From chemistry-request@server.ccl.net Fri Mar 24 01:04:00 2000 Received: from biol2.bio.nagoya-u.ac.jp ([133.6.127.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA02461 for ; Fri, 24 Mar 2000 01:03:59 -0500 Received: from [133.6.127.65] (jupiter [133.6.127.65]) by biol2.bio.nagoya-u.ac.jp (8.9.2/8.9.2) with SMTP id NAA23701; Fri, 24 Mar 2000 13:57:09 +0900 (JST) Date: Fri, 24 Mar 2000 13:57:09 +0900 (JST) Message-Id: <200003240457.NAA23701@biol2.bio.nagoya-u.ac.jp> To: "Yanni Wang" From: shinoda@biol2.bio.nagoya-u.ac.jp (Kazuki Shinoda) Subject: Re: Re: CCL:Program to convert CHARMM force field file to AMBER format Cc: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Yanni, I am sorry for lating to summarize. Unforturnately, however, I have got no replies from anyone about my question yet. So I cannot inform you of any information. Sorry, again. Best regards, Kazuki > >Dear Kazuki, > > You have ever submitted the following question on CCL. Would you like to >summarize the answers you got? > > Best regards! > > >On Jan 25, 8:57pm, Kazuki Shinoda wrote: > > Subject: CCL:Program to convert CHARMM force field file to AMBER format > > Dear CCLers, > > > > Does anyone have a program to convert CHARMM format > > force field file to AMBER format ? > > > > Best regard, > > > > Kazuki > > ================================================ Kazuki Shinoda, MC2 Division of Biological Science, Graduate school of Science Nagoya University, Chikusa, Nagoya 464-8602, Japan E-mail : shinoda@biol2.bio.nagoya-u.ac.jp URL: http://bio.nagoya-u.ac.jp:8001/~kazuki/kazuki.html ================================================ From chemistry-request@server.ccl.net Fri Mar 24 04:43:01 2000 Received: from uvaix7e1.comp.UVic.CA (root@uvaix7e1.comp.UVic.CA [142.104.5.107]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA03454 for ; Fri, 24 Mar 2000 04:43:00 -0500 Received: from p17-62.dialup.UVic.CA (p17-62.dialup.UVic.CA [142.104.17.62]) by uvaix7e1.comp.UVic.CA (8.9.3/8.9.3) with SMTP id AAA179604 for ; Fri, 24 Mar 2000 00:38:35 -0800 From: Roy Jensen To: CHEMISTRY@ccl.net Subject: SUMMARY: Dipole Moment from PES scan Date: Fri, 24 Mar 2000 00:38:40 -0800 Message-ID: <00amdsg1uke0d2giaq9esggmu0qk3ul407@4ax.com> X-Mailer: Forte Agent 1.7/32.534 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id EAA03455 My original question was: > Is there a way of getting Gaussian 94 to output the multipole moments > at each step of a relaxed or rigid PES scan? > Gaussian 98 is available but I have not used it. I received two responses. The response from Doug Fox at Gaussian proved to be definitive. Contrary to his hints at the difficulty, it wasn't that bad to implement! It would be nice if Gaussian, Inc. would leave up the online manual for the previous versions of Gaussian...it was hard to find the IOPs for Gaussian 94; they do not appear to be the same as in Gaussian 98. Roy Jensen ****************************************************************************** gaussian.com!fox@gaussian.com (Doug Fox) wrote: Dr. Jensen, There is no trivial way to request this. The structure of G94 and G98 computes the energy and checks if it is "optimized" and then loops back to update the structure. The population analysis is a separate program and it is not trivial to have it jump into the population analysis only at optimized points. It is on the list of requested features but it is not present even in G98. For a rigid scan you can make a nonstandard route which does the population analysis at every point. The basis non-standard route is, 1/38=1/1,8; 2/17=6,18=5/2; 3/11=9,25=1,30=1/1,2,3; 4//1; 5/5=2,38=4/2; 6/7=2,8=2,9=2,10=2,18=1,28=1/1; 1//8(1); 99/9=1/99; 2//2; 3/11=9,25=1,30=1/1,2,3; 4/5=5,16=2/1; 5/5=2,38=4/2; 1//8(-4); 99/9=1/99; and if you modify the final three lines as follows 5/5=2,38=4/2; 6/7=2,8=2,9=2,10=2,18=1,28=1/1; 1//8(-5); 99/9=1/99; you will get population analysis and multipole moments at each step. Best to start with the output from testrt for the case you want to get the basis set and other options set correctly. Then run a job like # NonStd 1/38=1/1,8; 2/17=6,18=5/2; 3/11=9,25=1,30=1/1,2,3; 4//1; 5/5=2,38=4/2; 6/7=2,8=2,9=2,10=2,18=1,28=1/1; 1//8(1); 99/9=1/99; 2//2; 3/11=9,25=1,30=1/1,2,3; 4/5=5,16=2/1; 5/5=2,38=4/2; 6/7=2,8=2,9=2,10=2,18=1,28=1/1; 1//8(-5); Your title and structure input follow. Check the G94 Programmer's Reference for details on the print options for l601 to tailor the output to get fewer features you don't want. ****************************************************************************** straka@chem.helsinki.fi (Michal Straka) wrote: Hi, I had the same problem I used Pop=Full but it gives an huge out file. I needed just one so I didn't bother, From chemistry-request@server.ccl.net Fri Mar 24 05:16:11 2000 Received: from sunu450.rz.ruhr-uni-bochum.de (sunu450.rz.ruhr-uni-bochum.de [134.147.64.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA03736 for ; Fri, 24 Mar 2000 05:16:10 -0500 Received: (qmail 29788 invoked from network); 24 Mar 2000 09:11:49 -0000 Received: from cvw.orch.ruhr-uni-bochum.de (HELO ?134.147.110.57?) (134.147.110.57) by mailhost.rz.ruhr-uni-bochum.de with SMTP; 24 Mar 2000 09:11:49 -0000 Mime-Version: 1.0 X-Sender: wuellcbd@mailhost.rz.ruhr-uni-bochum.de Message-Id: In-Reply-To: <862568AB.00469176.00@unomail.unomaha.edu> References: <862568AB.00469176.00@unomail.unomaha.edu> Date: Fri, 24 Mar 2000 10:11:39 +0100 To: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:Cluster information and Linux Alpha Cc: Chemistry@CCL.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" As to the possiblity to combine Alpha/Intel Clusters, note this statement coming from the vendors of LINDA: "However, Gaussian does not currently allow heterogenous execution. When the folks at Gaussian quoted "Linda for a heterogenous network" they are talking about a Linda distribution that runs independent problems on different networks." -- ---------------------------+------------------------------------------------ Christoph van Wullen | Fon (University): +49 234 32 26485 Theoretical Chemistry | Fax (University): +49 234 32 14109 Ruhr-Universitaet | Fon/Fax (private): +49 234 33 22 75 D-44780 Bochum, Germany | eMail: Christoph.van.Wuellen@Ruhr-Uni-Bochum.de ---------------------------+------------------------------------------------ From chemistry-request@server.ccl.net Thu Mar 23 18:32:06 2000 Received: from Mercury.acs.unt.edu (mercury.acs.unt.edu [129.120.220.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA00862 for ; Thu, 23 Mar 2000 18:32:05 -0500 Received: from jove.acs.unt.edu (10759@jove.acs.unt.edu [129.120.220.41]) by Mercury.acs.unt.edu (8.8.8/8.8.8) with ESMTP id QAA21403; Thu, 23 Mar 2000 16:27:48 -0600 (CST) Received: from localhost (tdp0006@localhost) by jove.acs.unt.edu (8.8.8/8.8.8) with ESMTP id QAA17424; Thu, 23 Mar 2000 16:25:41 -0600 (CST) Date: Thu, 23 Mar 2000 16:25:40 -0600 (CST) From: TREVOR D POWER To: Dave Price cc: Comp Chem Mailing List Subject: Re: CCL:MM vdW potential function derivation In-Reply-To: <38D8EBD8.6381D052@reading.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII You will want to take a look at: Norrby, P.-O.; Liljefors, T. J. Comp. Chem. (1998) 19,10 1146-1166 There is quite a lot in there about force field development. Cheers, Dr. David Power Department of Chemistry University of North Texas NT Station, Box 305070 Denton, TX 76203-5070 USA tdp0006@unt.edu On Wed, 22 Mar 2000, Dave Price wrote: > Dear CCLers, > I am trying to parameterise a system for use in molecular > mechanics/molecular dynamics/monte carlo calculations. I have seen > little in the literature about this (eg electron gas method, > HF/DFT calcs for torsional angles), has anyone published a comprehensive > review or have any very useful programs for this sort of thing? > I will summarise any answers I get if there is an interest. > (Please don't tell me to use the universal force-field). > Cheers, > Dave > > -- > ------------------------------------------------------------------------ > > Dr. David W. Price, Tel: +44 (0)118 9875123 extn 7415 > Department of Chemistry, Fax: +44 (0)118 9316331 > University of Reading, mailto:d.w.price@reading.ac.uk > Whiteknights, > READING http://www.chem.rdg.ac.uk/g50/mmrg/dave/dave.html > RG6 6AD > U.K. > > ------------------------------------------------------------------------ > > > -= 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 Fri Mar 24 05:49:46 2000 Received: from fsuj20.rz.uni-jena.de (fsuj20.rz.uni-jena.de [141.35.1.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA03920 for ; Fri, 24 Mar 2000 05:49:45 -0500 Received: from pc04.chemie.uni-jena.de (pc04.chemie.uni-jena.de [141.35.29.60]) by fsuj20.rz.uni-jena.de (8.9.1a/8.9.1) with ESMTP id KAA20394 for ; Fri, 24 Mar 2000 10:45:21 +0100 (MET) Received: from pc04.chemie.uni-jena.de by pc04.chemie.uni-jena.de (8.8.8/1.1.22.3/02Dec99-0338PM) id KAA0000015794; Fri, 24 Mar 2000 10:45:21 +0100 (MET) Sender: goeller@pc04.chemie.uni-jena.de Message-ID: <38DB3930.10AA9EE2@pc04.chemie.uni-jena.de> Date: Fri, 24 Mar 2000 10:45:20 +0100 From: Andreas Goeller X-Mailer: Mozilla 4.5 [en] (X11; I; OSF1 V4.0 alpha) X-Accept-Language: German, de, en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Summary: UV/vis visualisation Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all, here's the summary of my question about simulating UV/vis spectra: ________________________________________________________________________ *The original question: *from semiempirical calculations I get transition energies (say, in *wavenumbers, lam) and oscillator strengths (osc), i.e. a line spectrum. *The osc are proportional to the surface below one extinction curve. I *can model this curve approximately by using a Gauss curve f(x), and by *summation over all curves (g(x)) I get something comparable to an *experimental spectrum. The function is * *g(x)= sum_i(osc_i*(fx_i)) *f(x)= 1/(sigma*sqrt(2*pi))*exp(-0.5*((x-x0)/sigma)**2) * *Can anybody give me a hint about reasonable choices for sigma, the *standard deviation? The smaller sigma, the steeper the curve. * _________________________________________________________________________ >>>>>>>>>>>>>>>>>>>>>> There seems to be no quantitative relationship one can use. There are empirical factors that work. >>>>>>>>>>>>>>>>>>>>>> _________________________________________________________________________ From:"Paul N. Day MLPJ CON" It seems like with the normalization coefficient you have put on f(x), you will always get f(x)=1. I think you want to model the absorption spectrum with a gaussian such as epsilon=epsilon(max)*exp(-0.5*((x-x0)/sigma)**2) where epsilon(max) is the extinction coeficient at the line maximum with frequency x0. Then when you integrate this over x and multiply by the appropriate constant (4.33e-9 in customary units), you will get the oscillator strength. sigma is related to the linewidth at half-max, gamma, by sigma = 0.5*gamma/sqrt(2*ln2) It seems like the usual practice is to choose an arbitrary value for the line-width based on experiment. In a paper by Albota, et al (Science 281, 1653(1998)), for the calculations they use 0.1 eV for the linewidth. The linewidth is related to the decay rate of the state and is affected by temperature, solvent, etc. I do not know of a rigorous theoretical method for getting the linewidth, but I would be interested in hearing about any that you hear about. Thanks, Paul _________________________________________________________________________ From: Demetrio Antonio da Silva Filho - doutorado I do the same as you to fit the UV-Vis peaks that we get from QC calculations ( I have a fortran CODE do to that and I can send the code to you if you want). The value of sigma depends on the resolution of the article that you have to compare your results. I have an article which the experimental resolution was 10nm. So I use the same! Hope it helps! Demetrio Filho _________________________________________________________________________ From: Sérgio Emanuel Galembeck Some years ago I simulate some spectra of organic substances using a Gaussian, and I considered sigma an empirical parameter that are ajusted in order to reproduce experimental spectra. There some softwares that calculate a Gaussian using absorption and oscillator stenghts, as synspec. _________________________________________________________________________ From: Scott McMillan I've looked into this issue. I also use Gaussians for each individual excitation. In my case, I looked at the half-width of Gaussians fit to the experimental spectrum and used something similar to that. I found that a half-width between 500 and 1000 cm-1 works well. If you have experimental spectra, you could also trying fitting the half-widths although you could have a lot of fitting parameters. I don't know of a way to determine the width of the Gaussians a priori. Please send me a summary of the responses to your question. Thanks. _________________________________________________________________________ From: Stefan Grimme to my expierience, the band width at 1/e height is about 0.3-0.5 eV for larger molecules if measured in solution. >>>>>>>>>>>>>>>>>>>>>>> I mailed back to Demetrio: >it would be nice if I could have your source for reasons of comparison. >What exactly do you mean with sigma=10nm. The std. dev. or the line >width? and got the answer: ______________________________________________________________________________ 10nm is my dd, and it's your (sigma)^2 To run the the code, after compilation, you should have an archive called fort.1 with the energy in one column and the dipole oscilator strenght in the other. The archive fort.2, that will be created after running the program, will contains the spectrum with gaussians. Hope it helps! Demetrio FIlho f(x)= 1/(sigma*sqrt(2*pi))*exp(-0.5*((x-x0)/sigma)**2) Here is the code! implicit real*8(a-h,o-z) dimension energy(600),weight(600) c energy(i) e' a energia da transicao em eV ou comprimento de onda c em nanometros c weight(i) e' a forca de oscilador c dd e' a largura da gaussiana em eV ou nanometros c nn the number of transitions to be read read(1,*)nn,dd READ(1,*)( energy(I),weight(i),i=1,NN) eini=energy(1)-100.d0 emax=energy(nn)+100.d0 de=1.d0 e=eini pi=3.1415927d0 den=dsqrt(2.d0*pi)*dd dd=dd*dd npoint=(emax-eini)/de do i=1,npoint f=0.d0 do j=1,nn w=weight(j) ene=energy(j) if(dabs(e-ene).le.500.d0) f=f+w*exp(-0.5*(e-ene)**2/dd) enddo f=f/den write(2,*)e,f e=e+de enddo stop end -- Andreas Goeller --------------------------------------------------------------- Dr. Andreas Goeller Institut fuer Physikalische Chemie Friedrich-Schiller-Universitaet Lessingstr. 10 phone: +49(0)-3641-948352 D-07743 Jena fax: +49(0)-3641-948302 (secretary) Germany email: goeller@pc04.chemie.uni-jena.de http://www.uni-jena.de/chemie/photo/goeller/goeller.html --------------------------------------------------------------- Dr. Andreas Goeller ehemals Computer Chemie Centrum email: goeller@organik.uni-erlangen.de http://www.organik.uni-erlangen.de/clark/goeller/goeller.html --------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Mar 24 11:28:12 2000 Received: from tca7.dl.ac.uk (tca7.dl.ac.uk [193.62.112.105]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA06317 for ; Fri, 24 Mar 2000 11:28:11 -0500 Received: from localhost by tca7.dl.ac.uk; (5.65v4.0/1.1.8.2/06Oct95-0132PM) id AA00990; Fri, 24 Mar 2000 15:10:58 GMT Sender: hgs@dl.ac.uk Message-Id: <38DB8581.207618C9@dl.ac.uk> Date: Fri, 24 Mar 2000 15:10:58 +0000 From: Georg Schreckenbach Reply-To: h.g.schreckenbach@dl.ac.uk Organization: CLRC Daresbury Laboratory X-Mailer: Mozilla 4.05 [en] (X11; I; OSF1 V4.0 alpha) Mime-Version: 1.0 To: Computational Chemistry List Subject: frequency calculations for metal complexes Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, having been off-line for a while, I just came across an old (mid Feb. or so) summary in the CCL archives. I thought that I should add a little comment. The old summary is about the use of ECP basis sets for metal complexes. In this summary, somebody claims that one cannot calculate frequencies for metal complexes if an ECP basis set is used. This is definitely not correct anymore since, e.g., Gaussian98 has analytical second derivatives for ECPs. Thus, frequency calculations are, indeed, possible in these cases! (and I have done a lot of them lately ...) Best regards, Georg From chemistry-request@server.ccl.net Fri Mar 24 11:28:57 2000 Received: from tca7.dl.ac.uk (tca7.dl.ac.uk [193.62.112.105]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA06329 for ; Fri, 24 Mar 2000 11:28:53 -0500 Received: from localhost by tca7.dl.ac.uk; (5.65v4.0/1.1.8.2/06Oct95-0132PM) id AA00994; Fri, 24 Mar 2000 15:11:45 GMT Sender: hgs@dl.ac.uk Message-Id: <38DB85B0.25A42697@dl.ac.uk> Date: Fri, 24 Mar 2000 15:11:45 +0000 From: Georg Schreckenbach Reply-To: h.g.schreckenbach@dl.ac.uk Organization: CLRC Daresbury Laboratory X-Mailer: Mozilla 4.05 [en] (X11; I; OSF1 V4.0 alpha) Mime-Version: 1.0 To: Computational Chemistry List Subject: all-electron Gaussian basis for actinides Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear everybody, does anyone know of ALL-ELECTRON Gaussian basis sets for actinide elements, published or unpublished? I'd be particularly interested in the early actinides, Th thru' Am, say. I have already searched the CCL archives and the EMSL basis set repository but with no success. I know, of course, that one would normally use ECPs or related methods for these heavy elements. (... and there are a couple of ECP basis sets in the EMSL library ...) I also know that the ADF program provides all-electron SLATER basis sets for these elements. Would it, perhaps, be possible to use the basis sets that were developed for four-component relativistic methods? If so, would they have to be modified? (I suppose so ... e.g. take the large component only?) Where are they to be found? I'll summarize as usual. Thank you, and best regards, Georg From chemistry-request@server.ccl.net Fri Mar 24 12:12:01 2000 Received: from yeager5.chem.tamu.edu (yeager5.chem.tamu.edu [165.91.176.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA06620 for ; Fri, 24 Mar 2000 12:12:01 -0500 Received: (from noj@localhost) by yeager5.chem.tamu.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) id RAA28678; Fri, 24 Mar 2000 17:07:45 +0100 ("MET) Date: Fri, 24 Mar 2000 17:07:45 +0100 ("MET) Message-Id: <200003241607.RAA28678@yeager5.chem.tamu.edu> From: noj malcolm To: h.g.schreckenbach@dl.ac.uk CC: chemistry@ccl.net In-reply-to: <38DB85B0.25A42697@dl.ac.uk> (message from Georg Schreckenbach on Fri, 24 Mar 2000 15:11:45 +0000) Subject: Re: CCL:all-electron Gaussian basis for actinides Reply-To: noj@yeager5.chem.tamu.edu X-Beard: Beard v5.3 X-Child: Bethany Georg, you will find some references in a recent paper by Tilson, Shepard, Naleway, Wagner and Ermler (JCP 112#5 (2000) p2292) the basis sets employed seem to be private communications unfortunately, but you may get soemwhere by getting in touch with the authors. noj -- -------------------------------------------------------------------------- Dr. N.O.J. Malcolm e-mail:noj@yeager5.chem.tamu.edu Department of Chemistry Texas A&M University College Station TX 77845 U.S.A -------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Mar 24 14:10:08 2000 Received: from NPD1.NPD.UFPE.BR (npd1.npd.ufpe.br [150.161.6.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA07338 for ; Fri, 24 Mar 2000 14:09:56 -0500 Received: from mail.npd.ufpe.br ([150.161.40.38]) by npd.ufpe.br (PMDF V5.1-4 #20469) with ESMTP id <01JNF0O8KOZK000EWI@npd.ufpe.br> for chemistry@ccl.net; Fri, 24 Mar 2000 16:01:51 GMT-3 Date: Fri, 24 Mar 2000 16:12:32 -0300 From: Patricia Farias Subject: SOCC/trans.dipole moments (Br2) Sender: pati@[150.161.40.38] To: chemistry@ccl.net Message-id: <38DBBE20.45609034@mail.npd.ufpe.br> Organization: UFPE MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.5-23cl i686) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Dear CCL members, My research field involves Potodissociation Dynamics (theoretical work) and I would be very grateful if someone could provide me the following experimental data concerning Br2 (molecular bromine): -transition dipole moments -spin orbit coupling constants Thanks for any help Patricia Farias DQF-UFPE Recife-Brasil