From chemistry-request@server.ccl.net Thu Mar 28 08:32:06 2002 Received: from relay2.uni-heidelberg.de ([129.206.210.211]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2SDW5p29792 for ; Thu, 28 Mar 2002 08:32:05 -0500 Received: from akcomba.oci.uni-heidelberg.de (akcomba.oci.uni-heidelberg.de [129.206.40.111]) by relay2.uni-heidelberg.de (8.12.1/8.12.1) with ESMTP id g2SDVtjf022454 for ; Thu, 28 Mar 2002 14:31:55 +0100 (MET) Received: by akcomba.oci.uni-heidelberg.de with Internet Mail Service (5.5.2650.21) id ; Thu, 28 Mar 2002 14:39:38 +0100 Message-ID: <31404621DE99D3119A16525400E1A5A80B06AE@akcomba.oci.uni-heidelberg.de> From: "Remenyi, Rainer" To: "'chemistry@ccl.net.'" Subject: CCL: Summary TD-DFT Date: Thu, 28 Mar 2002 14:39:34 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Hello, last week I posted the following question: Dear all, I have got a question about TD-DFT output in G98. What do the numbers below ?Spin exactly mean and how can one extract an assignment for the transitions from a TD-DFT calculation in G98. Output example from TD-DFT: CIS wavefunction symmetry could not be determined. Excited State 5: ?Spin -?Sym 2.2048 eV 562.34 nm f=0.0225 65B -> 75B 0.13525 68B -> 75B 0.22273 69B -> 75B -0.51298 70B -> 75B 0.17038 71B -> 75B 0.53289 72B -> 75B -0.41843 73B -> 75B -0.23022 74B -> 75B 0.23340 Here is the summary of the answers, and thanks to the poeple who replied: Hello Rainer, ?Spin and ?sym should be the spin and symmetry of the 5th excited state (in your example). The fact that there are "?" mean that G98 couldn't determine both ot them. The spin is not difficult to determine from your calculation. The reason why you have ?sym, I guess, is because G98 was not able to determine the symmetry of all the orbitals: you should have somewhere in your output file a list of orbitals with their symmetry. Some of them should be of the form ?A or ?B... Now to determine the symmetry of your state you need the symmetries of the 65B and 75B orbitals. The symmetry of the excited state is simple the inner product |65> X |75>. Check the table of multiplication of the symmetry your are working with... Sometimes its much more difficult to determine the symmetry of the excited state: if you have a transition between degenerated orbitals for example... But obviously its not your case. the numbers (e.g. 0.13525) is just the coefficient of the corresponding slater determinant into the total wave function of the excited state. Basically, it's roughly equivalent to a CI decomposition. Hope this help, Pascal Dr. Pascal Boulet Queen Mary, University of London Centre for Computational Science Department of Chemistry Mile End Road London, E1 4NS UK Phone: (+44) (0)20 7882 7759 fax: (+44) (0)20 7882 7794 Hi Rainer, Sorry about the late reply but your e-mail bounced. Dear Rainer: Output for a TD-DFT calculation for a closed shell species generally contains spin multiplicity and state symmetries, e.g. - Excited State 1: Singlet-A2 3.7169 eV 333.57 nm f=0.0000 20 -> 21 0.66862 .. But for a calculation on an open shell species, G98 uses the unrestricted-DFT procedure ("different [Kohn-Sham] MOs for alpha and beta spin") which means that the computed states are more or less spin-contaminated. In this case, G98 does not print a spin multiplicity, e.g. - Excited State 1: ?Spin -A2 1.0282 eV 1205.70 nm f=0.0000 24B -> 25B 1.03710 24B -> 27B -0.16586 .. Hence, ?Spin indicates than the spin multiplicity is not well defined and is not available. The numbers below ?Spin are the CI coefficients of the excited configurations listed to the left: 24B -> 25B, and so on (meaning, e.g.: the configuration derived by promoting an electron from beta spin-MO no. 24 to beta spin-MO no. 25). A large coefficient means that the configuration in question has a large weight in the state wave function. You may notice that in the example I give above, one of the coefficients exceeds unity, indicating that for TD calculations on open shell systems G98 does not normalize the states in the usual sense. - In my opinion, it would have been VERY HELPFUL if Gaussian would compute and print spin data for excited states, just as for the ground state where the expectation value of S**2 is given. In the example you quote in your query, not even the wave function symmetry is printed, evidently because of a failure; if you look up the MO symmetries given in the printout, you will probably find that Gaussian failed to deduce symmetry labels for some of the MOs. I am not quite sure of what you mean when you say "how can one extract an assignment for the transitions from a TD-DFT calculation in G98". To me, an 'assignment' means an assignment of experimentally observed transitions to theoretically predicted ones, and such an assignment can of course not be extracted from the G98 output. Do you mean: How can the calculated transitions be explained in terms of orbital contributions? If this is your question, you must look up the orbitals involved in the leading configurations listed in the output (the keyword POP=REGULAR gives you the five highest occupied and the five lowest unoccupied MOs; consult the manual). Good Luck! Yours, Jens >--< P.S. Please say hello to dear old Heidelberg! I spent the years 1979-1984 in Heidelberg as a member of Professor Gleiter's group. 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 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= There was a discussion of ?Spin in the TD-DFT output about 5 months ago on CCL - maybe you'll find your answer in the summary of that discussion. In short, I believe that the conclusion is that ?Spin is related to the weight of a particular excitation in a given state. In order to assign the excitations I always look at the output orbitals (e.g., using Molden) and assign the state according to the excitation with the highest nominal ?Spin value. If you get any better suggestions please let me know because manually visualizing the orbitals is quite time consuming. Cheers, Theis Solling Dr. Theis I. Solling California Institute of Technology M/C 127-72 1200 E. California Blvd. Pasadena, California 91125 Ph. (626)-395-6741 Dr. Remenyi, This happens most commonly when the SCF orbitals cannot be labeled properly. Look back after the end of the SCF and see if any of the orbitals, 65,68-74 and then 75 are labeled. Even if not all of them are labeled the first group must be the same any one will do. Then if the reference is a singlet then the product will be the symmetry. Otherwise you need to look at the full orbital set. Since this is a beta-beta excitation the spin state should be the same as the ground state. Rainer Remenyi Anorganisch-Chemisches Institut Im Neuenheimer Feld 270 69120 Heidelberg Germany phone ++ 49 6221 54 8653 fax ++ 49 6221 54 6617 e-mail: remenyi@akcomba.oci.uni-heidelberg.de From chemistry-request@server.ccl.net Thu Mar 28 03:27:42 2002 Received: from amiga.chemie.uni-konstanz.de ([134.34.112.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2S8Rfp26872 for ; Thu, 28 Mar 2002 03:27:42 -0500 Received: (from jochen@localhost) by amiga.chemie.uni-konstanz.de (8.11.6/8.8.7) id g2S8GhT16798; Thu, 28 Mar 2002 09:16:43 +0100 From: Jochen Buehler Message-ID: <15522.53610.904000.938134@amiga.chemie.uni-konstanz.de> Date: Thu, 28 Mar 2002 09:16:42 +0100 To: "Dr. Daniel Glossman-Mitnik" Cc: "Computational Chemistry List" Subject: CCL:gaussian 98 compilation on sgi In-Reply-To: <008201c1d601$4a0a87c0$2601010a@cimav.edu.mx> References: <008201c1d601$4a0a87c0$2601010a@cimav.edu.mx> X-Mailer: VM 6.96 under 21.1 (patch 14) "Cuyahoga Valley" XEmacs Lucid Dr. Daniel Glossman-Mitnik writes: > Dear netters: > > I have trying to compile Gausssian 98 Rev. A11.2 on a Silicon > Graphics O2 (R12000 - 400 MHz) with no luck. I have tried the > sgi.make makefile that came with the software, and I have also > tried the modified version that´s published in the WebMO.net > web page. The compilers came with the machine are f77 version > 7.0 and C version 7.0. I've compiled A.9 on several SGIs running IRIX 6.5.x using the MIPSPro 7.3.x compilers (as stated on http://www.gaussian.com/g98_req.htm). Maybe the 7.0.x compilers are too old and no longer supported? Never needed to do more on IRIX machines than starting the g98 build with the bldg98 script... Regards, Jochen -- Jochen Buehler, Dipl.-Chem EMail: jochen@amiga.chemie.uni-konstanz.de AG Prof. Dr. Daltrozzo buehler@chemie.uni-konstanz.de Fachbereich Chemie Phone: +49-7531-882095 Universitaet Konstanz Fax: +49-7531-88792095 78457 Konstanz, Germany From chemistry-request@server.ccl.net Thu Mar 28 05:47:59 2002 Received: from jeeves.ccdc.cam.ac.uk ([131.111.113.44]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2SAlwp28461 for ; Thu, 28 Mar 2002 05:47:58 -0500 Received: from odin.ccdc.cam.ac.uk ([131.111.113.134] helo=ccdc.cam.ac.uk) by jeeves.ccdc.cam.ac.uk with esmtp (Exim 3.12 #1 (Debian)) id 16qXRh-0005zt-00 for ; Thu, 28 Mar 2002 10:47:53 +0000 Sender: cole@ccl.net Message-ID: <3CA2F4D8.FF8D0AE2@ccdc.cam.ac.uk> Date: Thu, 28 Mar 2002 10:47:52 +0000 From: Jason Cole Organization: CCDC X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX 6.5 IP32) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: GOLD ouput files filtering References: <3CA2EC21.40F0F7B9@ccdc.cam.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Yogesh, Glad to hear that you like the program. Unfortunatly, there is no easy way from within gold to minimise the overall output that it produces. What you see is what you get. Most of our users write wrapper scripts to achieve this, that read the files as they are produced and delete those that they dont want. This has the advantage of allowing flexibility in selection - a user is able to select docked solutions on the basis of properties unrelated to golds own scoring function, which can be specific to a particular system. Your question is, however, probably one of the more common development requests that we get for gold. It poses one difficult issue; what to throw away? Different users have different requirements - some would like to save all information for the best N dockings, some would like to only save the top ranked solution for all dockings. Others would just like to save everything but in a compressed format rather than the current rather verbose format that gold uses - this is necessary for re-ranking for example. I'd value any feedback on this issue, form any user of Gold who has this problem - what would users prefer? Also, what do users extract from the various log files in GOLD, that could be condensed down into a more compact format? Would a set of 'stub' example scripts written in python or perl be useful? Jason CCDC From chemistry-request@server.ccl.net Thu Mar 28 10:16:43 2002 Received: from mailimailo.univ-rennes1.fr ([129.20.131.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2SFGhp31405 for ; Thu, 28 Mar 2002 10:16:43 -0500 Received: from nom-wqalwr69vp7 (pc-theo11.spm.univ-rennes1.fr [129.20.75.136]) by mailimailo.univ-rennes1.fr (8.9.3/jtpda-5.3.3) with ESMTP id QAA19287 for ; Thu, 28 Mar 2002 16:15:53 +0100 (MET) Message-Id: <4.2.0.58.20020328155715.00b7b120@mailhost.univ-rennes1.fr> X-Sender: bleguenn@mailhost.univ-rennes1.fr X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.0.58 Date: Thu, 28 Mar 2002 16:16:22 +0100 To: CHEMISTRY@ccl.net From: Boris Le Guennic Subject: Extended Huckel parameters Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL'ers Extended Huckel parameters I found in different programs (Cacao, Yaehmop...) for the boron atom are the following: 2s -15.2 1.3 2p -8.2 1.3 Has anyone got a better set of parameters for this atom? Thanks in advance Boris Le Guennic From chemistry-request@server.ccl.net Thu Mar 28 16:34:34 2002 Received: from cardinal3.Stanford.EDU ([171.64.15.251]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2SLYYp05113 for ; Thu, 28 Mar 2002 16:34:34 -0500 Received: (from liviu@localhost) by cardinal3.Stanford.EDU (8.11.6/8.11.6) id g2SLYLh07126; Thu, 28 Mar 2002 13:34:21 -0800 Date: Thu, 28 Mar 2002 13:34:21 -0800 (PST) From: Liviu Mihail Mirica To: Subject: TD-DFT Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, i also have a question on TD-DFT calculations using Gausssian. i tried to do a calculation with the following input, it worked for one molecule, but not for the rest of them (all are broken symmetry calculations). # gfinput iop(6/7=3) # TD(Nstates=10) UB3LYP/6-311G* SCFcyc=1000 # scf=(tight,vshift=500,NOVARACC,NOINCFOCK) # int=finegrid pop=full guess=read geom=check it gives me this error message: **** Fatal Problem: The smallest alpha delta epsilon is -0.48647432D-01 **** Fatal Problem: The smallest beta delta epsilon is -0.48637465D-01 Does anyone have any idea how i can solve this problem? Thanks, Liviu Mirica ************************** Liviu Mihail Mirica tel: 650-497-3188 Escondido Village, 35 B email: liviu@leland.stanford.edu Stanford, CA 94305, USA From chemistry-request@server.ccl.net Thu Mar 28 17:10:42 2002 Received: from web20503.mail.yahoo.com ([216.136.226.138]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g2SMAfp05775 for ; Thu, 28 Mar 2002 17:10:42 -0500 Message-ID: <20020328221032.34127.qmail@web20503.mail.yahoo.com> Received: from [40.0.40.7] by web20503.mail.yahoo.com via HTTP; Thu, 28 Mar 2002 14:10:32 PST Date: Thu, 28 Mar 2002 14:10:32 -0800 (PST) From: Kaiming Wang Subject: Any good paper on Grid-based interactions? To: chemistry@ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1240982236-1017353432=:31681" --0-1240982236-1017353432=:31681 Content-Type: text/plain; charset=us-ascii Hello, I wonder if you can tell me some good articles on the methods of grid-based potential calculations. The more detail and more updated, the better. Thanks a lot. Kaiming --------------------------------- Do You Yahoo!? Yahoo! Movies - coverage of the 74th Academy Awards® --0-1240982236-1017353432=:31681 Content-Type: text/html; charset=us-ascii

Hello,

I wonder if you can tell me some good articles on the methods of

grid-based potential calculations. The more detail and more updated, the better.

Thanks a lot.

Kaiming

 


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