From chemistry-request@server.ccl.net Mon Apr 19 00:00:44 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA03634; Mon, 19 Apr 1999 00:00:44 -0400 Received: from tachyon.gw.ansto.gov.au (firewall-user@anstogw.gw.ansto.gov.au [137.157.8.253]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id XAA03210 Sun, 18 Apr 1999 23:57:39 -0400 (EDT) Received: by tachyon.gw.ansto.gov.au; id NAA05554; Mon, 19 Apr 1999 13:57:38 +1000 (EST) Received: from hadron.ansto.gov.au(137.157.13.219) by tachyon.gw.ansto.gov.au via smap (3.2) id xma005427; Mon, 19 Apr 99 13:57:24 +1000 Received: from b34_env_khz.ansto.gov.au (sn80-5.dhcp.ansto.gov.au [137.157.82.5]) by hadron.ansto.gov.au (8.9.3/8.9.3) with SMTP id NAA17691 for ; Mon, 19 Apr 1999 13:57:23 +1000 (EST) Message-Id: <2.2.32.19990419035724.0069e2e0@pop.ansto.gov.au> X-Sender: khz@pop.ansto.gov.au X-Mailer: Windows Eudora Pro Version 2.2 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 19 Apr 1999 13:57:24 +1000 To: chemistry@www.ccl.net From: Kate Harle Subject: searching for email Hi I am searching for the email address of Jeff Hey, who did his undergrad and PhD in chemistry at Monash University, Australia. I noticed that a Jeff Hey sent a message to this address in January (found this reference on the web) and was wondering if it was the same Jeff. If so, could he please contact me on my email address below. thankyou Kate Kate Harle Environment Division (Bld 34) ANSTO PMB 1 Menai, NSW 2234 Australia Ph. 61-2-9717-3880 FAX 61-2-9717-9270 http://home.ansto.gov.au/ From jkl@ccl.net Fri Apr 16 09:10:23 1999 -0400 Received: from gatekeeper.eastman.com (gatekeeper.eastman.com [164.89.253.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA28693 Fri, 16 Apr 1999 09:10:20 -0400 (EDT) Received: by gatekeeper.eastman.com; id JAA19861; Fri, 16 Apr 1999 09:13:27 -0400 (EDT) Received: from emngw1.eastman.com(164.89.254.2) by gatekeeper.eastman.com via smap (3.2) id xma018767; Fri, 16 Apr 99 09:12:47 -0400 Received: by eastman.com id AA750430 (5.67b/IDA-1.5 for chemistry@www.ccl.net); Fri, 16 Apr 1999 09:09:09 -0400 Received: from ntmcon02.emn.com by eastman.com with SMTP id AA770904 (5.67b/SMI-4.1 for ); Fri, 16 Apr 1999 09:09:07 -0400 Received: by ntmcon02.emn.com with Internet Mail Service (5.5.2232.9) id <2WFLTBXP>; Fri, 16 Apr 1999 09:09:08 -0400 Message-Id: From: "Wilson, Bruce E" To: "'chemistry@www.ccl.net'" Subject: Summary: Plotting 2D or 3D data and seeing chemical structure Date: Fri, 16 Apr 1999 09:09:06 -0400 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Type: text/plain Several people responsed to my original request for information regarding software which would allow one to plot 2D or 3D data and easily see the chemical structures associated with data points. The results are summarized below. A number of people asked me to not use their names in any summary, so I've taken the liberty of summarizing responses, rather than including them explictly. 1) A number of people recommended the combination of Spotfire (http://www.spotfire.com) with Isis (http://www.mdli.com). A demo version of Spotfire can be downloaded from their web site, though that version doesn't have the structure capability in it. It does, however, illustrate the graphing and analysis capabilities of the software. Spotfire does, however, appear to be limited to 2D graphs. 2) A number of people also recommended Diva and/or Tsar, from Oxford Molecular (http://www.oxmol.co.uk). Diva is the desktop product which has the graphics capabilities, while Tsar has the features for multivariate regression and QSAR type analysis. 3) Contrary to my original information and experience, it is possible to get at least close to what I was looking for with the MSI Cerius2 QSAR tools (http://www.msi.com). In particular, this requires turning on the label row by pickable and it appears to work best with the 3D plots, rather than 2D. 4) A few people also recommended the tools from Tripos (http://www.tripos.com), particulary the Tripos Molecular Spreadsheet and the HQSAR tools. 5) There is a project called CACTVS at the University of Erlangen (http://www2.ccc.uni-erlangen.de/software/cactvs/) which appears to be a toolkit by which one could get to any of a number of ends, including the ones I had in mind. At least on a first pass, it is not the most appropriate solution (yet) for my particular situation in an industrial environment with some very short deadlines. Anyone in academia or with a longer timescale, however, might do well to more seriously consider this toolkit. 6) This area appears to be one where there is also ongoing activity. I received a few responses from people who are doing development work in this area and who will likely have related products at some point in the future. Opinions and judgements expressed are my own, and I very much thank those who took the time to respond to my question. ====================================================== Bruce E. Wilson (bewilson@eastman.com) Eastman Chemical Company, Chemicals Research Division Lincoln St, B-150B, Box 1972 Kingsport, TN 37662-5150, USA Office: (423) 229-8886; FAX: (423) 229-4558 From jkl@ccl.net Fri Apr 16 11:52:39 1999 -0400 Received: from MIT.EDU (SOUTH-STATION-ANNEX.MIT.EDU [18.72.1.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA29631 Fri, 16 Apr 1999 11:52:36 -0400 (EDT) Received: from MASS-TOOLPIKE.MIT.EDU by MIT.EDU with SMTP id AA18977; Fri, 16 Apr 99 11:52:26 EDT Received: by mass-toolpike.mit.edu (8.8.7/4.7) id LAA04916; Fri, 16 Apr 1999 11:52:32 -0400 (EDT) Message-Id: <199904161552.LAA04916@mass-toolpike.mit.edu> To: chemistry@www.ccl.net Subject: sum: consistancy failure Date: Fri, 16 Apr 1999 11:52:32 EDT From: Ning Xie Hi, all, My thanks go to the people who replied my question. They are: 1. Doug Fox: gaussian.com!fox@lorentzian.com who suggested: "My best guess for the problem is that you will need a much better grid. Try INT=GRID=UltraFine."; 2. Peter Huesser who wrote: "I had the same problem a few years ago. If I remember right "SCF=NoVarrAcc" was the solution or Int=Rys1E or both."; 3. Han Zuilhof who wrote: "In our research on analogous polyDIacetylenes and oligomeric derivatives of this, convergence could -as in many other cases that one wants to study with large basis sets- be best achieved in a stepwise manner: start with a HF/3-21G single point, follow-up with guess=read with a B3LYP/6-31G* & loose scf criteria, and finish off with the B3LYP/6-311G** computation. (Do use the polarization functions, as the description will be significantly worse without them.) Once you have a B3LYP/6-311G** wavefunction on the starting geometry, our experience is that this will then rarely yield problems further on in the optimization in G94 (Gaussian 98 will likely be similar), even with much larger systems (upto C80)." and 4. Wai-To Chan who suggested: " Try the option scf=NoVarAcc to see if you can get around. If it is a single point calculation then specify scf=(NoVarAcc,tight). Note that tight is the default anyway for geometry optimisation. Hope this would solve your problem." The original question is: Hi, all, I'm trying to use BLYP/6-311g** to calculate the thermodynamic properties of polyacetylenes (C2H2 to C20H2 or even higher with respect to the number of carbons). The job is terminated shortly after it is started and gives a "consistency failure #2 in CalDSu" message in the log file. I changed the basis set to 6-311g and use SCF=QC and it still does not work. Any suggestion is appreciated. Thank you very much. Regards, ning The last part of the log file is Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. Requested convergence on MAX density matrix=1.00D-06. Integral accuracy reduced to 1.0D-05 until final iterations. Problem detected with inexpensive integrals. Switching to full accuracy and repeating last cycle. Warning! Spurious integrated density: NE= 74 NElCor= 0 Integral= 0.00000 Tolerance=1.00D-03 Consistency failure #2 in CalDSu. Error termination via Lnk1e in /usr2/g98/l502.exe. Job cpu time: 0 days 0 hours 0 minutes 38.5 seconds. File lengths (MBytes): RWF= 19 Int= 0 D2E= 0 Chk= 1 Scr= 1 I applied a combination of the suggestions and it worked with C12. Neither suggestion worked alone though. Thanks again. ning From jkl@ccl.net Fri Apr 16 14:02:22 1999 -0400 Received: from asp.biogeo.uw.edu.pl (grzesb@asp.biogeo.uw.edu.pl [148.81.33.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA28006 Fri, 16 Apr 1999 07:25:45 -0400 (EDT) Received: (from grzesb@localhost) by asp.biogeo.uw.edu.pl (8.8.7/8.8.7) id NAA29392; Fri, 16 Apr 1999 13:26:55 +0200 From: Grzegorz Bakalarski Message-Id: <199904161126.NAA29392@asp.biogeo.uw.edu.pl> Subject: G94 and new IBM AIX 4.3 (Power 2) To: chemistry@www.ccl.net Date: Fri, 16 Apr 1999 13:26:55 +0200 (EEST) Cc: grzesb@asp.biogeo.uw.edu.pl (Grzegorz Bakalarski) Dear CCLers, I have a problem with installing G94 on a new IBM RS6K (Power 2) with AIX 3.2 and new compilers. The problem is that IBM made many changes in OS and compilers so I'm not not able to run binary code (exe) compiled on older machine & OS. G94 (D or E) almost compiles on a new machine (there are problems with fstatfs routine in mdutil.c). When I make neccessery changes I could compile to the end. However the code did not want to run - it stopped after reading link1 (%) lines of input. My question is: DID ANYBODY OF YOU SUCCEED IN COMPILING G94 ON RS6K WITH AIX 4.3 ? IF YES, COULD YOU SHARE NEEDED KNOWLEDGE HOW TO DO IT ? Thank a lot for any help. Regards, G.Bakalarski Warsaw University P.S. The latest supported AIX for G94 is probably 4.1.3! New G98 is ported to AIX 4.3, however changes in a code are significant ... I contacted with Gaussian and they don't plan to port G94 to new AIX, however say it should be possible .... From chemistry-request@server.ccl.net Mon Apr 19 05:15:26 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA06863; Mon, 19 Apr 1999 05:15:26 -0400 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA04125 Mon, 19 Apr 1999 05:12:17 -0400 (EDT) Received: from ac.rwth-aachen.de (pae102.ac.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-12 #30440) with ESMTP id <01JA7RF7ZZLW0004Q9@mail.rwth-aachen.de> for CHEMISTRY@www.ccl.net; Mon, 19 Apr 1999 11:11:00 +0200 Date: Mon, 19 Apr 1999 11:10:00 +0200 From: Krzysztof Radacki Subject: Re: CCL:PGI Users Guide Sender: root@mail.rwth-aachen.de To: CCL Message-id: <371AF2E8.7A1824F@ac.rwth-aachen.de> Organization: Inst.Inorg.Chem., RWTH Aachen, Germany MIME-version: 1.0 X-Mailer: Mozilla 4.08 [en] (X11; I; Linux 2.0.36 i586) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit References: Artem Masunov wrote: > > Dear Krzys > It looks like you are suggesting a useful thing. > But what do you mean? If FTP command, I do not think FTP connection to WWW > server is possible. If browser command, which browser and version has it? > Artem > > > If the only one problem is "download them one after the other" why you didn't > > use wget? > > > > regards > > > > Krzys Radacki Wget it's unix program (also available as compilled with egcc for Windows, I'm useing it under linux). I don't know what system you use but it should be available for each one (it's GPL'ed). Syntax is like: wget -r -nH http://support.rz.rwth-aachen.de/Manuals/PGC/ and you get all PGI manual on your HD. Any browser and you can use like on-line doc. From jkl@ccl.net Sat Apr 17 13:48:17 1999 -0400 Received: from jg1.bchem.temple.edu (jg1.bchem.temple.edu [155.247.44.101]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA29471 Sat, 17 Apr 1999 13:48:13 -0400 (EDT) Received: by jg1.bchem.temple.edu (931110.SGI/911001.SGI) for CHEMISTRY@www.ccl.net id AA10513; Sat, 17 Apr 99 05:00:21 -0700 Date: Sat, 17 Apr 99 05:00:21 -0700 From: gabriel@jg1.bchem.temple.edu (Dr. Jerome L. Gabriel) Message-Id: <9904171200.AA10513@jg1.bchem.temple.edu> To: CHEMISTRY@www.ccl.net Dear CCL I would appreciate some help in finding references and/or computer programs that would help in the prediction of the metabolic breakdown of drugs and other pharmacological compounds. Thank you, Jerome L. Gabriel Director Molecular Modeling Facility Temple University Medical School Philadelphia, PA 19140 gabriel@jg1.bchem.temple.edu From chemistry-request@server.ccl.net Mon Apr 19 05:55:02 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA07525; Mon, 19 Apr 1999 05:55:02 -0400 Received: from jupiter.t30.physik.tu-muenchen.de (jupiter.t30.physik.tu-muenchen.de [129.187.186.90]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id FAA04186 Mon, 19 Apr 1999 05:51:55 -0400 (EDT) Received: from minerva.t30.physik.tu-muenchen.de by jupiter.t30.physik.tu-muenchen.de via ESMTP (950215.SGI.8.6.10/931108.SGI.ANONFTP) for id LAA09017; Mon, 19 Apr 1999 11:51:41 +0200 Received: (rieger@localhost) by minerva.t30.physik.tu-muenchen.de (8.6.10/8.6.9) id JAA11377; Mon, 19 Apr 1999 09:51:41 GMT Date: Mon, 19 Apr 1999 11:51:41 +0200 (MDT) From: Bernd Rieger X-Sender: rieger@minerva.t30.physik.tu-muenchen.de To: ccl Subject: ccl:g98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I did a UHF/LANL2MB SP calculation with G98 on a triplet state. After the SCF has converged i found that the energie of the alpha HOMO was higher than the alpha LUMO. The same for beta orbitals. Alpha occ. eigenvalues -- -0.22532 -0.21631 -0.08415 Alpha virt. eigenvalues -- -0.10304 0.00737 0.01977 0.03175 0.03827 Beta occ. eigenvalues -- -0.09456 Beta virt. eigenvalues -- -0.10780 -0.07132 0.02100 0.02998 0.03074 What happened? Is it possible that the VShift has something to do with it? I could not set it to zero even with SCF=(VShift=0). Also the symmetry of the orbital is not found correctly at the end of the SCF. Does anybody know why this happened? To confirm that it is indeed a triplett I did also a SP for the singlet and found that the HF energie was 0.45886 Hartree lower for the triplett. This seems quite a lot to me, almost 13 eV. I did the calculation on 2 different platforms, can that cause the big difference? Thanks in advance Bernd +--------------------------------------------------------------------+ | Bernd Rieger Phone:089 289 13768 | | Physic Department T38, TU Muenchen Fax: 089 289 12444 | | James-Franck-Strasse | | 85748 Garching email: brieger@physik.tu-muenchen.de | +--------------------------------------------------------------------+ From chemistry-request@server.ccl.net Mon Apr 19 07:20:31 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA08266; Mon, 19 Apr 1999 07:20:31 -0400 Received: from ns.dsm.nl (ns.dsm.nl [163.175.153.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA04357 Mon, 19 Apr 1999 07:17:22 -0400 (EDT) From: Steven.Creve@dsm-group.com Received: from dsm-fw1. (dsm-fw1.dsm.nl [163.175.153.254]) by ns.dsm.nl (8.8.6/MQT) with SMTP id NAA03270 for ; Mon, 19 Apr 1999 13:25:36 +0200 (METDST) Received: from localhost (root@localhost) by dsm-om1.dsm.nl (8.8.6/MQT) with SMTP id NAA05906 for CHEMISTRY@www.ccl.net;Mon, 19 Apr 1999 13:14:28 +0200 (METDST) X-OpenMail-Hops: 5 Date: Mon, 19 Apr 1999 13:16:03 +0200 X-OpenMail-Transport-Id: <02C52371B1073075/NL/400net/DSM/371B0FF0.10DD.3604.000> Message-Id: <"371B0FF0.10DD.3604.000*Creve_Steven_SJR//RESEARCH/NL/400net/DSM"@MHS> Subject: CCL:FMM in G98 MIME-Version: 1.0 TO: CHEMISTRY@www.ccl.net Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 7bit Hi, has anyone experience with the fast multipole method in Gaussian98? In my case (single point on a 204 basis functions system) it doesn't seem to work. Steven From chemistry-request@server.ccl.net Mon Apr 19 10:25:24 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA10877; Mon, 19 Apr 1999 10:25:23 -0400 Received: from ns.dsm.nl (ns.dsm.nl [163.175.153.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA05027 Mon, 19 Apr 1999 10:22:13 -0400 (EDT) From: Steven.Creve@dsm-group.com Received: from dsm-fw1. (dsm-fw1.dsm.nl [163.175.153.254]) by ns.dsm.nl (8.8.6/MQT) with SMTP id QAA09991 for ; Mon, 19 Apr 1999 16:30:39 +0200 (METDST) Received: from localhost (root@localhost) by dsm-om1.dsm.nl (8.8.6/MQT) with SMTP id QAA09431 for CHEMISTRY@www.ccl.net;Mon, 19 Apr 1999 16:19:29 +0200 (METDST) X-OpenMail-Hops: 5 Date: Mon, 19 Apr 1999 16:20:40 +0200 X-OpenMail-Transport-Id: <01428371B3BB8019/NL/400net/DSM/371B3ABB.10DD.3C6B.000> Message-Id: <"371B3ABB.10DD.3C6B.000*Creve_Steven_SJR//RESEARCH/NL/400net/DSM"@MHS> Subject: CCL:Re: CCL:FMM in G98 -Reply MIME-Version: 1.0 TO: CHEMISTRY@www.ccl.net Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 7bit Let me reformulate my questions: I'm using BP86 on 204 basis function system. It takes 2 hours and 22 minutes. If I use BP86 FMM it takes 2 hours and 20 minutes. Should I expect a considerable speed-up for this size of systems? Steven Creve From chemistry-request@server.ccl.net Mon Apr 19 10:34:33 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA11155; Mon, 19 Apr 1999 10:34:33 -0400 Received: from ns.dsm.nl (ns.dsm.nl [163.175.153.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA05103 Mon, 19 Apr 1999 10:31:24 -0400 (EDT) From: Steven.Creve@dsm-group.com Received: from dsm-fw1. (dsm-fw1.dsm.nl [163.175.153.254]) by ns.dsm.nl (8.8.6/MQT) with SMTP id QAA10301 for ; Mon, 19 Apr 1999 16:39:36 +0200 (METDST) Received: from localhost (root@localhost) by dsm-om1.dsm.nl (8.8.6/MQT) with SMTP id QAA11194 for CHEMISTRY@www.ccl.net;Mon, 19 Apr 1999 16:28:25 +0200 (METDST) X-OpenMail-Hops: 5 Date: Mon, 19 Apr 1999 16:29:43 +0200 X-OpenMail-Transport-Id: <01428371B3DD7028/NL/400net/DSM/371B3D1B.10DD.3CE3.000> Message-Id: <"371B3D1B.10DD.3CE3.000*Creve_Steven_SJR//RESEARCH/NL/400net/DSM"@MHS> Subject: CCL:SGI Visual Workstation MIME-Version: 1.0 TO: CHEMISTRY@www.ccl.net Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 7bit Hi, does anyone out there has any experience with computational chemistry on the WindowsNT Silicon Graphics Visual Workstations (320 or 540)? Any information is wellcome Steven Creve From chemistry-request@server.ccl.net Mon Apr 19 10:59:54 1999 Received: from asia.chimfarm.unipg.it (asia.chimfarm.unipg.it [141.250.13.18]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA11478 for ; Mon, 19 Apr 1999 10:59:53 -0400 Received: from asia.chimfarm.unipg.it (localhost [127.0.0.1]) by asia.chimfarm.unipg.it (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id WAA10820 for ; Fri, 16 Feb 1996 22:56:21 +0100 Sender: antonio@asia.chimfarm.unipg.it Message-ID: <3124FD84.41C6@asia.chimfarm.unipg.it> Date: Fri, 16 Feb 1996 22:56:20 +0100 From: Antonio Macchiarulo Organization: Istituto di Chimica e Tecnologia del Farmaco X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Dynamics traj.files in mpeg Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, I would like suggestions on programs that are able to convert tripos dynamics trajectory files in .mpeg . Thanks in advance. -- ********************************************************* * Dr. Antonio Macchiarulo * * Istituto di Chimica e Tecnologia del Farmaco * * Universita' degli Studi di Perugia * * Via del Liceo 1, 06100 * * Perugia (ITALY). * * E_mail: antonio@asia.chimfarm.unipg.it * * Voice: ++ 39 75 5855114. * ********************************************************* From chemistry-request@server.ccl.net Mon Apr 19 12:53:42 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA12611; Mon, 19 Apr 1999 12:53:42 -0400 Received: from aragorn.ics.muni.cz (aragorn.ics.muni.cz [147.251.4.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA05676 Mon, 19 Apr 1999 12:50:28 -0400 (EDT) Received: from monoceros.physics.muni.cz (mplonka@monoceros.physics.muni.cz [147.251.27.2]) by aragorn.ics.muni.cz (8.8.5/8.8.5) with ESMTP id SAA09236 for ; Mon, 19 Apr 1999 18:50:14 +0200 (MET DST) Received: (from mplonka@localhost) by monoceros.physics.muni.cz (8.8.5/8.8.5) id SAA10943 for chemistry@www.ccl.net; Mon, 19 Apr 1999 18:50:14 +0200 From: Miroslav Plonka Message-Id: <199904191650.SAA10943@monoceros.physics.muni.cz> Subject: g98, precision To: chemistry@www.ccl.net Date: Mon, 19 Apr 1999 18:50:13 +0200 (CEST) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCL, I would appreciate an advice how to increase the precision of the Gaussian 98 job. I would like to improve the result in the calculation of the coordinates (the displacements) of atoms during vibrational excitations in molecule when frequency job is calculated (e.g. # MNDO Opt=Z-matrix Test Freq). The default is 2 decimals, I need 3-4 decimals. Thank you very much. Regards -------------------------------------- Miroslav Plonka, PhD Dept. of Theor. Phys. and Astroph. Faculty of Science, Masaryk University Kotlarska 2, 611 37 Brno Czech Republic Tel.:+420-5-41129456 -------------------------------------- From chemistry-request@server.ccl.net Mon Apr 19 16:37:57 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA14731; Mon, 19 Apr 1999 16:37:57 -0400 Received: from quartz.super.arizona.edu (quartz.Super.Arizona.EDU [128.196.131.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id QAA06443 Mon, 19 Apr 1999 16:34:43 -0400 (EDT) Received: from localhost (fan@localhost) by quartz.super.arizona.edu (8.8.7/8.8.7) with SMTP id NAA19614 for ; Mon, 19 Apr 1999 13:34:37 -0700 (MST) X-Authentication-Warning: quartz.super.arizona.edu: fan owned process doing -bs Date: Mon, 19 Apr 1999 13:34:37 -0700 (MST) From: Hua-Jun Fan X-Sender: fan@quartz.super.arizona.edu Reply-To: Hua-Jun Fan To: CCL Subject: summary: cluster calculations In-Reply-To: <36E60824.7D641749@farlep.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers, The original question and the replies received up to now are shown below(selected contents only). Many thanks to to David Case, Thomas Gray, and T.R. Hughbanks. Huajun ----origianl question------- I had question about using DSW-Xalpha methods in calculating Re6 cluster. I have read a paper about it and am interested in repeating the calculations. The authors's email address on the paper is not right. The paper is published by Dr. Arratia-perez on J. Chem.Phy. vol 110, num. 5, 1999 Feb issue about DSW-Xalpha calculation on Re cluster. I wonder if anyone have any suggestion/advice on the software availability, and a bit of detail about it how the calculations are performed, even the priciple about the methods, calculations. (I am quite new to this area, all I knew about it is not very many methods are available to do this kind of cluster) From paper, there is not much information in it. ---- replies ----- #############T.R. Hughbanks######### trh@mail.chem.tamu.edu We have performed a number of calculations on clusters in recent years. These days, we use primarily density functional theory. We have used the DMol and DSolid modules within the MSI suite of programs (formerly the Biosym package). This method is computationally efficient, but the numerical grids used in evaluating the exchange and correlation functionals seem to me to be a bit suspect when numerical precision is concerned (i.e., as in a careful geometry optimization). The BLYP functional is built in to the version we have used, but not the B3LYP functional (the latest and most "popular" version). DFT methods are built into the latest Guassian packages, though they run slower than Hartree-Fock in Guassian's implementation (in which 3- and 4-center integrals are still evaluated, in DMol the electron density is expanded in auxilary functions so such integrals are avoided). If you want to do calculations in rhenium clusters, you will have to face the problem of what to do about relativistic effects. Ignoring such effects in 2nd row T.M.s is not too serious, but most experts will tell you that you can't really neglect them for 3rd row T.M.s. A fairly recent paper that compared Nb6X12 and Ta6X12 clusters appeared (in JACS or Inorg. Chem.). That is probably a good reference to look up in order to get you started thinking about DFT calculations On Re6-based clusters. #############David Case:############# case@scripps.edu You can try to reach Dr. Arratia-Perez at the following e-mail address: lhernand@plantina.inia.cl However, this address is about 10 months old, and may still not work. (It looks like there is just a typo in the e-mail address in the JCP paper.) The code for the DSW-Xalpha program is available from our anonymous ftp site: ftp://ftp.scripps.edu/pub/case/dsw.tar.Z There should be a README file (I think in the dsw directory). This points you to the instructions (in main.f or somewhere like that). You will probably need to study how the non-relativistic program works first, as it has much fuller documentation. I hope you will be able to get in touch with Dr. Arratia-Perez, since he would be an excellent source of help. To understand the method, you should trace back to previous papers of Arratia-Perez. The basic algorithmic reference is the following: C. Y. Yang and D. A. Case. Dirac scattered wave calculations. Local Density Approximations in Quantum Chemistry and Solid State Physics, J. P. Dahl and J. Avery, eds. (Plenum, 1984), pp. 643-664. This might be a little hard to find now(!). The first calculations using the method were the following, which has a fair description of the approach: D. A. Case and C. Y. Yang. Relativistic scattered wave calculatons on UF6. J. Chem. Phys. 72, 3443-3448 (1980). ############Thomas Gray######## tgray@fas.harvard.edu Bursten, B. E.; et al. Isr. J. Chem. 1980, 19, 132. Woolley, R. G. Inorg. Chem. 1985, 24, 3519-3525. Hughbanks, T.; Hoffmann, R. J. Am. Chem. Soc. 1983, 105, 1150-1162. Hughbanks, T. Inorg. Chem. 1986, 25, 1492-1497. Saito, Y.; Tanaka, H. K.; Azumi, T. J. Phys. Chem. 1985, 89, 4413-4415. Azumi, T.; Saito, Y. . Phys. Chem. 1988, 92, 1715-1721. Imoto, H.; Saito, T.; Adachi H. Inorg. Chem. 1995, 34, 2415-2422. Robinson, L. M.; Bain, R. L.; Shriver, D. F.; Ellis, D. E. Inorg. Chem. 1995, 34, 5588-5596. Two recent reviews which discuss electronic structure calculations are: Saito, T. Adv. Inorg. Chem. 1996, 44, 45-92, and Prokopuk, N.; Shriver, D. F. Adv. Inorg. Chem. 1998, 46, 1-50. From chemistry-request@server.ccl.net Mon Apr 19 17:18:20 1999 Received: from www.ccl.net (www.ccl.net [192.148.249.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA15334; Mon, 19 Apr 1999 17:18:20 -0400 Received: from darkwing.uoregon.edu (genghis@darkwing.uoregon.edu [128.223.142.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA06609 Mon, 19 Apr 1999 17:15:08 -0400 (EDT) Received: from localhost (genghis@localhost) by darkwing.uoregon.edu (8.9.3/8.9.3) with SMTP id OAA09460; Mon, 19 Apr 1999 14:15:03 -0700 (PDT) Date: Mon, 19 Apr 1999 14:15:02 -0700 (PDT) From: "Dale A. Braden" To: Miroslav Plonka cc: chemistry@www.ccl.net Subject: Re: CCL:g98, precision In-Reply-To: <199904191650.SAA10943@monoceros.physics.muni.cz> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Miroslav, Using freq=hpmodes in the route section will give you 5 decimal places in the normal mode eigenvectors. Dale Braden Department of Chemistry University of Oregon Eugene, OR 97403-1253 genghis@darkwing.uoregon.edu