From chemistry-request@server.ccl.net Mon Jul 31 00:17:51 2000 Received: from arbornet.org (m-net.arbornet.org [209.142.209.161]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA14728 for ; Mon, 31 Jul 2000 00:17:50 -0400 Received: from localhost (mrdonkey@localhost) by arbornet.org (8.10.2/8.10.2) with ESMTP id e6V4GQb84090; Mon, 31 Jul 2000 00:16:26 -0400 (EDT) Date: Mon, 31 Jul 2000 00:16:26 -0400 (EDT) From: Mr Donkey To: Yubo Fan cc: CHEMISTRY@ccl.net Subject: Re: CCL:G98 job cannot work In-Reply-To: <39839313.9EE5F820@guomai.sh.cn> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Yubo, this usually means that the maximum shared memory (shmmax) is set too small. This can be aleviated by doing the following: echo 67108864 > /proc/sys/kernel/shmmax this sets the shmmax to 64 MB. As I don't know what is required by G98, this may still be too small. You could try increasing that number if it still doesn't work. once you find a value that works you can add this command to the end of /etc/rc.d/rc.local so it is automatically run whenever you turn on the computer. hope this helps. - Don Key mrdonkey@m-net.arbornet.org On Sun, 30 Jul 2000, Yubo Fan wrote: > Dear CCLers: > > I have met some problems when I ran G98 jobs on my machine. My machine > is a dual PII computer with 256MB memory and RedHat Linux 6.2 is > installed. G98 jobs can be run correctly if I don't use parallel option. > When I add the line '%nprocs=2' on the top of input files, the following > message was given. 'shmget failed.: Invalid argument' For I am a Linux > beginner, I cannot solve this problem. Could you please give me some > advice? > > Thanks in advance > > Sincerely yours, > > Y. Fan From chemistry-request@server.ccl.net Mon Jul 31 04:52:09 2000 Received: from kuku.excite.com (kuku-rwcmta.excite.com [198.3.99.63]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA15855 for ; Mon, 31 Jul 2000 04:52:08 -0400 Received: from cheeks.excite.com ([199.172.152.207]) by kuku.excite.com (InterMail vM.4.01.02.39 201-229-119-122) with ESMTP id <20000731085111.ETX11596.kuku.excite.com@cheeks.excite.com> for ; Mon, 31 Jul 2000 01:51:11 -0700 Message-ID: <6758557.965033471845.JavaMail.imail@cheeks.excite.com> Date: Mon, 31 Jul 2000 01:51:11 -0700 (PDT) From: Zilvinas Rinkevicius To: CHEMISTRY@ccl.net Subject: Gaussian ZINDO-1 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Excite Inbox X-Sender-Ip: 193.219.180.252 Dear CCL users, Can any one provide me with information howto obtain from output in G98 using ZINDO method CI coeficiants and overlap integrals. Thanking in advance, with best regards, Zilvinas Rinkevicius, Kaunas Technology University, Faculty of Fundamental Sciences, Studentu st. 50, Kaunas 3000, Lithuania. _______________________________________________________ Say Bye to Slow Internet! http://www.home.com/xinbox/signup.html From chemistry-request@server.ccl.net Mon Jul 31 09:14:39 2000 Received: from chemie.fu-berlin.de (root@bohr.chemie.fu-berlin.de [160.45.24.161]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA17791 for ; Mon, 31 Jul 2000 09:14:38 -0400 Received: from localhost (winkelma@localhost) by chemie.fu-berlin.de (8.9.3/8.9.3) with ESMTP id PAA10656 for ; Mon, 31 Jul 2000 15:14:25 +0200 Date: Mon, 31 Jul 2000 15:14:25 +0200 (CEST) From: Daniel Winkelmann To: Computational Chemistry List Subject: Q: Hydratisation of Aldehydes Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi all, we are looking for data concerning mechanism and kinetic properties for the hydratisation of acetaldehyde and propionaldehyde. Any newer literatur (theoretical or experimental) ? TIA, Daniel Winkelmann +------------------------------------------------------------------+ | Daniel Winkelmann | | AG Knapp, Institut fuer Kristallographie | | Freie Universitaet Berlin Tel. : +49 30 838-53890 | | Takustrasse 6 Fax. : +49 30 838-53464 | | D-14195 Berlin Email : winkelma@chemie.fu-berlin.de | +------------------------------------------------------------------+ From chemistry-request@server.ccl.net Mon Jul 31 05:51:18 2000 Received: from angelos.phc.chalmers.se (angelos.phc.chalmers.se [129.16.97.41]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA16105 for ; Mon, 31 Jul 2000 05:51:17 -0400 Received: from fkrs2.phc.chalmers.se (fkrs2.phc.chalmers.se [129.16.97.48]) by angelos.phc.chalmers.se (8.9.3/8.9.3) with ESMTP id LAA14323; Mon, 31 Jul 2000 11:51:01 +0200 Received: (from svedung@localhost) by fkrs2.phc.chalmers.se (8.8.8/8.8.8) id LAA17071; Mon, 31 Jul 2000 11:50:59 +0200 Date: Mon, 31 Jul 2000 11:50:57 +0200 (MDT) From: Harald Svedung To: Didier MATHIEU cc: chemistry@ccl.net Subject: Re: CCL:Specific Buckingham parameters in Tinker In-Reply-To: <3969845C.FD83E36@ripault.cea.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, To apply the "usual combination rules", the Buckingham parameters can be converted to "usual" equilibrium distance, rm, and well depth, eps, (plus the additional hardness parameter, B ): A = 6 eps Exp(B) / (B-6) C = B eps rm^6 / (B-6) The B parameter typically varies between 10 and 15 depending on the system and it might be that some combination rule could be applied. >From preliminary calcualtions it's seen that the hetrogenous values for noble gas combinations falls between the corresponding homogenous vales as expected. An overlap integral treatment might give a suitable candidate combination rule. To avoid the "inner attractive trap" in the Buckingham potential, it can be modified as E=Aexp(-BR/rm)-C/((R/rm)^2+(0.25)^2)^3 I've found the value 0.25 to just cancel any tendency to form a local minima in the repulsive wall for B values down to 10. For what it's worth ;-) so long /Harald On Mon, 10 Jul 2000, Didier MATHIEU wrote: > Hello, > > As a first step in the modelling of a family of organic crystals, I > consider using the simple Buckingham potential of Gavezzotti and > Filippini (in: Computational Approaches in Supramolecular Chemistry, > G. Wipff, ed. Kluwer, pp. 51-62 (1994)). > However, the A,B,C parameters in the expression E=Aexp(-BR)-C/R^6 do not > obey the usual combinations rules. > On the other hand, it seems that the Tinker program I use does expect > such rules. > Is it nonetheless possible to specify independent A,B,C parameters for > each atom pair to the program, or is it necessary to modify the programs > in order to introduce the extra degree of freedom required ? > > Sincerely yours. > > -- > Didier MATHIEU > CEA - Le Ripault, BP 16 > 37260 Monts (France) > Tel. 33(0)2.47.34.41.85 > > > Harald Svedung (Ph.Lic.) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone: +46-31-240897, +46-709223206 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden www.che.chalmers.se/~svedung/ From chemistry-request@server.ccl.net Mon Jul 31 10:33:25 2000 Received: from ne059.cm.utexas.edu (ne059.cm.utexas.edu [146.6.145.59]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA18154 for ; Mon, 31 Jul 2000 10:33:24 -0400 Received: from ne057.cm.utexas.edu by ne059.cm.utexas.edu (AIX 3.2/UCB 5.64/4.03) id AA13638; Mon, 31 Jul 2000 09:27:26 -0500 Message-Id: <3985A906.DF449838@eeyore.cm.utexas.edu> Date: Mon, 31 Jul 2000 09:27:50 -0700 From: "Isaac B. Bersuker" X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en,zh,zh-CN,zh-TW Mime-Version: 1.0 To: Kasper Planeta Jensen Cc: "Isaac B. Bersuker" , Per-Ola Norrby , chemistry@ccl.net Subject: Re: CCL:TM force fields References: <397C5C3F.28DEEEDA@eeyore.cm.utexas.edu> <3981EB26.6F70A956@eeyore.cm.utexas.edu> <39823A46.37BBE83A@studentergaarden.dk> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit The point is that just the transferability does not work in TM compounds. There is no sense to continue the discussion until you reply specifically to the criticism of the force field idea in application to TM systems given, e.g., in the references I mentioned in my message: "... see see in Internat J. Quant. Chem. 1997,63,1051, and in Combined QM and MM Methods, Ed. J.Gao, M.A.Thompson, ACS Symposium Series 712, Washington 1998, pp 99-91". Regards I. B. Kasper Planeta Jensen wrote: > Dear Dr. Bersuker > > I reckon that transferability of parameters like bond distances, > (coordination-)geometries etc. > is not limited to the field of organic chemistry. Metal-ligand distances, force > constants, > torsion barriers etc. are similar in similar complexes. Hence, you can parameterize for > inorganic > compounds in the same way as for organic compounds. As long as transferability exists > in chemistry, force fields are possible that are not ad hoc per definition since they > generalize > this transfereability in terms of parameters. > > Yours, > Kasper > > "Isaac B. Bersuker" wrote: > > > Dear Dr. Norrby: > > > > Instead of getting iritated and offended, you better respond to the specific > > criticism of the force field idea in application to TM systems. This is SCIENCE, > > let me remind you, and the main condition of its progress is open discussion and > > proof of statements. I proved my statements in the references I gave earlier (that > > you deleted) and I would expect you to show that my proof is wrong. Just stating > > that one made calculations with good results does not prove anything, with > > arbitrary parameters (changed from one compound to another) everybody can get any a > > priori desired results. > > > > And, please, don't reffer to "authorities". I respect them all and their point of > > view, but the scientific truth is more important. > > > > Regards > > Isaac > > > > Per-Ola Norrby wrote: > > > > > Isaac B. Bersuker wrote: > > > > > > >I repeat my firm conviction that, in general, there are > > > >no force fields for transitiom metal systems (see my latest book ... > > > > > > (The rest of the message deleted). > > > > > > I've seen this comment a couple of times now, and I'm getting > > > irritated. This is a very sweeping statement, and insulting to those > > > who have produced good work in this area. It is only true if you > > > interprete it like "it is not possible to achieve infinite accuracy > > > for all possible TM complexes", but stated like that it would be > > > equally true of any method. For specific classes of complexes, it is > > > possible to get high accuracy with force field methods. It's just a > > > question of having a flexible enough force field and doing a careful > > > parameterization. Check out the book by Comba and Hambley, > > > "Molecular Modeling of Inorganic Compounds", a new edition is comming > > > out soon. We also have a review in press in Coord.Chem.Rev. on how > > > to do this parameterization (don't know when it's going to appear). > > > For some classical reviews, see: > > > > > > C.R. Landis, D.M. Root, T. Cleveland, in: K.B. Lipkowitz and D.B. > > > Boyd (Eds.), Reviews in Computational Chemistry, Vol. 6, VCH > > > Publishers, Inc., New York, 1995, p. 73-148. > > > > > > M. Zimmer, Chem. Rev. 95 (1995) 2629. > > > > > > P. Comba, Comments Inorg. Chem. 16 (1994) 133. > > > > > > B.P. Hay, Coordination Chemistry Reviews 126 (1993) 177. > > > > > > (Yes, I know, I left several out, this is just a selection based on > > > personal preference). > > > > > > The general force fields are also advancing. You can still > > > get whooping errors, and should validate carefully, but I've actually > > > been surprised several times by the results you can get without > > > specific parameterization. I'd like to point to UFF (not all > > > implementations though :-), VALBOND (not a complete force field, but > > > a very interesting addition to UFF), and the force fields in PCModel > > > and Spartan. There are others, but I don't have personal experience > > > with them. > > > > > > Per-Ola > > > -- > > > > > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > > * Per-Ola Norrby, Associate Professor > > > * The Royal Danish School of Pharmacy, Dept. of Med. Chem. > > > * Universitetsparken 2, DK 2100 Copenhagen, Denmark > > > * Tel. +45-35306506, fax +45-35306040 > > > * Email: peo@dfh.dk (preferred), peo@compchem.dfh.dk > > > * WWW: http://compchem.dfh.dk/PeO/ > > > > > > > -- > > Isaac B. Bersuker > > Institute for Theoretical Chemistry > > Department of Chemistry & Biochemistry > > The University of Texas at Austin > > Austin, TX 78712, USA > > Ph: (512) 471-4671 > > Fax: (512) 471-8696 > > Email: bersuker@eeyore.cm.utexas.edu > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Isaac B. Bersuker Institute for Theoretical Chemistry Department of Chemistry & Biochemistry The University of Texas at Austin Austin, TX 78712, USA Ph: (512) 471-4671 Fax: (512) 471-8696 Email: bersuker@eeyore.cm.utexas.edu From chemistry-request@server.ccl.net Mon Jul 31 12:46:24 2000 Received: from dcmail1.dowcorning.com (dcmail1.dowcorning.com [208.154.221.50]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA18753 for ; Mon, 31 Jul 2000 12:46:24 -0400 From: peter.qian@dowcorning.com Received: from dcmailfw.dowcornusa.com (unverified) by dcmail1.dowcorning.com (Content Technologies SMTPRS 4.1.5) with ESMTP id for ; Mon, 31 Jul 2000 12:36:57 -0400 Received: from corpnt83.dowcornusa.com (unverified) by dcmailfw.dowcornusa.com (Content Technologies SMTPRS 4.1.5) with ESMTP id for ; Mon, 31 Jul 2000 12:38:39 -0400 Received: by smtp.dowcornusa.com with Internet Mail Service (5.5.2650.21) id ; Mon, 31 Jul 2000 12:46:01 -0400 Message-ID: To: chemistry@ccl.net Subject: Information on software and publications on thermal and electrica l conductivity modeling Date: Mon, 31 Jul 2000 12:45:59 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Dear CCL members: I am interested in seeking information regarding software and publications on modeling thermal and electrical conductivities. Thanks in advance for you reply. Peter Qian Dow Corning Corporation * Voice: (517)496-6938 Interface Expertise Center, CO41D1 * Fax: (517)496-5121 Midland, MI 48686 * e-mail: peter.qian@dowcorning.com * http://www.dowcorning.com/ From chemistry-request@server.ccl.net Mon Jul 31 14:53:09 2000 Received: from darwin-le0.sepracor.com ([64.14.72.225]) by server.ccl.net (8.8.7/8.8.7) with SMTP id OAA19424 for ; Mon, 31 Jul 2000 14:53:09 -0400 Received: from mailhost.sepracor.com by darwin-le0.sepracor.com via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 31 Jul 2000 18:47:47 UT Received: from getmail.sepracor.com by lovelace-hme1.sepracor.com via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 31 Jul 2000 18:44:01 UT Received: by getmail.sepracor.com with Internet Mail Service (5.5.2650.21) id ; Mon, 31 Jul 2000 14:51:13 -0400 Message-ID: From: Gerry Tanoury To: "'chemistry@ccl.net'" Subject: summary: restarting a transition state search Date: Mon, 31 Jul 2000 14:51:05 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id OAA19425 Dear CCLers: Approximately a week ago, I inquired about some difficulties I had when attempting to restart a TS search from a .chk file on G98W at a specific step. I recieved six responses within 2 hrs of my request being sent! Nearly all the responses instructed me to remove the Z-matrix before resubmitting. When I tried that, I got a "consistency failure: NVar= 205 MaxSV= 102 Left= 42296 ICheck=84432 LenOG= 84551." error message. However, I was able to solve the problem by a rather circuitous route: Convert the .chk file at step=10 to a .gjf using the newZmat utility Open the new file with GaussView for Windows. Submit this new structure with the opt=calcfc keyword. This did work, and a transition structure was located. Special thanks to those who responded so quickly: Uwe Richter Steven Bachrach Tim Jödicke Tanja van Mourik Dave Shobe Sue Kong Krzysztof Radacki Laurence Cuffe Huajun Fan Gerald J. Tanoury gtanoury@sepracor.com From chemistry-request@server.ccl.net Mon Jul 31 19:17:44 2000 Received: from chala.q1.fcen.uba.ar (chala.q1.fcen.uba.ar [157.92.31.25]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA20768 for ; Mon, 31 Jul 2000 19:17:39 -0400 Received: from localhost (damian@localhost) by chala.q1.fcen.uba.ar (8.9.3/8.9.3) with ESMTP id WAA05174; Mon, 31 Jul 2000 22:38:01 +0200 Date: Mon, 31 Jul 2000 22:38:01 +0200 (MEST) From: =?X-UNKNOWN?Q?Dami=E1n_Scherlis?= To: help@gaussian.com cc: chemistry@ccl.net Subject: HF + UHF in g98 In-Reply-To: <20000712101537.B132991@gershwin> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello. I've run into a problem when trying to run an open shell calculation using both HF and UHF in the Route Section: when I do this the program performs a ROHF calculation. On the other side, g98 works fine if I specify whether HF or UHF. Is that due to the fact that since UHF is the default for HF, the redundancy is misunderstood ?