From chemistry-request@ccl.net Tue Sep 14 12:09:46 2004 Received: from web21205.mail.yahoo.com (web21205.mail.yahoo.com [216.136.131.248]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i8EH9gwE016714 for >ccl.net>; Tue, 14 Sep 2004 12:09:43 -0500 Message-ID: <20040914171935.74903.qmail<>web21205.mail.yahoo.com> Received: from [129.109.59.107] by web21205.mail.yahoo.com via HTTP; Tue, 14 Sep 2004 10:19:35 PDT Date: Tue, 14 Sep 2004 10:19:35 -0700 (PDT) From: IEJMD >yahoo.com> Subject: IEJMD Preprint Server To: CCL >ccl.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=1.1 required=7.5 tests=FVGT_m_MULTI_ODD2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net The IEJMD Preprint Server was launched at http://www.biochempress.com/iejmd_pi.html The purpose of the IEJMD Preprint Server is to extend the process of peer-review by collecting comments, questions for authors, or reviews from the IEJMD readers. These comments will supplement the usual peer-review process. Papers submitted for publication in the Internet Electronic Journal of Molecular Design (IEJMD), http://www.biochempress.com, are currently deposited in the IEJMD Preprints server, http://www.biochempress.com/iejmd_pi.html Recent papers from the IEJMD Preprint Server: 11. On the Mechanism of Glycoside Hydrolysis by the Family GH-90 Phage P22 Tailspike Protein Wim Nerinckx, Tom Desmet, and Marc Claeyssens 10. Tautomerism and Mass Spectra of Thiomorpholides Patricia E. Allegretti, Facundo Namor, Eduardo A. Castro, and Jorge J. P. Furlong 9. Sweet and Taste Modifying Proteins - Comparative Modeling and Docking Studies of Curculin, Mabinlin, Miraculin with the T1R2-T1R3 Receptor Ravi Kant, R. Mohan Babu, and S. Ramakumar 8. Investigation of the Electronic Structure of Antitumor Drugs. I. QSAR Study for 2-(4-Aminophenyl)benzothiazoles Shabaan A. K. El-roby and Rifaat Hilal We would appreciate receiving your comments, questions for authors, or reviews for the IEJMD Preprints; please send all comments by E-mail to iejmd<>yahoo.com Best regards, John Paul T. Smith Assistant Editor Internet Electronic Journal of Molecular Design (IEJMD) ISSN 1538-6414 Publisher: BioChem Press http://www.biochempress.com _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com From chemistry-request@ccl.net Tue Sep 14 04:33:29 2004 Received: from nibbel.kulnet.kuleuven.ac.be (nibbel.kulnet.kuleuven.ac.be [134.58.240.41]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i8E9XSwE025117 for ; Tue, 14 Sep 2004 04:33:28 -0500 Received: from localhost (localhost [127.0.0.1]) by nibbel.kulnet.kuleuven.ac.be (Postfix) with ESMTP id 733F94B6A1 for ; Tue, 14 Sep 2004 11:43:27 +0200 (CEST) Received: from antonius.kulnet.kuleuven.ac.be (antonius.kulnet.kuleuven.ac.be [134.58.240.73]) by nibbel.kulnet.kuleuven.ac.be (Postfix) with ESMTP id 16B904B630 for ; Tue, 14 Sep 2004 11:43:27 +0200 (CEST) Received: from agr-ccc-splash.agr.kuleuven.ac.be (dhcp-105-184.agr.kuleuven.ac.be [10.33.105.184]) by antonius.kulnet.kuleuven.ac.be (Postfix) with ESMTP id D38C54C2C5 for ; Tue, 14 Sep 2004 11:43:26 +0200 (CEST) Message-Id: <6.1.1.1.2.20040914112253.024e96b8[at]u0043641.kuleuven.be> X-Sender: u0043641[at]u0043641.kuleuven.be (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 6.1.1.1 Date: Tue, 14 Sep 2004 11:43:43 +0200 To: cheMISTRY[at]ccl.net From: Eric Breynaert Subject: CCL:g03 optimised geometry becomes unoptimised after freq calculation - SUMMARY - Problem not solved Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed X-Virus-Scanned: by KULeuven Antivirus Cluster X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i8E9XTwE025124 Dear Ccl'ers On Mon, Sep 06, 2004 at 01:11:35PM +0200, eric breynaert wrote: > dear ccl'ers, > > I'm doing dft (ub3lyp/lanl2dz) calculations on technetium compounds. After > a geometry optimisation, i always run a stabe=(opt) and then a freq > calculation. > > Item Value Threshold Converged? > Maximum Force .000043 .000450 YES > RMS Force .000007 .000300 YES > Maximum Displacement .000646 .001800 YES > RMS Displacement .000162 .001200 YES > Predicted change in Energy=-3.998357D-08 > Optimization completed. > -- Stationary point found. > > Stable reports ->wavefunction stable under the perturbations considered > At the end of the freq calculation the geom optimisation params become > > Item Value Threshold Converged? > Maximum Force .004051 .000450 NO > RMS Force .001202 .000300 NO > Maximum Displacement .126525 .001800 NO > RMS Displacement .018760 .001200 NO > Predicted change in Energy=-1.029330D-03 > > Can anyone explain this ? What happens ? Among others i got the following reply from help[at]gaussian.com > Clearly something is different here and I suspect that the SCF converged > to a different energy. When you say that the Stable reported a stable SCF > was this STABLE=OPT and perhaps it found an initial instability and then > optimized further to find the true ground state? In this case you would > need to reoptimize the structure before running the FREQ calculation. After checking this, if found that stable did find an instability in the wavefunction, so i did a re-optimisation (optimised within 12 steps) and then i ran a stable=(opt) calculation again. This time stable again found an instability, so again i did a reoptimisation. Only this time i didn't reach an optimised structure within 198 steps. When i look at the energy changes and the rms gradient i can only conclude that the inital geometry i started with after the last stable=(opt) calculation was more optimised than all other steps of this last optimisation calculation. This is a link to a screenshot of the report gaussview generates. http://splash.studentenweb.org/OptPlot.jpg All comments on this issue are highly appreciated. Regards, Eric Breynaert -- Eric Breynaert Labo voor Colloodchemie Kasteelpark Arenberg 23 B-3001 Leuven Tel: +3216321457 Fax: +3216321998 From chemistry-request@ccl.net Tue Sep 14 03:04:40 2004 Received: from hotmail.com (bay22-f11.bay22.hotmail.com [64.4.16.61]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i8E84TKo015738 for ; Tue, 14 Sep 2004 03:04:29 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 14 Sep 2004 01:12:55 -0700 Received: from 210.83.210.9 by by22fd.bay22.hotmail.msn.com with HTTP; Tue, 14 Sep 2004 08:12:55 GMT X-Originating-IP: [210.83.210.9] X-Originating-Email: [liuxin_dut~at~hotmail.com] X-Sender: liuxin_dut~at~hotmail.com From: "Liu Xin" To: chemistry~at~ccl.net Subject: CCL: basis sets to study UV of MnS GeS2 and HgS Date: Tue, 14 Sep 2004 08:12:55 +0000 Mime-Version: 1.0 Content-Type: text/plain; charset=gb2312; format=flowed Message-ID: X-OriginalArrivalTime: 14 Sep 2004 08:12:55.0888 (UTC) FILETIME=[A3B61D00:01C49A32] X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi! I am trying to study the UV spectra of MnS, GeS2 and HgS. During my calculations with TD in g98W, I find that the LanL2dz basis set shipped with g98 is not good enough. So, I hope that I can get some useful information from you. Any suggestions or instructions will be appreciated and will be quated in my future works. I am looking forward for your kindly help! Sincerely your Xin, Liu From chemistry-request@ccl.net Tue Sep 14 09:42:24 2004 Received: from mailhub130.itcs.purdue.edu (mailhub130.itcs.purdue.edu [128.210.5.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i8EEgNwE032160 for ; Tue, 14 Sep 2004 09:42:23 -0500 Received: from [128.46.108.125] (frny117bpc05.ecn.purdue.edu [128.46.108.125]) by mailhub130.itcs.purdue.edu (8.12.10/8.12.10/scan-smtp) with ESMTP id i8EEqLVO003187 for ; Tue, 14 Sep 2004 09:52:21 -0500 Message-ID: <414705A6.9080509_at_purdue.edu> Date: Tue, 14 Sep 2004 09:52:22 -0500 From: Aaron Deskins User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.2) Gecko/20040803 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry_at_ccl.net Subject: Periodic frequency calculations References: <000501c499e6$60f17060$0200a8c0@planaria> In-Reply-To: <000501c499e6$60f17060$0200a8c0@planaria> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello fellow CCL'ers, I'm attempting some frequency (phonon) calculations with the VASP periodic DFT program. I'm hoping that those knowledgable with these type of calculations can help me out. After doing some reading, I think I have the basic theory down. First atom positions are perturbed from equilibrium to get the matrix, D(R), with elements of form d^2(V)/dr1dr2, or second partial derivatives of energy with respect to displacements 1 and 2. Next Bloch's theorem is applied to get the dynamical matrix: D(k) = Sum [ D(R)*exp[-i*dot(k,R)]. One can diagonalize the dynamical matrix to get the phonon spectrum. Does this sound right? In practice, VASP only calculates the spectrum at the gamma point, so in this case D(k) = D(R). In theory the code could be modified to include other k-points if needed. What is the relationship between IR frequencies from experiment and the calculated phonon spectrum? Is there a special relationship between the IR frequencies and the gamma point? Any help, suggestions, comments, references, etc. are appreciated. Aaron Deskins Purdue University Chemical Engineering From chemistry-request@ccl.net Tue Sep 14 13:47:39 2004 Received: from collapsed.wormhole.hu (collapsed.wormhole.hu [195.70.35.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i8EIlcwE024586 for ; Tue, 14 Sep 2004 13:47:38 -0500 Received: from szilva (helo=localhost) by collapsed.wormhole.hu with local-esmtp (Exim 4.34 #1 (Debian)) id 1C7IUe-00044u-DG; Tue, 14 Sep 2004 20:57:32 +0200 Date: Tue, 14 Sep 2004 20:57:31 +0200 (CEST) From: szilva_at_computer.org X-X-Sender: szilva_at_collapsed.wormhole.hu To: Mark Thompson , CCL Subject: CCL:Note to ArgusLab users Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Sender: Szilveszter JUHOS X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Mon, 13 Sep 2004, Mark Thompson wrote: > I have accepted a position as Chief Scientist for Biosciences at > Fujitsu. Great, congratulations for the new job! > You are of course free to continue to use ArgusLab 3.1 and 4.0 and to > redistribute it to your friends and colleagues as you see fit. However, > I won't be making bug fixes or adding new features after Sept. 27th. What about putting it to opensource (sourceforge.net)? Being a UNIX-addicted person I neved had a look on Argus[Lab|Dock] but sounds as an interesing project. Some of those people already using it would be happy to jump into the code. Cheers: Szilva From chemistry-request@ccl.net Tue Sep 14 15:50:52 2004 Received: from smtp.ucla.edu (smtp.ucla.edu [169.232.48.137]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i8EKooiU003015 for ; Tue, 14 Sep 2004 15:50:51 -0500 Received: from mail.ucla.edu (mail.ucla.edu [169.232.48.135]) by smtp.ucla.edu (8.12.11/8.12.11) with ESMTP id i8EL0q8T031881 for ; Tue, 14 Sep 2004 14:00:52 -0700 Received: from [137.78.33.197] (varies04012101237.jpl.nasa.gov [137.78.33.197]) (authenticated bits=0) by mail.ucla.edu (8.12.11/8.12.11) with ESMTP id i8EL0pq3028871 for ; Tue, 14 Sep 2004 14:00:52 -0700 Message-ID: <41475C03.3030704.-at-.ucla.edu> Date: Tue, 14 Sep 2004 14:00:51 -0700 From: Douglas Sievers User-Agent: Mozilla Thunderbird 0.6 (X11/20040708) X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL Subject: 1-D Periodic Boundary Conditions in Gaussian 03 or CPMD References: In-Reply-To: Content-Type: text/plain; charset=US-ASCII; format=flowed Content-Transfer-Encoding: 7bit X-Probable-Spam: no X-Spam-Hits: 0 X-Scanned-By: smtp.ucla.edu X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi CCLers, Since I haven't received any response from Gaussian support since asking this question over a week ago, I thought I would try the list. Does anyone know how to output all energies and eigenvalues for all of the k-points in a PBC calculation? I am trying to do a 1-dimensional calculation on their "test molecule" in the manual with a minimal basis set. I tried using IOp(5/98=1), which according to the manual should output everything, but it didn't work. I also tried #P for extra output and Pop=Full, hoping to recover more data, but without success. Here is the input file: %chk=neo5.chk #P HF/3-21g PBC(NKPoint=5) IOp(5/98=1) Pop=Full neoprene, [-CH2-CH=C(Cl)-CH2-] optimized geometry 0 1 C,-1.9267226529,0.4060180273,0.0316702826 H,-2.3523143977,0.9206168644,0.9131400756 H,-1.8372739404,1.1548899113,-0.770750797 C,-0.5737182157,-0.1434584477,0.3762843235 H,-0.5015912465,-0.7653394047,1.2791284293 C,0.5790889876,0.0220081655,-0.3005160849 C,1.9237098673,-0.5258773194,0.0966261209 H,1.772234452,-1.2511397907,0.915962512 H,2.3627869487,-1.0792380182,-0.752511583 Cl,0.6209825739,0.9860944599,-1.7876398696 TV,4.8477468928,0.1714181332,0.5112729831 In the output I am geting fields like this, which I believe are maybe supposed to be the HOMO and LUMO at each k (each Cycle appears to be a single k-point), but there is no reference to k anywhere and I don't know what all the extra symbols mean: Cycle 1 Pass 0 IDiag 1: E= (Non-Variational) Sum_Occ: Avg-Min 2.81146D-03 Max-Avg 1.54567D-03 Dif 4.35713D-03 (eV) Alpha HOCO: -8.752273 LUCO: -4.373880 indirect gap: 4.378393 direct gap: 4.378393 (eV) Diagonalized old Fock matrix for initial guess. Cycle 1 Pass 1 IDiag 1: ... Sum_Occ: Avg-Min 9.82218D-02 Max-Avg 8.15760D-02 Dif 1.79798D-01 (eV) Alpha HOCO: -6.665804 LUCO: 6.526957 indirect gap: 13.192761 direct gap: 13.192761 (eV) GapD= 2.000 DampG=2.000 DampE=0.250 DampFc=0.5000 IDamp=-1. Damping current iteration by 5.00D-01 RMSDP=3.53D-03 MaxDP=9.16D-02 OVMax= 0.00D+00 Cycle 2 Pass 1 IDiag 1: ... Sum_Occ: Avg-Min 6.94870D-02 Max-Avg 5.54877D-02 Dif 1.24975D-01 (eV) Alpha HOCO: -8.634730 LUCO: 4.809102 indirect gap: 13.443832 direct gap: 13.443832 (eV) RMSDP=1.41D-03 MaxDP=3.63D-02 DE=-9.83D-02 OVMax= 0.00D+00 Has anyone had this same problem? Also, if anyone knows how to use CPMD instead I would appreciate a rough draft of an input file if available. Thank you, Doug >On Mon, 13 Sep 2004, Mark Thompson wrote: > > > >>I have accepted a position as Chief Scientist for Biosciences at >>Fujitsu. >> >> > >Great, congratulations for the new job! > > > >>You are of course free to continue to use ArgusLab 3.1 and 4.0 and to >>redistribute it to your friends and colleagues as you see fit. However, >>I won't be making bug fixes or adding new features after Sept. 27th. >> >> > >What about putting it to opensource (sourceforge.net)? Being a >UNIX-addicted person I neved had a look on Argus[Lab|Dock] but sounds as >an interesing project. Some of those people already using it would be >happy to jump into the code. > >Cheers: >Szilva > > > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY.-at-.ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST.-at-.ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow.-at-.nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > >