.net for rich@censa.org by www.ccl.net (8.8.3/950822.1) id DAA18383; Fri, 15 Aug 1997 03:37:27 -0400 (EDT) Received: from lysa (lysa.teamscience.com [199.232.114.18]) by venus.star.net (8.8.5/8.7.3) with SMTP id DAA13863; Fri, 15 Aug 1997 03:36:15 -0400 Message-Id: <3.0.32.19970815033906.0092f660@star.net> X-Sender: richlysa@star.net X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Fri, 15 Aug 1997 03:39:54 -0400 To: ldoyle@teamscience.com From: "Rich Lysakowski, Ph.D." Subject: Invitation to Open House of Collaborative Electronic Notebook Systems (CENS) Consortium Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 8bit =========================================================== This message is being sent to multiple mailing lists. We apologize for any duplicates you may receive. =========================================================== Dear Colleague, We request your attendance at an End User Open House of the Collaborative Electronic Notebook Systems (CENS) Consortium. PURPOSE OF THE MEETING: to disclose to you the strategies, products, processes, and schedules for the CENS Consortium’s Knowledge, Software and Hardware Deliverables. From this meeting you will get a lot of useful information about electronic notebook systems and the CENS Consortium’s work that will help you decide about your company’s level of membership and participation. MEETING TIME: 1:30 PM to 4:45 PM , Thursday, September 11, 1997 This immediately follows the American Chemical Society’s (ACS) Symposium on ELECTRONIC NOTEBOOKS AND INTRANETS at the Las Vegas Convention Center, >from 9 AM until 12 noon. MEETING PLACE: The CENS Consortium Open House will be held in the Capri 1 Room at the Riviera Hotel, in Las Vegas, Nevada on September 11 >from 1:30 PM until 4:45 PM. The Open House Agenda follows below. The Riviera Hotel & Casino is located at 2901 Las Vegas Boulevard South. COST TO YOU: Free to Confirmed Attendees. Free lunch will be provided to the first 40 confirmed attendees!! INTENDED AUDIENCE: Scientists, engineers, attorneys, librarians, records managers, archivists, intellectual property specialists, information technology and laboratory automation experts. ACTION REQUIRED BY YOU: Please send e-mail to Leslie Doyle at CENSA (ldoyle@censa.org) to register and to have the CENS Consortium Nondisclosure Agreement sent to you. See below for details. -------------------------------------------------------------- THE ACS SYMPOSIUM ON ELECTRONIC NOTEBOOKS AND INTRANETS: Dr. Rich Lysakowski will chair the ACS Symposium on "Electronic Notebooks and INTRANETS" as part 8 of the 12-part series of symposia designed to forward research and bring commercially supported electronic notebooks into global usage. In Las Vegas, many experts will present technical and legal research results and their views on commercial products applied to this area. Alternatively, see http://www.censa.org/CENSAp/ACSsym, papers 54 to 59 for Symposium details. See www.lib.uchicago.edu/~atbrooks/CINF/cinflas.htm, for abstracts of all ACS' CINF papers at the Las Vegas Meeting. See www.acs.org/meetings/lasvegas/welcome.htm for ACS Meeting details. The Las Vegas Convention Center is located at 3150 Paradise Road. The ACS Symposium and the CENS Consortium Open House will give you a solid view of the state of industry for electronic notebook systems and collaborative computing in science. For more information on CENS and CENSA, please see http://www.censa.org -------------------------------------------------------------- WORK OF THE CENS CONSORTIUM: To better understand the Consortium's work -- think about having a "collaborative electronic lab notebook system" that your teams of scientists worldwide can use to reliably capture, manage, securely share and permanently archive and retrieve ALL common data and records generated in R&D and testing labs. Then embed this tool into powerful, easy-to-use enterprise scalable frameworks that easily support complex R&D project data management and collaboration. Then include powerful tools that make it easy to integrate all your existing software tools. This integrated vision is a major goal of the Collaborative Electronic Notebook Systems Consortium. THE CENS CONSORTIUM'S MISSION: to drive creation of open, commercially available, reasonably-priced and supported advanced software to support intra-enterprise R&D team project data management and collaboration, focusing short-term on complete electronic notebook systems that meet end user, and corporate scientific, patent, regulatory, and technical requirements. CENSA is using the best available processes and methods for accelerating development work by handling most operational details for Members, such as eliminating unnecessary and costly preliminary meetings. Many other steps are being taken to speed development and reduce costs to Members. At this meeting you will learn about the processes being used to fulfill the Consortium’s mission, including: 1) Prioritizing the functional and business requirements for R&D team computing and collaborative electronic notebook systems, in a few months, rather than years proposed by others; 2) Rapidly assessing commercially available and emerging technologies, with the objective of building upon more than one set of base platforms, middleware, and desktop components; 3) Contracting with the best qualified vendors to enhance or construct the necessary base platforms, tools, and applications so they become robust and full-function R&D Team Computing Systems with electronic notebooks; 4) Overseeing and administering the development and testing processes for the resulting software; 5) Pre-testing and certifying the software and hardware deliverables in the CENS Consortium Testbed Laboratory before it ships to Members; and 6) Issuing certified products to Consortium Members at substantial discounts. We are also sponsoring CENS Program Groups, which are CENS groups focused on regulatory processes and technology development. Key deliverables include detailed System Specifications, Statements of Best Practices, and SOPs for Fully Electronic Records Management and Recordkeeping in Regulated Industries. Some Members have told us that the CENS Program Groups alone are worth the price of joining. The Consortium is selecting base platforms and vendors based on the rigorous screening process developed by Members. Vendors and systems include those for electronic notebooks and recordkeeping, groupware, document management, the World Wide Web, LIMS, instrument interfacing, chemical, biological, spectroscopic, and materials data management, and other tools. The CENS Consortium emphasizes an open process, driven by end user and vendor needs, to result in products marketed by Consortium Vendors with truly open, modular and extensible designs, using or defining standards wherever possible. If you want to know more about CENS and the CENS Consortium, we wholeheartedly invite you and your company to attend this Open House. Please feel free to call if you have any questions. We look forward to seeing you on September 11, and working with you in the near future as part of the Collaborative Electronic Notebook Systems Consortium. Sincerely, Rich Lysakowski, Ph.D., Executive Director, The Collaborative Electronic Notebook Systems Consortium Phone: 617-935-9600; fax: 617-935-3113; E-Mail: rich@censa.org; Web: www.censa.org ============================================================== P.S. THIS MEETING IS ONLY OPEN TO END USER COMPANIES IN THE CHEMICAL, PHARMACEUTICAL, BIOTECHNOLOGY, AGRICHEMICAL, FOOD AND BEVERAGE, OIL AND GAS,CONSUMER PRODUCTS, ENVIRONMENTAL, AND RELATED INDUSTRIES. THIS MEETING IS NOT OPEN TO COMPUTER, SOFTWARE OR SERVICE VENDORS OF ANY KIND. HOWEVER, FUTURE MEETINGS WILL BE OPEN TO VENDOR MEMBERS. To attend this disclosure meeting, you must return a current CENSA NONDISCLOSURE AGREEMENT signed by a legal representative of your company, because we will be disclosing significant proprietary information that took years to develop. This is the only way to be confirmed as an attendee. Please send e-mail to Leslie Doyle at CENSA (ldoyle@censa.org) to have the CENSA Nondisclosure Agreement sent to you. No person can attend the Consortium meeting without a signed agreement received by CENSA at least two days ahead of the meeting. Please call 617-935-9600 if you need further clarification or questions about this. If you have recently signed this agreement then you have already fulfilled this requirement for attendance. Copyright 1997 - CENSA, All Rights Reserved Internationally ============================================================== MEETING AGENDA FOR THE COLLABORATIVE ELECTRONIC NOTEBOOK SYSTEMS (CENS) CONSORTIUM OPEN HOUSE 1:30 PM to 4:45 PM , Thursday, September 11, 1997, Las Vegas, Nevada Free Lunch served at 12:30 PM to the first 40 confirmed attendees!! MEETING AGENDA - Introductions of Consortium Participants and Meeting Attendees - Collaborative Electronic Notebook Systems (CENS) & The CENS Consortium - Business Problems The CENS Consortium is Solving - R&D Team Computing Consortium Deliverables - Legal and Regulatory Program - Technical Program Knowledge Deliverables - Software and Hardware Systems and Tools - CENSA Technical Architecture for Electronic Notebook Systems - Project Management, Product Management and Delivery Processes - Consortium Research and Development Schedule - Fiscal and Human Resources Required From Participants - Closing the Loop on Your Company’s Participation - General Discussion and Next Steps for Your Company --------------------------------------------------------- EVENING CLOSED-DOOR MEETING - FOR CONSORTIUM MEMBERS ONLY Reviews of: - System Functional Specifications for Notebook Clients, Servers, and Integration Tools - Consortium Technical Architecture - Progress on Engineering Work and Schedules - Progress on Vendor RFPs and Vendor Participation - Other Ongoing Work with Vendors - Consortium Membership Activities - Discussion of Next Steps Message sent using MailDelay Daemon started at 5:00 PM EST. From Eugene.Leitl@lrz.uni-muenchen.de Fri Aug 15 05:17:47 1997 Received: from sunsrv5.lrz-muenchen.de for Eugene.Leitl@lrz.uni-muenchen.de by www.ccl.net (8.8.3/950822.1) id EAA18738; Fri, 15 Aug 1997 04:47:45 -0400 (EDT) Received: from sun6.lrz-muenchen.de by sunsrv5.lrz-muenchen.de; Fri, 15 Aug 97 10:47:45 +0200 Received: by sun6.lrz-muenchen.de (5.x/SMI-SVR4) id AA00268; Fri, 15 Aug 1997 10:47:46 +0200 Date: Fri, 15 Aug 1997 10:47:46 +0200 (MET DST) From: Eugene Leitl X-Sender: ui22204@sun6 To: chemistry Subject: which MD package to turn to for starters? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I just downloaded the sources from "The Art of Molecular Dynamics Simulation" by D.C. Rapaport, from http://www.cup.cam.ac.uk/onlinepubs/ArtMolecular/ArtMoleculartop.html (actually, from ftp://ftp.cup.cam.ac.uk/pub/science/ArtMolecular/artmdsim.tar.gz ) Is there a free nontrivial MD package for Linux out there, to get started quickly? I'm interested in solvated linear (bio)polymers, especially proteins. A quick & dirty trajectory renderer for X would be also very nice to have. My hardware is currently very puny: 32 MBytes RAM, K5/166, RedHat 4.2. (I intend to upgrade to 128 MBytes K6/233 quite soon though, then turning to DSP boards (SHARC, 'C6x) for crunch assistance, so raw horsepower should not be a problem in the future). Roughly, systems of which size/duration are accessible with my current configuration (K5/166, 32 MBytes RAM)? ______________________________________________________________________________ icbmto:N 48 10'07'' E 011 33'53'' http://www.lrz-muenchen.de/~ui22204 From isao@akina1.aki.che.tohoku.ac.jp Fri Aug 15 07:17:47 1997 Received: from akina1.aki.che.tohoku.ac.jp for isao@akina1.aki.che.tohoku.ac.jp by www.ccl.net (8.8.3/950822.1) id GAA19240; Fri, 15 Aug 1997 06:34:19 -0400 (EDT) Received: by akina1.aki.che.tohoku.ac.jp (8.6.12+2.5Wb7/2.7W) id TAA10825; Fri, 15 Aug 1997 19:31:26 +0900 Message-Id: <199708151031.TAA10825@akina1.aki.che.tohoku.ac.jp> To: chemistry@www.ccl.net Subject: [Q] Tight Binding Molecular Dynamics with Periodic Boundary. Cc: isao@aki.che.tohoku.ac.jp Date: Fri, 15 Aug 1997 19:31:25 +0900 From: "Isao Gunji .Sendai. Japan" Dear CCLers, I'm japanese graduate student. Sorry for consuming some of your valuable time. Please give some answers if you like. I want to do tight binding molecular dynamics(TBMD) calculation about the system with periodic boundary condition(PBC) such as surface or bulk(2 or 3 dimension). Especially, I am very interested in the oxide surface as many think so. So in the first place, I searched papers of TBMD with PBC about oxide system by Current Content. But I couldn't find such papers. There are a few papers about TBMD with periodic boundary condition, though there are many papers about TBMD about Si cluster(some about big cluster). I studied TBMD with cluster model by the paper, Journal:J. Phys.:Condens. Matter 2 (1990) 1509-1520. title: Molecular dynamics using the tight-binding approximation. author: K. Lassonen and R. M. Nieminen. This paper is good for me to understand what I shoud do when I want to TBMD calculation about Si cluster. Let me in main subject. I have some questions and requests. (1) Is there free program about TBMD with *PBC* ?(If you know, please teach me.) (2) Is TBMD with PBC hard to program ? (What part is difficult in compariosn with TBMD about Cluster system?) (3) Is TBMD method suitable for oxide? ( If it is not, What is the reason.) I don't have a perfect command of English( neither physics.;-) ) So , if I didn't use appropriate words in upper sentence, please point it out. Please sent all answers to my e-mail. Many thanks! I will summarize mails which are sent to me, and send the mail to here. -->isao@aki.che.tohoku.ac.jp Thank you for your reading my mail. From tevelde@scm.com Thu Aug 14 04:34:15 1997 Received: from gallium.chem.vu.nl for tevelde@scm.com by www.ccl.net (8.8.3/950822.1) id EAA12029; Thu, 14 Aug 1997 04:07:25 -0400 (EDT) Received: from thallium.chem.vu.nl by gallium.chem.vu.nl (5.64/AUX-3.1.1) id AA07182; Thu, 14 Aug 97 10:07:23 MET DST X-Sender: tevelde@chem.vu.nl Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 14 Aug 1997 10:07:24 +0100 To: chemistry@www.ccl.net From: tevelde@scm.com (Bert te Velde) Subject: Re: CCL:ADF: AE-Fit-functions (answer) >original question: > >>Has anybody developed fit-functions for the all-electron-basis >>to be used in ADF? I ask this question because we would like to >>do a geometry-optimization in an electric field by hand (coordinate >>driving) In our opinion it is important to take into account the >>inner shells too to explain a molecular electrostriction. >>Are there other opinions? > >answer from Christoph Schwittek: > >> Two comments on your question. First, you can make the fit basis >>yourself. Any combination of two basis functions contributes to the >>density, and hence must be represented by the fit basis. For instance, >>if your basis has two p-sets with coefficients alpha1 and alpha2, >>then there is a d-type contribution in the density with coefficient >>alpha1 + alpha2 that must be represented by the fit basis (in fact, >>there are two more d-type contributions, with coefficients 2*alpha1 >>and 2*alpha2). We had in Calgary an old utility program with ADF >>that would calculate from a given basis set all the possible combinations >>for the fit and their respective overlap, so that one can choose a reasonabl= >e >>fit basis from that. The program is called "alphas" -- maybe you can >>obtain it or its successor from Amsterdam. I have occasionally >>created basis sets with smaller cores, and consequently had to >>make a new fit basis each time. >> Second, as you know, ADF uses numerical integration throughout. >>While this works well normally, I would be careful with all-electron >>calculations of heavy atoms because the very steep density near >>the nucleus might well strain the integration scheme over the limit, >>at least this was my experience sometimes. Admittedly, I haven't >>played with the detailed integration parameters here, and one can >>probably do a lot by just increasing the integration accuracy around >>the nuclei only. 1. about the numerical integration: ADF2.1 and later versions monitor the actually used functions in a calculation to determine the integration grid within the atomic core regions, so the fear for inadequate precision when using steeper functions is not needed anymore. It might have been for earlier versions when the program used fixed assumptions about what kind of steep functions would occur for the different elements of the periodic table. 2. the generation of all fitfunctions that would be needed according to the products-of-basisfunctions principle can of course easily be generated by any simple program. If there are people interested we may upgrade our own variety of such a program a little so as to include it in the packet as one of the utility programs. This is not the end of the story, however, since fitsets generated in this fashion are often close to linear dependency and one really has to remove some functions to avoid numerical trouble. In addition, this basis-products principle applies rigorously to single atoms but is not exact anymore when considering products of basisfunctions centered on different atoms. The limiting decaying behaviour is still correct but the true representation of the involved charge-density has more terms that may play a role closer to the nuclei and in the bonding region, and in particular components with higher l-values. Therefore, we ourselves use the products-principle only for a first set-up of fitsets. The method we actually use when developing fitsets is to use the products-of-basisfunctions only to determine the steepest and the most diffuse fitfunction on each atom(type), for each l-value separately, up to l=4, and then fill in the 'gap' between steep and diffuse in an even-tempered way, using an overlap criterion for 'adjacent' fitfunctions in the sequence to define some kind of 'density' of functions on the range: the higher this density the more accurate the total set, but also the more expensive the calculation, (and finally: too many functions will again result in numerical stability problems due to linear dependency). S-sets (l=0) are always chosen rather dense, and the numbers of used functions decrease with increasing l,first because these are less important and secondly because they imply a rapidly increasing computational effort (each s-fitfunction has only one "m"-component, each p: 3 components, each d: 5, etcetera) 3. We are currently looking into some re-investigation project on basis and fit sets, including the development of fitsets for the all-electron basis (in first instance only for the lighter elements). The problem is not so much to just create a bunch of fitfunctions and type them into the database, but to do large numbers of test calculations to assess the precision in practical terms: deviation of energy and other properties from some limiting value. Best regards ----------------------------------------------------------------------- Bert te Velde SCIENTIFIC COMPUTING & MODELLING phone: +31-20-4447625 Chemistry Department, Vrije Universiteit fax: +31-20-4447643 De Boelelaan 1083 email: tevelde@chem.vu.nl 1081 HV Amsterdam; The Netherlands ----------------------------------------------------------------------- From nathalie@chbs.ciba.com Thu Aug 14 06:17:32 1997 Received: from gatekeeper.chbs.ciba.com for nathalie@chbs.ciba.com by www.ccl.net (8.8.3/950822.1) id GAA12517; Thu, 14 Aug 1997 06:05:09 -0400 (EDT) Received: from cgchm.is.chbs by gatekeeper.chbs.ciba.com; (5.65v3.2/1.1.8.2/12Mar96-0208PM) id AA14464; Thu, 14 Aug 1997 12:04:39 +0200 Received: from camm1.ph.chbs by Central.CHBS.CIBA.COM id AA26090; Thu, 14 Aug 1997 12:05:09 +0200 (5.65c8/Ciba2.0-C1.1) Received: by camm1.ph.chbs (940816.SGI.8.6.9/940406.SGI/camm.ph.chbs-1.0) for chemistry@www.ccl.net id MAA10968; Thu, 14 Aug 1997 12:07:47 +0200 Date: Thu, 14 Aug 1997 12:07:47 +0200 From: nathalie@chbs.ciba.com (Nathalie Vancampenhout K136.4.96) Message-Id: <199708141007.MAA10968@camm1.ph.chbs> To: chemistry@www.ccl.net Subject: geom. optimiz. of macrolide Dear all, I am trying to optimiza the geometry of a macrolide with the s-e method AM1. The geometry doesn't reach a convergence...Is there someone with any experience with such of problem? Thanks for helpinf Nathalie From bausch@chem.vill.edu Thu Aug 14 18:17:39 1997 Received: from rs6chem.chem.vill.edu for bausch@chem.vill.edu by www.ccl.net (8.8.3/950822.1) id RAA16929; Thu, 14 Aug 1997 17:46:42 -0400 (EDT) Received: from [153.104.73.18] (bausch.chem.vill.edu [153.104.73.18]) by rs6chem.chem.vill.edu (8.8.5/8.8.5) with SMTP id RAA13073 for ; Thu, 14 Aug 1997 17:52:56 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 14 Aug 1997 05:47:17 -0500 To: chemistry@www.ccl.net From: bausch@chem.vill.edu (Joseph W. Bausch) Subject: compiling G94 on a linux machine Anybody out there wish to lend their expertise helping a semi-newbie get G94 compiled on a linux machine? OK, for those of you that are willing to read further! Here is what we have to the best of my knowledge. DualPentiumPro w/ linux 2.0.30, f2c version 960717, gcc version 2.7.2.2, and libc 5.4.33 These are supposedly higher versions than Gaussian's home page says we need. I have gotten G94 ver E2 off a 8 mm tape onto another unix machine (my linux box doesn't have a tape drive), then ftp over the source. I have followed the instructions that came with the rev E2 exactly as they are written, but the build part only runs a short while before stopping. I won't post the entire log file, but here are the first few lines. I am wondering if the last lines of this indicative of a problem with my libc? uname -a Linux linux 2.0.30 #5 Tue Aug 12 13:28:21 EDT 1997 i686 set makeflag = set makename = make setenv TMPDIR . if ( ( == ) || ( == all ) ) then @ dolink = 1 @ delexe = 1 @ doutil = 1 @ resutil = 0 else if ( ( == nolink ) || ( == utilonly ) ) then @ doprof = 0 @ dop1 = 0 @ doi8 = 0 if ( == prof ) then if ( == profi8 ) then if ( == ibmp1 ) then if ( == i8 ) then if ( != ) then if ( 0 && ( ! 1 ) ) then set utilname=util.a endif if ( 1 ) then touch delete_me.exe rm -f -r delete_me.exe util.a endif if ( `hostname` == sun4 ) then hostname if ( -e /usr/convex/bin/cc ) then cc -o gau-machine bsd/machine.c ./cca03508.i:1: numeric constant with no digits ./cca03508.i:1: numeric constant with no digits ./cca03508.i:1: invalid #line ./cca03508.i:51: numeric constant with no digits ./cca03508.i:51: numeric constant with no digits ./cca03508.i:51: invalid #line ./cca03508.i:82: numeric constant with no digits ./cca03508.i:82: numeric constant with no digits ./cca03508.i:82: invalid #line ./cca03508.i:216: numeric constant with no digits ./cca03508.i:216: numeric constant with no digits ./cca03508.i:216: invalid #line ./cca03508.i:240: numeric constant with no digits ./cca03508.i:240: numeric constant with no digits ./cca03508.i:240: invalid #line ./cca03508.i:259: numeric constant with no digits ./cca03508.i:259: numeric constant with no digits ./cca03508.i:259: invalid #line ./cca03508.i:261: numeric constant with no digits ./cca03508.i:261: numeric constant with no digits ./cca03508.i:261: invalid #line ./cca03508.i:278: numeric constant with no digits ./cca03508.i:278: numeric constant with no digits ./cca03508.i:278: invalid #line ./cca03508.i:299: numeric constant with no digits ./cca03508.i:299: numeric constant with no digits ./cca03508.i:299: invalid #line ./cca03508.i:318: parse error at null character ./cca03508.i:318: virtual memory exhausted endif (rest deleted) If posting the rest of the log file is needed, I can do so. Thanks for any help you can provide! Joe ---------------------------------------------------------------------------- Joseph W. Bausch, Ph.D. Assistant Professor of Chemistry Department of Chemistry Villanova University Villanova, PA 19085-1699 Voice: 610-519-4872 FAX: 610-519-6347 (preferred) or 610-519-7167 Email: bausch@rs6chem.vill.edu WWW: http://rs6chem.vill.edu/faculty/bausch.htm ---------------------------------------------------------------------------- From schiffer@h1tw0036.hoechst.com Fri Aug 15 11:17:51 1997 Received: from backup.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id LAA20603; Fri, 15 Aug 1997 11:08:35 -0400 (EDT) Received: by backup.hoechst.com id RAA22789; Fri, 15 Aug 1997 17:04:28 +0200 Received: from unknown(134.81.76.36) by backup id sma022781; Fri Aug 15 17:03:49 1997 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id RAA05491; Fri, 15 Aug 1997 17:07:23 +0200 Message-ID: <33F470AA.41C6@h1tw0036.hoechst.com> Date: Fri, 15 Aug 1997 17:07:22 +0200 From: "Dr. Heinz Schiffer" Organization: Hoechst Corporate Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Computational Chemistry List CC: "Haeser, Marco, Dr." Subject: diradical singlets Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello all, does anyone out there has experience with the calculation of singlet states of diradicals within density functional theories ? If so, it would be very nice to get some information of it. To be more specific : I have only an unrestricted (or spin-polarized) DFT code available to handle open-shell systems. Within an unrestricted procedure you can only calculate electronic states, which can be described by a single Slater determinant. The triplet state of a diradical is therefore no problem, because the triplet state can, e.g., be described by a single Slater determinant (a_a,b_a). a_a is orbital a with alpha spin, b_a is orbital b with alpha spin. The energy is h_aa + h_bb + J_ab - K_ab. h_aa and h_bb are the expectation values of the one-electron operators with orbitals a and b, respectively. J_ab and K_ab are the usual Coulomb and exchange energies. The singlet state of a diradical represents a problem in so far, as it is described by a linear combination of two Slater determinants : 1/sqrt(2) * [ (a_a,b_b) - (a_b,b_a) ]. a_a and b_a as above, a_b and b_b are orbitals a and b with beta spin. The energy is h_aa + h_bb + J_ab + K_ab. Within an unrestricted (or spin-polarized) procedure, you cannot use two determinants. Within the Roothaan open-shell formalism of the Hartree-Fock method and the corresponding formalism of the Kohn-Sham method, you can ! But as I mentioned above, I do not have acces to such a program. Now, there is a trick : The energy of the single Slater determinant (a_a,b_b) is : h_aa + h_bb + J_ab. If you take that expression two times and substract the energy of the triplet state from it, you end up with the same energy expression as for the singlet state ! So, I tried to do an unrestricted DFT calculation for the mixed state, described by the single Slater determinant (a_a,b_b). And I got tremendous convergence problems : after several thousand iterations (with and without DIIS, level shifts, damping, etc.) I always end up with a wild oszillatory behaviour in the energy. Therefor my question, if anyone has experience with such calculations. Ciao, Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com From korkin@qtp.ufl.edu Fri Aug 15 12:18:59 1997 Received: from qtp.ufl.edu for korkin@qtp.ufl.edu by www.ccl.net (8.8.3/950822.1) id LAA26675; Fri, 15 Aug 1997 11:37:07 -0400 (EDT) Received: from white7 by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id LAA11053; Fri, 15 Aug 1997 11:36:34 -0400 Message-Id: <199708151536.LAA11053@qtp.ufl.edu> Date: Fri, 15 Aug 1997 11:36:44 -0400 (EDT) From: Anatoli Korkin Reply-To: Anatoli Korkin Subject: Re: CCL:geom. optimiz. of macrolide To: nathalie@chbs.ciba.com Cc: chemistry@www.ccl.net MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: O1rRwBtzSXrD1uZDXtqlow== X-Mailer: dtmail 1.2.0 CDE Version 1.2 SunOS 5.6 sun4c sparc Natalie, There can be many reasons why your structure does not converge. It is hard to give general advices witout seeing the case. It is the same as asking for a diagnosis by telephone tellling that someone has a fiver. One simple reason can be two close conformations or two close electronic states which oscilate. Series of separate partial optimization of parameters which have different force constants (e.g. optimization of dihedral angles separately from others) may help. Other suggestion is using different algorithms for optimizations, modifying maimal step in optimization, etc. Even a better definition of z-matrix can be crucial. If this does not help, you need to see a doctor :-) Good luck, Anatoli > > Dear all, > I am trying to optimiza the geometry of a macrolide with the s-e method AM1. > The geometry doesn't reach a convergence...Is there someone with any > experience with such of problem? > Thanks for helpinf > Nathalie > > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- > From ccl@www.ccl.net Mon Aug 11 18:17:00 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id RAA28183; Mon, 11 Aug 1997 17:52:39 -0400 (EDT) Received: from kodakr.kodak.com for mckelvey@kodakr.kodak.com by bedrock.ccl.net (8.8.6/950822.1) id RAA27176; Mon, 11 Aug 1997 17:52:38 -0400 (EDT) Received: from mail.rl.kodak.com by kodakr.kodak.com with SMTP id AB02614 (5.67b/IDA-1.5 for ); Mon, 11 Aug 1997 17:50:11 -0400 Received: from mozart.rl.kodak.com by mail.rl.kodak.com (8.8.3/1.1.10.5/17Jan97-0515PM) id SAA10076; Mon, 11 Aug 1997 18:03:03 -0400 (EDT) Received: from stomper (stomper.rl.kodak.com [150.220.76.39]) by mozart.rl.kodak.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id RAA16971; Mon, 11 Aug 1997 17:51:50 -0400 Message-Id: <33EE9A11.5125@kodak.com> Date: Mon, 11 Aug 1997 05:50:25 +0100 From: John McKelvey Reply-To: mckelvey@kodakr.kodak.com Organization: Eastman Kodak Company X-Mailer: Mozilla 3.0 (WinNT; I) Mime-Version: 1.0 To: chemistry@ccl.net Cc: mckelvey@kodakr.kodak.com Subject: Mail Lists Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit CCler's: Where can one find info for Netscape V3.o about creating mailing lists that is noticably clearer than Netscape 3.0 Help, and the related printed info in your (MY!) bookstore? Thanks, John -- ************************************ * John McKelvey * * Imaging Research and Development * * Building 83 * * Research Laboratories * * Eastman Kodak Company * * Rochester, NY 14650-2216 * * (V)716-477-3335 * * (F)716-722-2327 * * (E)McKelvey@Kodak.COM * ************************************ From baker@terminator.chem.uiowa.edu Fri Aug 15 14:17:53 1997 Received: from ns-mx.uiowa.edu for baker@terminator.chem.uiowa.edu by www.ccl.net (8.8.3/950822.1) id NAA27611; Fri, 15 Aug 1997 13:27:28 -0400 (EDT) Received: from terminator.chem.uiowa.edu (terminator.chem.uiowa.edu [128.255.69.76]) by ns-mx.uiowa.edu (8.8.5/8.8.5) with SMTP id MAA47070 for <@ns-mx.uiowa.edu:chemistry@www.ccl.net>; Fri, 15 Aug 1997 12:27:29 -0500 Received: by terminator.chem.uiowa.edu (940816.SGI.8.6.9/940406.SGI) id MAA16048; Fri, 15 Aug 1997 12:28:34 -0700 Date: Fri, 15 Aug 1997 12:28:34 -0700 (PDT) From: "Nathan A. Baker" To: CCL Subject: Gaussian 94 Question... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi -- I am trying to perform a NMR analysis of a molecule by reading in the wavefunction from a checkpoint file. I do not want Gaussian 94 to recompute the wavefunction, simplu calculate the shielding tensors. I was wondering if ayone had suggestions as to how this may be accomplished. I've tried %Chk=file %NoSave #Guess=(Read,Only) NMR title 0 1 coordinates but I immediately receive an error that NMR calculations can only be performed on single points. The input file %Chk=file %NoSave #Guess=Read NMR etc. will read in the molecule and estimate the nuclear repulsion energy, one-electron integrals, etc., but just after printing the smallest eigenvalue of the overlap matrix, the program terminates with the error: RdChkP: Unable to locate IRWF=0 Number= 522. Error termination via Lnk1e in /usr/local/g94/l401.exe. Any ideas? Thanks in advance. ----------------------------------------------- Nathan Baker * baker@terminator.chem.uiowa.edu HELP! MY TYPEWRITER IS BROKEN! -- E. E. CUMMINGS ----------------------------------------------- From gford@post.smu.edu Fri Aug 15 14:39:42 1997 Received: from post.cis.smu.edu for gford@post.smu.edu by www.ccl.net (8.8.3/950822.1) id NAA27507; Fri, 15 Aug 1997 13:18:56 -0400 (EDT) Received: by post.cis.smu.edu (/\==/\ Smail3.1.28.1 #28.3) id ; Fri, 15 Aug 97 12:18 CDT Message-Id: Date: Fri, 15 Aug 97 12:18 CDT From: "George P. Ford" Reply-To: "George P. Ford" To: jianwang@cgl.ucsf.edu Cc: CHEMISTRY@www.ccl.net Subject: CCL:Empirical solvation model Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Mailer: POPmail 2.3b2 Jian Wang wrote: > > Could someone points to me some empirical methods to > estimate free solvation energy of a molecule in > aqueous solution? > There are a couple of purely empirical methods for estimating solvation free energies. All use some kind of atom, group, or bond additivity. The scheme published by Cabani et al also predicts enthalpies and heat capacities of solution. Hine's method [2], based on Benson-like group contributions, is very accurate at the cost of a somewhat narrower range of applicability. We published an extension of Hine's method to organic onium ions [3] that worked quite well. [1] Cabani, S.; Gianni, P.; Mollica, V.; Lepori, L, J. Solution Chem., 1981, 10, 563-595. [2] Hine, J.; Mookerjee, P. K., J. Org. Chem., 1975, 40, 292-298. [3] Ford, G. P.; Dcribner, J. D., J. Org. Chem., 1983, 48, 2226-2233. > There are many solvation models to calculate solvation > free energy such as QM SCRF methods, AMSOL, PB, > GBSA, MD, MC and etc. What we would like to know is > the performance of empirical methods, i.e., what are > their standard errors over a large set of experimental > data or over other theoretical results, where an empirical > approach will break down. This is an interesting question. Most published comparisons of theoretical and experimental hydration energies are dominated by simple monofunctional compounds. Here the empirical methods are far more accurate than even highly parameterized methods like SM2. Unfortunately the most interesting chemistry invovles complex polyfunctional compounds where empirical methods should fail to some degree because of direct and/or indirect interaction between the substituents. On the other hand QM-based methods should be partly immune to this. We've tried to look into this in more detail. Unfortunately there just do not seem to be enough accurate experimental hydration data for appropriate polyfunctional compounds available. ============================================================================ George P. Ford | email: gford@smu.edu Department of Chemistry | web: http://www.smu.edu/~gford/ Southern Methodist University | telephone: (214)768-2479 Dallas, Texas 75275 | fax: (214)768-4089 ============================================================================ From elewars@alchemy.chem.utoronto.ca Fri Aug 15 18:17:52 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id SAA10850; Fri, 15 Aug 1997 18:01:06 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id SAA14152 for chemistry@www.ccl.net; Fri, 15 Aug 1997 18:01:01 -0400 (EDT) Date: Fri, 15 Aug 1997 18:01:01 -0400 (EDT) From: "E. Lewars" Message-Id: <199708152201.SAA14152@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: MACROLIDE Hello, your email address (nathalie. etc) doesn't work, so I'm using the CCL net. If you send me an ASCI drawing of the molecule I'll see what I can do; if it works I'll send you the Cartesians of the opt struct. e.g. send CH2-CH2 / \ O=C CH2 | \ O CH-CH3 / | CH2 CH-CH-CH2 etc etc etc E. Lewars ========= What program are you using in your attempted opt? ====