From chemistry-request@www.ccl.net Thu Mar 11 04:18:22 1999 Received: from cleo.univ-reims.fr (cleo.univ-reims.fr [193.50.208.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA26036 Thu, 11 Mar 1999 04:17:47 -0500 (EST) From: cyrille.bertrand@univ-reims.fr Received: from centre01.univ-reims.fr (centre01.univ-reims.fr [193.50.208.1]) by cleo.univ-reims.fr with SMTP (8.7.1/8.7.1) id KAA22120 for ; Thu, 11 Mar 1999 10:12:10 +0100 (MET) Received: from localhost by centre01.univ-reims.fr with SMTP (1.38.193.4/16.2) id AA03079; Thu, 11 Mar 1999 09:09:52 GMT Date: Thu, 11 Mar 1999 09:09:52 +0000 (WET) To: CHEMISTRY@www.ccl.net Subject: Spin Orbit Coupling Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I'm looking for the Spin-orbit coupling value between the singlet and triplet of the 1,4-diradical coming from the addition of 3(acrolein) to 1(C2H4). Any references will be appreciated. From chemistry-request@www.ccl.net Thu Mar 11 04:20:32 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA26048 Thu, 11 Mar 1999 04:20:32 -0500 (EST) Received: from oxmail.ox.ac.uk (oxmail1.ox.ac.uk [129.67.1.1]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id EAA10896 for ; Thu, 11 Mar 1999 04:20:29 -0500 (EST) Received: from ermine.ox.ac.uk ([163.1.2.13]) by oxmail.ox.ac.uk with esmtp (Exim 2.10 #1) id 10L1dX-0001M1-00; Thu, 11 Mar 1999 09:20:15 +0000 Received: from oums0054 (helo=localhost) by ermine.ox.ac.uk with local-smtp (Exim 2.12 #1) id 10L1dX-0000d9-00; Thu, 11 Mar 1999 09:20:15 +0000 Date: Thu, 11 Mar 1999 09:20:15 +0000 (GMT) From: "Ivan I. Oleinik" To: Fernando Vila cc: Computational Chemistry List Subject: Re: CCL:G:Damped Coulomb Potential Summary In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Fernando, Explicit calculation of matrix element of the 'dumped Coulomb potential' (error function/R) with gaussians is in the paper of G. Lippert, J. Hutter and M. Parrinello " A hybrid Gaussian and plain wave denisty functional scheme", Mol Phys 92 (1997) pp 477-487. They have error function in the local part of the pseudopotential. On page 481 they write: " erf(a|r-R|) V(r) = ------------- |r-R| can be regarded as the Coulomb potential originating from a Gaussian charge centered at R". Formula (34) immediately gives the answer. Ivan Oleinik ------------------------------------------------------------------------ Ivan I. Oleinik E-mail : ivan.oleinik@materials.ox.ac.uk Department of Materials University of Oxford Parks Road Oxford OX1 3PH Tel : +44 (0)1865 283325 United Kingdom Fax : +44 (0)1865 273764 ------------------------------------------------------------------------ > ------------------------------------------------------------------------ > > On Wed, 10 Mar 1999, Fernando Vila wrote: > Dear Fellows; > > I would like to thank all the people that replied to me request. Right > after I sent my e-mail to the list I decided to give it a new try. At the > very beginning of my equations I found an error that was complicating > everything. After I fixed that the integrals turned out to be > embarrassingly easy, easier than those including only the Coulomb > potential. The references you sent will be useful to double check my > results. > > My original question was: > > Dear Fellows, > > For the past weeks I have been trying to calculate the matrix elements > for a damped Coulomb potential to no avail. The potential has the form: > > erf(a|r-R|) > V(r) = ------------- > |r-R| > > where r and R are position vectors and erf(t) is the error function: > > 2 t > erf(t) = -------- int exp(-x^2) dx. > PI^(1/2) 0 > > The matrix elements then are of the form: > > erf(a|r-R|) gij > = int gi V(r) gj dr = int ----------------- dr > |r-R| > > Here gi are spherical Gaussians and gij is the resulting Gaussian from the > Gaussian Product Theorem. > > I have tried using techniques similar to those used for the calculation of > the pure Coulomb potential (based on Fourier or Laplace transforms) but > the usual cancellation is not complete. > > Any pointers to papers, books or web pages are welcome.. The complete > solution is also very much welcome.. :-) > > Thanks to all in advance, Fer. > > Here is a summary of the replies I received: > > ========================================================================== > From: koelmel > > Hi, > > Lecture Notes in Chemistry, vol. 48, authored by C. Pisani, R. Dovesi > and C. Roetti, titled > "Hartree-Fock Ab Initio Treatment of Crystalline Systems" > (1988, springer) > > may be a useful reference. What you're looking for is mentioned > on page 60. > > One way is to convert 1/r into an integral using the Laplace transform > trick, then change the order of integration, I think. > > Hope this helps somewhat > > Cheers, > Christoph > > ========================================================================== > From: Frank Jensen > > Try looking up some of Peter Gill's work in > recent years. They have played with screened > Coulomb potentials. > Frank > > > ========================================================================== > From: Norge Cruz Hernandez > > Hi , > > Try to see : > > S. Obara and A. Saika. > J. Chem. Phys. 84(7), 3963 > > best regard > Norge > > ========================================================================== > From: "Jeremy P. Dombroski" > > Dear Fernando: > > This is work that myself, Professor Peter Gill and Dr Ross Adamson have > spent considerable time on (in particular, the latter). We have recently > published an article in J. Comp. Chem. and if you contact Ross at > ross@theor.ch.cam.ac.uk he may provide you with a preprint should the > article not yet be in print. > > Q-Chem 1.2 performs O(N) damped Coulomb SCF calculations, including > energies, optimizations and frequencies using what we have called the > CASE approximation where we replace all occurrences of the Coulomb > operator with the so-called Damped Coulomb potential. > > May I ask where your research interest lies in this damped Coulomb > potential? > > Regards, > Jeremy Dombroski > > > ========================================================================== > From: "Jan H. Jensen" > > Hello, > I believe Peter Gill at Cambridge has worked on something quite > similar. I don't have any references on hand. > > Best regards, > > Jan Jensen > > ******************************************************************************* > Fernando D. Vila > Department of Chemistry Voice (412)624-8691 > University of Pittsburgh Fax (412)624-8552 > Box 90 Chevron Science Center E-mail fer@theory6.chem.pitt.edu > Pittsburgh, PA 15260, USA WWW http://www.pitt.edu/~fer > ******************************************************************************* > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: chemistry-request@www.ccl.net > -- Original Sender From: Address: fer@theory6.chem.pitt.edu > 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 chemistry-request@www.ccl.net Thu Mar 11 08:38:29 1999 Received: from arnold.chem.uoa.gr (arnold.chem.uoa.gr [195.134.76.50]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA00271 Thu, 11 Mar 1999 08:38:27 -0500 (EST) Received: from localhost (jkerk@localhost) by arnold.chem.uoa.gr (8.8.8/8.8.8) with SMTP id PAA09137 for ; Thu, 11 Mar 1999 15:34:12 +0200 (EET) Date: Thu, 11 Mar 1999 15:34:12 +0200 (EET) From: "I. Kerkines" Reply-To: "I. Kerkines" To: chemistry@www.ccl.net Subject: MRCI Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear colleagues, Does anybody know of any reviews or related papers on second order CI (SOCI)? Thanks in advance, I will summarize for the list. Sincerely, ************************************************************ * Ioannis S. Kerkines * * M.Sc. Student in Physical Chemistry * * Department of Chemistry / University of Athens * * Panepistimiopolis Tel: ++30 1 727-4569 * * Zographou, 157 10 FAX: ++30 1 723-3219 * * HELLAS (Greece) Email: jkerk@arnold.chem.uoa.gr * ************************************************************ From chemistry-request@www.ccl.net Wed Mar 10 03:40:57 1999 Received: from mail.chemie.fu-berlin.de (root@mail.chemie.fu-berlin.de [160.45.24.23]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA09740 Wed, 10 Mar 1999 03:40:56 -0500 (EST) Received: from Dirac.Chemie.FU-Berlin.DE(dirac.chemie.fu-berlin.de[160.45.24.166]) (2286 bytes) by mail.chemie.fu-berlin.de via sendmail with P:smtp/R:bind_hosts/T:inet_zone_bind_smtp (sender: ) id for ; Wed, 10 Mar 1999 09:40:48 +0100 (CET) (Smail-3.2.0.101 1997-Dec-17 #18 built 1999-Feb-17) Received: by Dirac.Chemie.FU-Berlin.DE (Smail3.2.0.98) id ; Wed, 10 Mar 1999 09:40:47 +0100 (MET) Message-Id: From: knapp@chemie.fu-berlin.de (Ernst-Walter Knapp) Subject: graduate student position in comp. chem. To: CHEMISTRY@www.ccl.net Date: Wed, 10 Mar 1999 09:40:47 +0100 (MET) X-Mailer: ELM [version 2.4 PL24 ME8d] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Graduate position (BAT 2A half) in Computational (Bio)(physics)chemistry At the Chemistry Department of the Free University of Berlin, there is a position to do PhD work available. Beside research work, during the terms also two hours per week tutorial work in German language needs to be done. Our group in Computational Biophysics/Biochemistry is active in modeling and computer simulation of proteins. One focus is protein folding and structure prediction, where we develop our own methods. But we also calculate vibrational spectra, protonation pattern, proton and electron transfer processes and reaction mechanisms in proteins using different methods. Further details can be obtained from our home page: http://userpage.chemie.fu-berlin.de/~knapp/ Our group members are from chemistry, biochemistry, physics and mathematics. If you are interested to do such interdisciplinary research work, please contact me by email: Knapp@Chemie.FU-Berlin.de |---------------------------------------------------------------------| | Dr. Ernst-Walter Knapp | | Freie Universitaet Berlin Tel.: +49 30 838 4387 | | Fachbereich Chemie Fax.: +49 30 838 3464 | | Institut fuer Kristallographie | | Takustrasse 6 E-mail: Knapp@Chemie.FU-Berlin.de | | D-14195 Berlin | | Germany www: http://userpage.chemie.fu-berlin.de/~knapp/ | |---------------------------------------------------------------------| From chemistry-request@www.ccl.net Wed Mar 10 06:50:12 1999 Received: from oxmail.ox.ac.uk (oxmail2.ox.ac.uk [163.1.2.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA10400 Wed, 10 Mar 1999 06:49:48 -0500 (EST) Received: from ermine.ox.ac.uk ([163.1.2.13]) by oxmail.ox.ac.uk with esmtp (Exim 2.10 #1) id 10KhUN-00027q-00 for chemistry@www.ccl.net; Wed, 10 Mar 1999 11:49:27 +0000 Received: from oums0010 (helo=localhost) by ermine.ox.ac.uk with local-smtp (Exim 2.12 #1) id 10KhUN-0007Fd-00 for chemistry@www.ccl.net; Wed, 10 Mar 1999 11:49:27 +0000 Date: Wed, 10 Mar 1999 11:49:27 +0000 (GMT) From: Andrew Horsfield Reply-To: Andrew Horsfield To: CCL mail list Subject: Non-radiative transitions Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have just implemented the "fewest switches" algorithm of John Tully for carrying out non-adiabatic molecular dynamics in an LCAO code (which can use either tight binding or density functional theory). I plan to use this code to study non-radiative transitions in silicon. My first problem is to find some simple systems for which answers are already known in order to debug the code. Ideally I would like to use a hydrocarbon or silicon based system since I have reliable tight binding models for these. Does anyone know of calculated or experimental non-radiative transition rates for such systems? Best regards, Andrew +----------------------------------------------------+ Andrew Horsfield e-mail: horsfield@fecit.co.uk FECIT, 2 Longwalk Road, Stockley Park, Uxbridge, Middlesex UB11 1AB, United Kingdom. phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422 +----------------------------------------------------+ From chemistry-request@www.ccl.net Wed Mar 10 07:47:51 1999 Received: from Sun.Farlep.Net (Sun.Farlep.Net [208.244.48.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA10524 Wed, 10 Mar 1999 07:47:49 -0500 (EST) Organization: Farlep-Internet Received: from farlep.net (L101.Farlep.Net [208.244.49.227]) by Sun.Farlep.Net (8.9.1/8.9.1/Farlep-Mail-1.6) with ESMTP id OAA14572; Wed, 10 Mar 1999 14:47:31 +0200 (EET) Message-ID: <36E60824.7D641749@farlep.net> Date: Wed, 10 Mar 1999 08:50:29 +0300 From: "Victor E. Kuz'min" X-Mailer: Mozilla 4.5 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CCL , BAYARD Francois , VARNEK Alexandre Subject: CCL:SUMMARY:Drawings--->Structure Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 8bit Dear CCL'ers, The original question and the replies received up to now are shown below. My big thanks to to Lewis Jardine, Tamas Gunda, Doug Henry, Rob Williams. best regards, VEK --------------------------------------------------q--- > Dear Colleagues, > Whether there is a software for conversion of a graphics image of > molecular structure ( for example: *.gif, *.jpg, …. etc) in files such > as *.mol, *.hin, *.pdb, ….? This is a peculiar kind of OCR for the > structural formulas. It will enable for scanned drawings to get the > structural file. Is it possible? I shall be grateful for any guidelines > or tips. > > With best regards, > VEK ------------------------------------------------------ --------------------------------------------------r1-- > Hello Victor > > This functionality will be added to ChemSymphony in the near future. > We have already added it to an application that we are developing > to access Daylight and it will be migrated to standard ChemSymphony > Beans in the near future. > > However, we will only be covering .JPG & .PNG as there are > licensing and royalty problems with using GIFs (also it is > an out-of-date format). Secondly we do not have a .hin filter > at the present, although we have provided documentation on how > to write and add extra filters. > > See our website for the range of beans available. > > Cheers > Lewis > > > --- --- > Dr. Lewis Jardine | e-mail: lewis@cherwell.com > ChemSymphony Team Leader | Phone: +44 (0)1865 784810 > Cherwell Scientific Publishing | Fax: +44 (0)1865 784801 > Oxford Science Park | http://www.cherwell.com/ > OX4 4GA, UK | http://www.chemsymphony.com/ > --- --- > > ------------------------------------------------------ --------------------------------------------------r2-- > As far as I remember, there is a program called Kekule somewhere > out there, which was designed to convert scanned structural images > to molfiles > > Hope this helps > > Tamas > > > ************************************************************************ > Dr Tamas E. Gunda phone: (+36-52) 316666-2479 > Research Group of Antibiotics fax : (+36-52) 310936 > L. Kossuth University e-mail: tamasgunda@tigris.klte.hu > POBox 36 http://www.klte.hu/~gundat > H-4010 Debrecen > Hungary > ************************************************************************ ------------------------------------------------------ --------------------------------------------------r3-- > Subject: > RE: CCL:Drawings--->Stuctural file > Date: > Fri, 5 Mar 1999 08:51:03 -0800 > From: > Doug Henry > Organization: > Farlep-Internet > To: > "'Victor E. Kuz'min'" > > > > > The Kekule Program from Oxford Molecular (www.oxmol.com) does this. > ------------------------------------------------------ --------------------------------------------------r4-- > Kekule is supplied by Oxford Molecular. You can find more information > at: > > http://www.oxmol.co.uk/prods/kekule/ > > I hope this is what you need. > > Thanks, > Rob > > -- > > --------------------------------------------------------------------- > Dr Rob Williams Tel: (+44) 1865 784600 > Deputy Engineering Manager Fax: (+44) 1865 784601 > Oxford Molecular Limited E-mail: rwilliams@oxmol.co.uk > --------------------------------------------------------------------- -- >____< >____< >____< >____< >____< >____< /|@\/@|\ /|@\/@|\ /|@\/@|\ /|@\/@|\ /|@\/@|\ /|@\/@|\ (\____/) (\____/) (\____/) (\____/) (\____/) (\____/) --"--"-------"--"-------"--"-------"--"-------"--"-------"--"---- Victor E. Kuz'min National Academy of Science of Ukraine Head Scientist A.V.Bogatsky Phys.- Chem. Institute Deputy Head of Department of Thermodynamics & Theoretical Chemistry 86 Lustdorfskaja doroga, 270080, Odessa, Ukraine Home: Office: 38(0482) 631389 38(0482) 225127 Fax 38(0482) 652012 mailto:victor@farlep.net mailto:vek@pci.farlep.net From chemistry-request@www.ccl.net Wed Mar 10 12:48:26 1999 Received: from sg1503.chemie.uni-marburg.de (sg1503.Chemie.Uni-Marburg.DE [137.248.151.215]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA14438 Wed, 10 Mar 1999 12:48:20 -0500 (EST) Received: from pc15105 (pc15105.Chemie.Uni-Marburg.DE [137.248.151.180]) by sg1503.chemie.uni-marburg.de (8.9.3/8.9.2/schn) with SMTP id SAA17668; Wed, 10 Mar 1999 18:47:11 +0100 (MET) From: "Stefan Fau" To: "Joseph W. Bausch" Cc: "CCL" Subject: RE: G:getting data from vibrational frequencies Date: Wed, 10 Mar 1999 18:49:20 +0100 Message-ID: <000401be6b1e$5385ef70$b497f889@pc15105.chemie.uni-marburg.de> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 In-Reply-To: Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by www.ccl.net id MAA14439 Dear JWB, you can create a distorted geometry by manually adding the vector of the chosen vibrational mode to the coordinates as given in the Standard Orientation. You can also use a small program called xvibs (available in the CCL archive) for the same purpose. It will produce a set of geometries that are distorted in varying degrees (geoms for a "video"), but you can delete unwanted geometries. I think you may get 6 numbers per line. In that case you are interested in the first three numbers. Alternatively you can use "molden -A" and the z-matrix editor (Gaussian style). The "-A" prevents molden from reordering the atoms when creating the new z-matrix. You can then alter the most important variables manually. > I have an optimized geometry (using Gaussian94) of a highly symmetrical > molecule. A frequency calculation indicates that it is a saddle point, > with 4 imaginary frequencies. I have animated these frequencies using > MOLDEN. I would like to reoptimize this structure "following" the changes > as indicated by each of the four imaginary frequencies (I'm hoping that it > will lead down to a transition state). Is there any easy way to get > MOLDEN, or any other program, to give starting coordinates > corresponding to > the geometries just slightly perturbed from this optimized geometry? > > I'll summarize if there is sufficient interest, > JWB > bausch@chem.vill.edu ______________________________________________________________________ Dr. Stefan Fau Fachbereich Chemie, AK Frenking Philipps-Universität Marburg 35032 Marburg, Germany fau@chemie.uni-marburg.de From chemistry-request@www.ccl.net Wed Mar 10 18:32:39 1999 Received: from rs6chem.chem.vill.edu (rs6chem.chem.vill.edu [153.104.73.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA24367 Wed, 10 Mar 1999 18:32:38 -0500 (EST) 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 ESMTP id SAA15115 for ; Wed, 10 Mar 1999 18:32:18 -0500 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 10 Mar 1999 18:36:25 -0500 To: CHEMISTRY@www.ccl.net From: "Joseph W. Bausch" Subject: summary: getting data from vibrational frequencies Last night I posted the following to the CCL: -------- I have an optimized geometry (using Gaussian94) of a highly symmetrical molecule. A frequency calculation indicates that it is a saddle point, with 4 imaginary frequencies. I have animated these frequencies using MOLDEN. I would like to reoptimize this structure "following" the changes as indicated by each of the four imaginary frequencies (I'm hoping that it will lead down to a transition state). Is there any easy way to get MOLDEN, or any other program, to give starting coordinates corresponding to the geometries just slightly perturbed from this optimized geometry? -------- As usual, the CCL community has been a big help! It turns out that the MOLDEN program does just what I need, as indicated below by the author of MOLDEN. The other responses I got are also quite informative, so I have included them all. Thanks to everyone that responded, JWB --- #1 From: Gijs Schaftenaar molden has a commandline flag '-w opt' where opt can be 1 or 2, '-w 1' will make molden write out a freqN.dat file with a series of xyz geometries when you select a frequency, '-w 2' does the same only now the file contains a series of mopac z-matrices. (molden can read these files back in, now use the 'Select Point' section to display them). The molden molden -d commandline flag will make molden print the equilibrium geometry and the Normal Mode displacements. Best Regards, Gijs Schaftenaar Author of Molden --- #2 From: chmmai@nus.edu.sg (Dr. Ida N. L. Ma) Excel. What you need is to get the geom in Standard orientation, and then the displacement vector of the mode you are interested in: final displacement = original coordinate +(factor)*displacement vector where factor is a number, representing how much you want to displace along the vector. The small the number, the smaller the displacement. --- #3 From: Matthias Hofmann Molecule can do what you ask for. This program was written for the Mac by Nico Hommes who is at the University of Erlangen, Germany. It allows you to specify how many pictures to be generated for the animation and each can be used for generating a new input geometry. In this way you can choose between a small or larger distortion. But the program is not free. For further information have a look at: http://www.ccc.uni-erlangen.de/hommes/molecule/index.html --- #4 From: Dmitry Khoroshun Molecule for Macintosh by van Eikema Hommes can do some steps along the specified directions. --- #5 From: Pablo Vitoria Garcia Viewmol will let you distort the molecule (and change the degree of perturbation) and save the new coordinates. I send you as an attachment some information about the program (which is freely available). --- #6 From: Stefan Konietzny there is a tool called xvibs. It produces a trajectory xyz file out of a frequency output. I use it with gOpenMol by Leif Laaksonen. For a chosen vibration you can cut out the desired orientation and put it back into your input, and hopefully the optimization goes down the hill. If you like i can send you the source. This is the beginning of the source: xvibs version 4.0.1 (August 1997) This program produces XYZ animation files for molecular vibrations represented by normal modes taken from output files from Aces2, Gamess, and Gaussian. The program autosenses what output file is given. It writes separate files, one simple cosine trajectory for particular normal mode. Vectors representing the normal coordinate are attached to the atoms, which is useful for a static picture. This program is not copyrighted. You are welcome to extend it, or send your files to basmith@pollux.chem.umn.edu and I will gladly extend it for you. Send bug reports to: basmith@pollux.chem.umn.edu -cut- Written in 1990 by Milan Hodoscek Institute of Chemistry, Ljubljana, Slovenia Modified for XMOL 1992 @NIH, Bethesda, MD Modified again Fred Brouwer Univ. of Amsterdam 1994 to include vectors (fred@org.chem.uva.nl (Fred Brouwer)) Modified to accept G94, Yos Ginting (Yos.Ginting@chem.utas.edu.au) Modified by Jan Labanowski, jkl@ccl.net to accept input from GAMESS and ACESS Rewritten by Bradley A. Smith, (http://pollux.chem.umn.edu/~basmith/, basmith@pollux.chem.umn.edu) --- #7 From: Elmar Gerwalin I use xvibs to do exactly this. xvibs is simple "C"-program , available as source code, but should be easily to compile: use: cc xvibs.c -lm See the file xvibs.c for further informations. Now for the thing you need: xvibs extrcats the normal modes from a g94-output and creates an "xyz"-file (don't worry :-) ) for each mode you tell him. (E.g. xvibs water.out 3 creates a file water.003.xyz (or something like that) which contains a series of 20 (!) cartesian coordinates for this mode. So , first, programs that can animate xyz-files (like xmol) can show the mode (like molden does) second: you can cut out the 10th (NOT the last, because it's a loop: the 20th is equal to the 1st) section of coordinates and use this as NEW gaussian input ! This works fine when you want to follow 1 mode. For more modes, I have no idea yet but to perform this procedure Oh, xvibs is available (free) anywhere in the Web. I don't know the Original source now, but you might find it at: http://www.uni-duesseldorf.de/ftp/ftp/share/xvibs/doc/ or: http://www.arl.hpc.mil/PET/cta/ccm/training/courses/scivis/xvibs/ or use a search engine.. --- #8 From: Karl Irikura I have an awk script that will displace the geometry along a selected normal mode. It's attached; I hope it helps! --- #9 From: "Stefan Fau" you can create a distorted geometry by manually adding the vector of the chosen vibrational mode to the coordinates as given in the Standard Orientation. You can also use a small program called xvibs (available in the CCL archive) for the same purpose. It will produce a set of geometries that are distorted in varying degrees (geoms for a "video"), but you can delete unwanted geometries. I think you may get 6 numbers per line. In that case you are interested in the first three numbers. Alternatively you can use "molden -A" and the z-matrix editor (Gaussian style). The "-A" prevents molden from reordering the atoms when creating the new z-matrix. You can then alter the most important variables manually. --- #10 From: "E. Lewars" Hello, concerning your inquiry about the 4th-order saddle point: I suppose you wish to relax it to a transition state (1st-order saddle) or to a minimum. I don't know of a program that will *automatically* decrease the symmetry and thus give an input geometry that when optimized will be a TS or a min. You may be able to break the symmetry by inspecting the Cartesians of your structure and then slightly altering a pair (or more than one pair) and reoptimizing. If you have a good graphical interface like Spartan has, you could alter bond lengths very simply in the builder, then reoptimize. If you used a Z-matrix you can break the symmetry by making previously equal parameters unequal. --- #11 From: jmmckel@ibm.net Perhaps take the optimized structure coordinates R for which you calculated the frequencies. One at a time add a small percentage of the FG eigenvectors for each of the four modes and reoptimize. Recently I read an article on the optimization of tetramethyl silane with high symmetry which was quite similar. Turns out that using the keyword "tight" eliminated the four imaginary frequencies and dropped the cymmetry to Cs with no imaginary frequencies. --- From chemistry-request@www.ccl.net Thu Mar 11 13:38:24 1999 Received: from ftpbox.mot.com (ftpbox.mot.com [129.188.136.101]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA03748 Thu, 11 Mar 1999 13:38:20 -0500 (EST) Received: [from pobox2.mot.com (pobox2.mot.com [129.188.137.195]) by ftpbox.mot.com (MOT-ftpbox 1.0) with ESMTP id MAA27687 for ; Thu, 11 Mar 1999 12:19:44 -0600 (CST)] Received: [from emailphx.sps.mot.com (emailphx.sps.mot.com [192.55.22.5]) by pobox2.mot.com (MOT-pobox2 1.0) with ESMTP id MAA24645 for ; Thu, 11 Mar 1999 12:18:17 -0600 (CST)] Received: from email.mot.com (zkorkin [223.189.20.185]) by act.sps.mot.com (8.8.6 (PHNE_14041)/8.8.6) with ESMTP id LAA02180 for ; Thu, 11 Mar 1999 11:19:39 -0700 (MST) Sender: korkin@act.sps.mot.com Message-ID: <36E819EB.1B3BEB08@email.mot.com> Date: Thu, 11 Mar 1999 12:30:51 -0700 From: Anatoli Korkin X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: CCL Subject: Avogadro's number Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, Last time I was visiting my dentist, he asked me how Avogadro could come with his number at that time. Shame to me I was not able to answer and I do not have a proper text book or a time to do this small history research. However, since this number links computational chemists to the "real world", I would appreciate if someone takes his time to send me a short story. I am sure someone has it in his lectures notes. It is probably interesting for other people, since we have many students on this list. Thank you in advance, Anatoli Korkin From chemistry-request@www.ccl.net Thu Mar 11 13:46:15 1999 Received: from neon.ch.pwr.wroc.pl (neon.ch.pwr.wroc.pl [156.17.2.212]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA04655 Thu, 11 Mar 1999 13:46:13 -0500 (EST) Received: from neon.ch.pwr.wroc.pl (localhost [127.0.0.1]) by neon.ch.pwr.wroc.pl (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id TAA27839 for ; Thu, 11 Mar 1999 19:32:43 +0100 (MET) Sender: jola@neon.ch.pwr.wroc.pl Message-ID: <36E80C4B.41C6@neon.ch.pwr.wroc.pl> Date: Thu, 11 Mar 1999 19:32:43 +0100 From: Jolanta Grembecka Organization: Wroclaw University of Technology X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Frozen atoms in G94 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I would like to fix some atoms to their starting positions during the optimization in G94. I know the possibitity how to do it in G98 - in input file after the atom name which shoul be frozen, you have to write value -1 and next give the cartesian cooridinates of the atom. However it does not work in G94. Does anybody know how to do it in G94 version? I known that I can froze some geometrical parametrs (torsion angles etc.) but I prefer rather fixing the atom position on its nuclei. Thank You very much for any suggestions. Jola Gremebcka Institute of Organic Chemistry Biochemistry and Biotechnology Wroclaw University of Technology From chemistry-request@www.ccl.net Thu Mar 11 13:47:11 1999 Received: from neon.ch.pwr.wroc.pl (neon.ch.pwr.wroc.pl [156.17.2.212]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA04752 Thu, 11 Mar 1999 13:47:05 -0500 (EST) Received: from neon.ch.pwr.wroc.pl (localhost [127.0.0.1]) by neon.ch.pwr.wroc.pl (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id TAA27932 for ; Thu, 11 Mar 1999 19:46:12 +0100 (MET) Sender: jola@neon.ch.pwr.wroc.pl Message-ID: <36E80F74.167E@neon.ch.pwr.wroc.pl> Date: Thu, 11 Mar 1999 19:46:12 +0100 From: Jolanta Grembecka Organization: Wroclaw University of Technology X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Torsional parameters for cff Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers I need to add torsional parameters for phosphoamidate bound to Cff97 force field because they are not included in this force field. Does enyone know what type of calculations I should perform to obtain appropriate parameters? I am also interested in findig of the literature in this subject. Thank You for help. Jola Grembecka Institute of Organic Chemistry Biochemistry and Biotechnology Wroclaw Univeristy of Technology From chemistry-request@www.ccl.net Thu Mar 11 15:50:23 1999 Received: from chrs1.chem.lsu.edu (chrs1.chem.lsu.edu [130.39.132.111]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id PAA08928 Thu, 11 Mar 1999 15:50:16 -0500 (EST) Received: from localhost by chrs1.chem.lsu.edu (AIX 4.1/UCB 5.64/4.03) id AA21230; Thu, 11 Mar 1999 14:49:48 -0600 Date: Thu, 11 Mar 1999 14:49:48 -0600 (CST) From: Chris Harwell To: Anatoli Korkin Cc: CCL Subject: Re: CCL:Avogadro's number In-Reply-To: <36E819EB.1B3BEB08@email.mot.com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 11 Mar 1999, Anatoli Korkin wrote: > Dear Colleagues, > > Last time I was visiting my dentist, he asked me how Avogadro > could come with his number at that time. i think he only came up with the idea of a mole and relatvie proportions. someone else actually came up with the number after boltzmann & maxwell came up with the necessary stat. mech. > number links computational chemists to the "real world", I > would appreciate if someone takes his time to send me a short > story. I am sure someone has it in his lectures notes. It for an excellent story. see asimov's chemistry. it has lots of short bio's and stories. charwel@chrs1.chem.lsu.edu From chemistry-request@www.ccl.net Thu Mar 11 17:00:29 1999 Received: from sp2n17.missouri.edu (sp2n17-t.missouri.edu [128.206.2.27]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA09346 Thu, 11 Mar 1999 17:00:28 -0500 (EST) Received: from [128.206.29.140] ([128.206.29.140]) by sp2n17.missouri.edu (8.9.0/8.9.0) with ESMTP id QAA593452; Thu, 11 Mar 1999 16:00:07 -0600 X-Sender: chemrh@pop.missouri.edu Message-Id: In-Reply-To: <36E819EB.1B3BEB08@email.mot.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 11 Mar 1999 16:01:37 -0600 To: Anatoli Korkin , From: "Robert E. Harris" Subject: Re: CCL:Avogadro's number Avogadro didn't come up with the number. He asserted that equal volumes of gases (under the same conditions) contqined equal numbers of molecules. The first really good estimates of the Avogadro constant came from the determination of the electron charge, which can be compared with Faraday's number (the charge on a mole of +1 ions) to give the Avogadro constant as the ratio. I think the modern value comes from the lattice spacing in high-ourity silicon compared with the density of the silicon. Robert E. Harris From chemistry-request@www.ccl.net Thu Mar 11 19:03:21 1999 Received: from salve5.salve.edu (salve5.salve.edu [198.49.179.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA10876 Thu, 11 Mar 1999 19:03:21 -0500 (EST) Received: from localhost (ascanio@localhost) by salve5.salve.edu (AIX4.3/UCB 8.8.8/8.7) with SMTP id SAA39696; Thu, 11 Mar 1999 18:53:50 -0500 Date: Thu, 11 Mar 1999 18:53:50 -0500 (EST) From: Ascanio DiPippo To: Anatoli Korkin cc: CCL Subject: Re: CCL:Avogadro's number In-Reply-To: <36E819EB.1B3BEB08@email.mot.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Avogadro was long dead and buried when a quantity was assigned to "equal volumes of gases contain equal numbers of particles' I recall that at one time there was thirteen(13) differewnt ways of determining 6.02...x 10ee23. The one I like best is from X-ray crystallagraphy KBr in a unit cubic or similar calculations. Students grasp this easily.