From chemistry-request@server.ccl.net Mon Jun 10 10:05:25 2002 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5AE5Oj16074 for ; Mon, 10 Jun 2002 10:05:24 -0400 Received: by smtp2.ruc.dk (Postfix, from userid 504) id 3D74B2F47DF; Mon, 10 Jun 2002 16:05:23 +0200 (CEST) Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by smtp2.ruc.dk (Postfix) with ESMTP id 7035C2F47DC; Mon, 10 Jun 2002 16:05:22 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id PAA12073; Mon, 10 Jun 2002 15:32:33 +0200 (MEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 10 Jun 02 16:05:22 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 10 Jun 02 16:05:19 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Peter Waaben Thulstrup" Date: Mon, 10 Jun 2002 16:05:14 +0100 Subject: CCL:G98 TD/CIS Opposite sign of the components of length- a Reply-To: spanget@ruc.dk Cc: chemistry@ccl.net X-Confirm-Reading-To: spanget@ruc.dk X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <374FD8A620E@virgil.ruc.dk> Hi Peter, hello again: > I have some questions regarding the output os CIS and TD jobs in G98 > (Rev. A7). I can't find anything on these issues in Gaussian > documentation or past CCL posts, although the questions are rather > simple. So I hope it makes sense... > > The output of TD and CIS calculations give the x, y, and z > components of the "Ground to excited state Transition electric > dipole moments", "Ground to excited state transition velocity dipole > Moments", and the "Ground to excited state transition magnetic > dipole Moments". > > 1) Why are the components of the electric and velocity derived > transition dipole moments oppositely signed? I thought that they > should be identical in a complete basis. I would have thought that > the sign ought to be the same. Which values should I trust? The "dipole length" and "dipole velocity" electronic transition moments, and , are far from identical (even in a complete basis); e.g., For a one-electron system we have r = {x,y,z} and p = -i{d/dx,d/dy,d/dz} (a.u.). is thus an imaginary quantity and Gaussian98 outputs the imaginary part, im[]. For the operators x and d/dx the following relations are valid for EXACT wavefunctions (since [H,x] = -d/dx): = (En - Em) ==> im[] = -(En - Em) Hence, and im[] should indeed have different signs, as printed by Gaussian98. Yours, Jens >--< NB! Please note new mail address: =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget@ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Mon Jun 10 10:26:53 2002 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5AEQrj16651 for ; Mon, 10 Jun 2002 10:26:53 -0400 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #11) id 17HQ8B-00016c-00 for chemistry@ccl.net; Mon, 10 Jun 2002 16:26:51 +0200 Message-ID: <3D04B6AD.40205@mpi-bpc.mpg.de> Date: Mon, 10 Jun 2002 16:24:45 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: CCL list Subject: two questions Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit 1. I am using the following input in order to calculate an electron density: %chk=tap_hf_opt.chk #P RB3LYP 6-31+G(d) Geom=Checkpoint Cube(40,Density) Guess=Read Density=Current methyl-TAP el.density calculation using optimized (hf 6-31g*) structure 0 1 In the output there is a line that says: "Warning! SCF SP cutoffs with diffuse functions may be unreliable. Consider SCF=Tight" Does anyone have experience with this and is able to explain to me what actually it is happening.? Can I simply ignore the warning or should I go for SCF=Tight? 2. I have the following input trying to calculate the frequencies of an optimized structure at the same level of theory: %chk=tap.chk #P Geom=AllCheck Guess=Read RB3LYP/6-31+G(d) FREQ POP=FULL GFPrint methyl-TAP optimization 0 1 The Gaussian job is broken by this error message: Not enough memory for a single radius per batch: NAngPt= 302 MaxPt= 216. Error termination via Lnk1e in /usr/local/g94/l1002.exe. Can anyone explain to me what is wrong? Thanks a lot in advance for any kind of advice. vlad -- Vlad Cojocaru Max Planck Institut for Biophysical Chemistry Deparment: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de From chemistry-request@server.ccl.net Mon Jun 10 11:19:34 2002 Received: from real.cyf-kr.edu.pl ([149.156.2.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5AFJXj17934 for ; Mon, 10 Jun 2002 11:19:33 -0400 Received: from kinga.cyf-kr.edu.pl (kinga.cyf-kr.edu.pl [149.156.2.32]) by real.cyf-kr.edu.pl (8.11.6/8.11.6) with ESMTP id g5AGFRp09756 for ; Mon, 10 Jun 2002 18:15:27 +0200 X-RAV-AntiVirus: This e-mail has been scanned for viruses on host: real.cyf-kr.edu.pl Received: (from mykrol@localhost) by kinga.cyf-kr.edu.pl (8.9.3/8.9.3) id RAA23175; Mon, 10 Jun 2002 17:15:23 +0200 (METDST) Date: Mon, 10 Jun 2002 17:15:20 +0200 (METDST) From: Marcin Krol To: chemistry@ccl.net Subject: QCOR in PME (CHARMM) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Charmm Users, I've tried to set up PME calculations of a neutral system (protein in water with counterions) and I'd like to know if I should bother about QCOR keyword (it should be reduced or set to zero for periodic systems in solution - that's what a manual says) or not. Is QCOR a net-charge correction (as described in the JCP 108, 7070 paper) keyword and it is ignored in neutral system simulation? I've also encountered another problem when doing paralell PME calculations. My job runs on two and four processors but fails to run on three. I get non 2**N PE count in transpose error, but my FFT value is 64 in each direction. Is there any way to force it run on three procs or not? Thank you in advance Marcin Krol From chemistry-request@server.ccl.net Mon Jun 10 12:08:56 2002 Received: from crane2.cf.ac.uk ([131.251.0.25]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5AG8uj18807 for ; Mon, 10 Jun 2002 12:08:56 -0400 Received: from thor.cf.ac.uk ([131.251.0.1]) by crane2.cf.ac.uk with esmtp (Exim 3.03 #1) id 17HRiu-0006IE-00; Mon, 10 Jun 2002 17:08:52 +0100 Received: from localhost (sacjap@localhost) by thor.cf.ac.uk (8.8.8/8.6.12) with ESMTP id RAA11376; Mon, 10 Jun 2002 17:08:52 +0100 (BST) Date: Mon, 10 Jun 2002 17:08:52 +0100 (BST) From: Jamie Platts X-Sender: sacjap@thor To: Vlad Cojocaru cc: CCL list Subject: Re: CCL:two questions In-Reply-To: <3D04B6AD.40205@mpi-bpc.mpg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII By default, Gaussian relaxes SCF convergence criteria for single-point (ie non-optimisation) jobs, to give reasonable energies in less cpu time. However, this can fall down when diffuse functions are present, since these might change substantially without affecting the energy much. More worryingly, the density (and hence any properties), will also be affected by such changes. I would advise that if you are interested in anything more than the final SCF energy then always used SCF=Tight. As for 2, L1002 solves the CPHF equations for the frequencies, so it seems your default setting doesn't give you enough memory to run this particular frequency job. Try increasing with something like: %Mem=256Mb ! exact figure depends on your machine %Chk=tap.chk #P ... If you can't assign enough memory for your particular molecule, you might have to use a smaller basis set and/or HF instead of B3LYP for your freq's. These are usually OK, as you can scale them to (almost) the correct value. There must be endless discussion of this in the CCL archives... Hope this helps, Jamie > 1. I am using the following input in order to calculate an electron density: > > %chk=tap_hf_opt.chk > #P RB3LYP 6-31+G(d) Geom=Checkpoint Cube(40,Density) Guess=Read > Density=Current > > methyl-TAP el.density calculation using optimized (hf 6-31g*) structure > > 0 1 > > > In the output there is a line that says: "Warning! SCF SP cutoffs with > diffuse functions may be unreliable. > Consider SCF=Tight" > Does anyone have experience with this and is able to explain to me what > actually it is happening.? Can I simply ignore the warning or should I > go for SCF=Tight? > > 2. I have the following input trying to calculate the frequencies of an > optimized structure at the same level of theory: > > %chk=tap.chk > #P Geom=AllCheck Guess=Read RB3LYP/6-31+G(d) FREQ POP=FULL GFPrint > > methyl-TAP optimization > > 0 1 > > > The Gaussian job is broken by this error message: > > Not enough memory for a single radius per batch: > NAngPt= 302 MaxPt= 216. > Error termination via Lnk1e in /usr/local/g94/l1002.exe. > > Can anyone explain to me what is wrong? > > Thanks a lot in advance for any kind of advice. > vlad > > -- > Vlad Cojocaru > Max Planck Institut for Biophysical Chemistry > Deparment: 060 > Am Fassberg 11, 37077 Goettingen, Germany > tel: ++49-551-201.1389 > e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de > > > > > -= 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 > > > > > > From chemistry-request@server.ccl.net Mon Jun 10 12:46:02 2002 Received: from smtp1.dti.ne.jp ([202.216.228.36]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5AGk1j19391 for ; Mon, 10 Jun 2002 12:46:01 -0400 Received: from b159504364 (PPP223.fukuoka-ip.dti.ne.jp [211.132.92.223]) by smtp1.dti.ne.jp (3.07) with SMTP id g5AGjqmg001997 for ; Tue, 11 Jun 2002 01:45:55 +0900 (JST) Message-ID: <001801c2109e$5690c2c0$df5c84d3@b159504364> From: "Telkuni" To: References: Subject: Suitable system for EHMO --summary Date: Tue, 11 Jun 2002 01:46:15 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hello CCLers, I have sent a question about Extended Huckel MO(EHMO) last week. Although there was only one reply, it is very available. (Thank you Dr.Lewars !) Here I send it again. ...Now, do you know the web site "Scirus http://www.scirus.com/"? The site was introduced by Dr.Shobe. Very useful! --------------------------------------------------- Telkuni Tsuru telkuni@venus.dti.ne.jp --- Original question --- > Hello CCLers, > > I have read the explanation of Extended Huckel MO(EHMO) method > on one book (Sorry, it is Japanese!) > > It said "EHMO isn't SCF, so it isn't available for the systems which have the > polarizability, especially not for the polypeptides. " > But, I saw some examples of other articles on which EHMO have been applied > to polar-systems. > > So I like to know the systems which are suitable or not-suitable for EHMO. > > I will summarize the responses. > > Thanks in advance. --- Reply --- Hello, An extended Hueckel method calculation can be run on *any* molecule. However, the EHM gives only qualitative, not quantitative, results. It is very poor for optimizing geometries, so an experimental geom or maybe a molecular mechanics geom is used as input. Relative energies of isomers from the EHM are not very good either. The main use of the EHM is to get the shapes and the ordering of energies of molecular orbitals; with good intuition this can be useful. EHM calculations are done mostly on polymers and "extended systems", i.e. solids. Physicists, Professor Hoffmann tells me, are always rediscovering the method. (The EHM is not SCF because the Fock matrix elements do not require an initial guess of the basis set coefficients; the Fock matrix thus does not have to be refined iteratively). For a good brief account and references, see I. N. Levine, "Quantum Chemistry", Prentice Hall, 2000. E. Lewars ===== From chemistry-request@server.ccl.net Mon Jun 10 08:41:24 2002 Received: from alpha5.iso.port.ac.uk ([148.197.254.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5ACfNj14943 for ; Mon, 10 Jun 2002 08:41:24 -0400 Received: from lu07.nwservers.iso.port.ac.uk ([148.197.251.180]) by alpha5.iso.port.ac.uk with esmtp (Exim 3.22 #2) id 17HO0H-001ApV-00; Mon, 10 Jun 2002 13:10:33 +0100 Received: from LU07/SpoolDir by LU07.nwservers.iso.port.ac.uk (Mercury 1.48); 10 Jun 02 13:10:22 +0100 Received: from SpoolDir by LU07 (Mercury 1.48); 10 Jun 02 12:56:33 +0100 From: Organization: University of Portsmouth To: "EuroQSAR 2002" Date: Mon, 10 Jun 2002 12:56:28 +0100 X-Distribution: Bulk MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Advice to registrants CC: martyn.ford@port.ac.uk Message-ID: <3D04A2D8.11893.341CDC@localhost> Priority: normal EuroQSAR 2002 EARLY BIRD REGISTRATION Reminder of deadline for discounted registration The deadline for registration to EuroQSAR 2002 at the discounted rates for academics, students and industrial scientists is Friday June 15th. Registrations received after that date will be charged at the full conference rates, details of which may be found on the conference web- site: www.euro-qsar.org From chemistry-request@server.ccl.net Mon Jun 10 10:33:45 2002 Received: from chuma.cas.usf.edu ([131.247.209.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5AEXij16887 for ; Mon, 10 Jun 2002 10:33:44 -0400 Received: from localhost (oleynik@localhost) by chuma.cas.usf.edu (8.9.3+Sun/8.9.3) with ESMTP id KAA22403 for ; Mon, 10 Jun 2002 10:33:44 -0400 (EDT) Date: Mon, 10 Jun 2002 10:33:44 -0400 (EDT) From: Ivan Oleynik To: chemistry@ccl.net Subject: LINUX CLUSTER Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, We are going to acquire a Linux cluster for running MPI type applications such as molecular dynamics, DFT plane wave and LCAO (such as MSI DMOL). We prefer to get as "turnkey" system as possible: we do not want to spend time studying hardware issues related to Beowulf DIY. I would really appreciate if someone could recommend a good vendor, who enthusiastically works with academics, understands and adequately responds to customer needs and requirements, provides good warranty support and, the most importantly, sells reliable state-of-the-art cluster systems. I would also like to get some technical advice regarding critical issues we need to keep in mind during the process of choosing configuration. To be specific, I am thinking of 24 node cluster with the following node configuration: dual AMD Athlon 2000+ (2100+) MP processor, 2Gb DDR SDRAM & 40Gb IDE hard drive. Obviously, the most important question is the choice of interconnect. I am aware of 3 standard options: Gigabit Ethernet, Myrinet, and Dolphi Wulfkit. I would appreciate very much if someone could share an experience regarding which of these 3 choices gives an optimum balance of performance (especially for heavy numerics) and price. Thanks very much, Ivan Oleynik ------------------------------------------------------------------------ Ivan I. Oleynik E-mail : oleynik@chuma.cas.usf.edu Department of Physics University of South Florida 4202 East Fowler Avenue Tel : (813) 974-8186 Tampa, Florida 33620-5700 Fax : (813) 974-5813 ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Mon Jun 10 11:18:07 2002 Received: from sina.com ([202.108.35.252]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g5AFI6j17879 for ; Mon, 10 Jun 2002 11:18:06 -0400 Received: (qmail 14099 invoked by uid 99); 10 Jun 2002 15:11:38 -0000 Message-ID: <20020610151138.14098.qmail@sina.com> From: chenghuiqc To: chemistry@ccl.net Subject: question on BSSE in G98 MIME-Version: 1.0 Date: Mon, 10 Jun 2002 23:11:38 +0800 X-Mailer: SinaMail 3.0Beta (FireToad) X-Priority: 3 Dear sir: When I use the keyword massage in Gaussian98 to do BSSE calculations the error information is: Warning! Spurious integrated density: NE= 18 NElCor= 0 Integral= 17.00628 Tolerance=1.00D-03 Consistency failure #2 in CalDSu. Error termination via Lnk1e in /raid5/shuhua/g98a11/g98/l502.exe. How can I handle this problem? thanks chenhui Nanjing university P.R.china ______________________________________ =================================================================== 劤읫출롤든綾錟芎 (http://mail.sina.com.cn) 劤읫롸잚斤口：랗癎懇끝浬寧浬，맡놔癎珂앎놔癎！ (http://classad.sina.com.cn/2shou/) From chemistry-request@server.ccl.net Mon Jun 10 11:22:57 2002 Received: from jacobus.chem.smu.edu ([129.119.201.27]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5AFMvj18050 for ; Mon, 10 Jun 2002 11:22:57 -0400 Received: from localhost (zmz@localhost) by jacobus.chem.smu.edu (8.11.6/8.11.6) with ESMTP id g5AFEVE03785 for ; Mon, 10 Jun 2002 10:14:31 -0500 Date: Mon, 10 Jun 2002 10:14:31 -0500 (CDT) From: Pearl Zheng To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, dear CCLers, We are working on docking molecules with thiolate into Zinc-Enzymes. It seems to us that FlexX( Sybyl GUI access ) always put carboxylate oxygen near to zinc instead of thiolate. A specific example is 1DD6( pdb code ), which has a thiolate ligand. Is anyone have suggestion of how to reproduce 1DD6 complex using FlexX? I appreciate any kind of suggestion. ---Mingzhu From chemistry-request@server.ccl.net Mon Jun 10 06:29:06 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5AAT6j13459 for ; Mon, 10 Jun 2002 06:29:06 -0400 Received: from localhost ([61.79.213.206]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.0) with SMTP id g5AAT2e11949 for ; Mon, 10 Jun 2002 06:29:03 -0400 (EDT) Message-Id: <200206101029.g5AAT2e11949@ccl.net> Reply-To: kigaker@yahoo.co.kr From: kigaker To: chemistry@ccl.net Subject: 키 성장,발육 전문 포털사이트[광고] Mime-Version: 1.0 Content-Type: text/html; charset="ks_c_5601-1987" Date: Mon, 10 Jun 2002 19:30:14 +0900 Copyright 2000(c)by 키가커닷컴.All rights reserved.

 

 

 

 

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From chemistry-request@server.ccl.net Mon Jun 10 13:52:58 2002 Received: from rhodopsin.usask.ca ([128.233.48.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5AHqwj20844 for ; Mon, 10 Jun 2002 13:52:58 -0400 Received: from pc.chemie.tu-darmstadt.de (localhost.localdomain [127.0.0.1]) by rhodopsin.usask.ca (8.11.6/8.11.6) with ESMTP id g5AHkLV13697 for ; Mon, 10 Jun 2002 11:46:21 -0600 Sender: thomas@localhost.localdomain Message-ID: <3D04E5ED.D335D0C3@pc.chemie.tu-darmstadt.de> Date: Mon, 10 Jun 2002 11:46:21 -0600 From: Thomas Exner X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.8-34.1mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: density matrix to MO coefficients Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I would like to ask, if somebody is aware of a method to get MO coefficients out of a given electron density matrix, i.e. an algorithm to express the density matrix as CCt where C is the matrix of MO coefficients for a given basis set (Ct is the transposed matrix of C). Any help is highly appreciated. Thank you and best wishes, Thomas -- ____________________________________________________________________ Dr. Thomas Exner Department of Physical Chemistry Physical Chemistry I University of Technology Darmstadt (TUD) Petersenstr. 20 Auf der Marienhoehe 5 64287 Darmstadt 64297 Darmstadt Germany Germany phone: +49-6151-16 2398 +49-6151-537165 fax: +49-6151-16 4298 e-mail: exner@pc.chemie.tu-darmstadt.de texner@gmx.net WWW: http://www.pc.chemie.tu-darmstadt.de/staff/exner/ Computational, Theoretical & Mathematical Chemistry Department of Chemistry University of Saskatchewan 110 Science Place 431 Edmund Park Saskatoon, SK, S7N 5C9 Saskatoon, SK, S7H 0Z4 Canada Canada phone: +1-306-966-5357 +1-306-382-5397 fax: +1-306-966-4730 ____________________________________________________________________