From owner-chemistry@ccl.net Fri Nov 26 03:23:01 2010 From: "Shirin Seifert shirin.seifert:gmail.com" To: CCL Subject: CCL: SHQ: First Excited State Message-Id: <-43229-101126032058-21758-hIpLNh51mGC+FRYbN9Gk/g*server.ccl.net> X-Original-From: Shirin Seifert Content-Type: multipart/alternative; boundary=0016e6dd961a82667d0495f0662a Date: Fri, 26 Nov 2010 11:50:51 +0330 MIME-Version: 1.0 Sent to CCL by: Shirin Seifert [shirin.seifert|a|gmail.com] --0016e6dd961a82667d0495f0662a Content-Type: text/plain; charset=ISO-8859-1 Dear CCLs I would like to compute the ET matrix element (gamma) for 1,6 heptadiene? Could you recommend some methods? Is there any value from experimental or theoretical studies in the literature? Thank you beforehand. Regards, S.S --0016e6dd961a82667d0495f0662a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCLs

I would like=A0 to compute the ET matrix element (gamma) f= or 1,6 heptadiene? Could you recommend some methods?
Is there any value = > from experimental or theoretical studies in the literature?

Thank yo= u beforehand.
Regards,
S.S
--0016e6dd961a82667d0495f0662a-- From owner-chemistry@ccl.net Fri Nov 26 04:14:00 2010 From: "MASLYK, MACIEJ MARCIN maciejmarcin.maslyk__ceu.es" To: CCL Subject: CCL:G: ODP: CCL:G: ODP: CCL:G: Gaussian output problem Message-Id: <-43230-101126035906-21118-zx+w+ZUe5URv62Rqd1oWAg+*+server.ccl.net> X-Original-From: "MASLYK, MACIEJ MARCIN" Content-Language: pl-PL Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Fri, 26 Nov 2010 10:03:15 +0100 MIME-Version: 1.0 Sent to CCL by: "MASLYK, MACIEJ MARCIN" [maciejmarcin.maslyk]_[ceu.es] Thanks Olli, the script is working. The thing is that in my input I have 200 sections with coordinates and this script changes stars for appropriate numbers in section 1 but in the second it doesn't change again from 10000 but continues from section 1. And so on. Do you know how to modify this script? Example: 9998 1 20001030 2.813824 -19.307495 32.184450 9999 1 20001030 1.933916 -20.325103 31.491169 **** 8 20001021 37.587292 -11.572024 28.812192 **** 1 20001030 37.333847 -11.927328 27.960694 **** 1 20001030 38.095189 -12.272395 29.221488 ble ble ble 9998 1 20001030 2.813824 -19.307495 32.184450 9999 1 20001030 1.933916 -20.325103 31.491166 **** 8 20001021 37.587292 -11.572024 28.812192 **** 1 20001030 37.333847 -11.927328 27.960694 **** 1 20001030 38.095189 -12.272395 29.221488 ble cble ble 9998 1 20001030 2.813824 -19.307495 32.184450 9999 1 20001030 1.933916 -20.325103 31.491166 **** 8 20001021 37.587292 -11.572024 28.812192 **** 1 20001030 37.333847 -11.927328 27.960694 **** 1 20001030 38.095189 -12.272395 29.221488 ....... more then 200 times So in every section of the file I want to have numbers from 10000 to ...... thanks regards Maciek Dr. Maciej Maslyk Universidad San Pablo CEU Urb. Montepríncipe, Ctra. Boadilla del Monte, Km. 5.300, 28668 Madrid, España Tel.- 91.372.64.31 - FAX.- 91.351.04.75 ________________________________________ Od: owner-chemistry+maciejmarcin.maslyk==ceu.es[*]ccl.net [owner-chemistry+maciejmarcin.maslyk==ceu.es[*]ccl.net] w imieniu Olli Lehtonen olehtone]~[chem.helsinki.fi [owner-chemistry[*]ccl.net] WysÅ‚ano: 24 listopada 2010 13:12 Do: MASLYK, MACIEJ MARCIN Temat: CCL:G: ODP: CCL:G: Gaussian output problem Sent to CCL by: Olli Lehtonen [olehtone . chem.helsinki.fi] Hi, Apparently you are using linux so with scripting language awk you can write BEGIN {atom=10000} { if (/^\ \*\*\*\*/) { sub("^\\ \\*\\*\\*\\*",atom); atom++; } print $0; } Assuming that script is contained in file called stars.awk you then give a command (output follows) awk -f stars.awk test.out 9995 1 20001030 -12.655571 46.600810 32.540627 9996 1 20001030 -12.533484 47.134581 33.952118 9997 8 20001021 2.441067 -19.529269 31.331119 9998 1 20001030 2.813824 -19.307495 32.184450 9999 1 20001030 1.933916 -20.325103 31.491166 10000 8 20001021 37.587292 -11.572024 28.812192 10001 1 20001030 37.333847 -11.927328 27.960694 10002 1 20001030 38.095189 -12.272395 29.221488 10003 8 20001021 23.735956 -43.072924 13.135294 10004 1 20001030 23.388276 -42.182008 13.115359 10005 1 20001030 22.974070 -43.624340 13.312930 where test.out contains your sample output. Just be aware that the script changes all **** (in the beginning of line with one extra space) with the running number so if you have the same problem someplace else in the output file it will change it there too. Hope it helps, Olli Oe Wed, Nov 24, 2010 at 10:20:47AM +0100, MASLYK, MACIEJ MARCIN maciejmarcin.maslyk^-^ceu.es wrote: > > Sent to CCL by: "MASLYK, MACIEJ MARCIN" [maciejmarcin.maslyk!A!ceu.es] > Thanks for help but I'm completely begginer in gaussian and also in linux so can you guys explain this thing with source code more precisely, please? > > Sam, I got 15 k atoms and 250 steps so it will kill me if I start changing stars to numbers manually :) > > regards > > Maciek > > -----Original Message----- > > From: owner-chemistry+closed==etsu.edu__ccl.net [mailto:owner-chemistry+closed==etsu.edu__ccl.net] On Behalf Of Maciej Maslyk maciejmarcin.maslyk .. ceu.es > Sent: Tuesday, November 23, 2010 8:45 AM > To: Close, David M. > Subject: CCL:G: Gaussian output problem > > > Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk-,-ceu.es] > Hi everyone, > could you help me with one problem, please? Every time I'm running G03 job I got problem with outputs. The problem is that I cannot extract structures because there are stars **** instead of atom numbers higher than 9999. Have you ever had this problem in your calculation if you had more than 9999 atoms in the system? > > It looks like this in output: > 9995 1 20001030 -12.655571 46.600810 32.540627 > 9996 1 20001030 -12.533484 47.134581 33.952118 > 9997 8 20001021 2.441067 -19.529269 31.331119 > 9998 1 20001030 2.813824 -19.307495 32.184450 > 9999 1 20001030 1.933916 -20.325103 31.491166 > **** 8 20001021 37.587292 -11.572024 28.812192 > **** 1 20001030 37.333847 -11.927328 27.960694 > **** 1 20001030 38.095189 -12.272395 29.221488 > **** 8 20001021 23.735956 -43.072924 13.135294 > **** 1 20001030 23.388276 -42.182008 13.115359 > **** 1 20001030 22.974070 -43.624340 13.312930 > > Do you have any suggestions? > > Thanks in advancehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Nov 26 05:30:00 2010 From: "Vincent Leroux vincent.leroux * loria.fr" To: CCL Subject: CCL: suggestions needed..... Message-Id: <-43231-101126024905-23246-Xz6VXRcPom54T6vxWSY95g()server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 26 Nov 2010 08:48:56 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux===loria.fr] Hi Rocky, I advise you not starting from scratch on such a difficult topic... this is simply insane IMHO. The CHARMm22 forcefield (the commercial version, not the one freely available from MacKerell et al.) contains parameters for those metals in combination with organic compounds. If you have InsightII installed on an old computer somewhere, you should dig into its data files to get the appropriate aminoh.rtf/parm.prm pair. That would give you a very good starting point for your studies - maybe after some tests you might find those parameters good enough for your work. Optimizing those might not be a sensible option already, so restarting from zero... Regards VL Le 25/11/10 16:52, rocky walden rocky.walden19%a%gmail.com a écrit : > Dear CCL users. > Thank you for your valuable time. > I am working on organometallic Compounds containing 6 carbon atoms > with a Metal atom Pt, Re, pd. > Now i am planning to optimize them geometrically. > I am also looking forward to continue my work focusing the > development of forcefields that which can explicitly to treat Metal > atoms (like Pt, Pd, Os, Re, Ru, Fe) containing Organic compounds. > So i kindly request all the computational chemistry experts. please > suggest me how to start from scratch for the development of the > forcefield for specially Metal atom containing Organic Compounds. > > I also kindly request you to post me some links or some references > literature. > This is very helpful to me. > > Excuse me for my bad english. > Thank you in advance. > > > Regards > Walden > > > From owner-chemistry@ccl.net Fri Nov 26 09:28:00 2010 From: "Herbert Fruchtl herbert.fruchtl[#]st-andrews.ac.uk" To: CCL Subject: CCL:G: Question on calculation of charge center of electrons in a molecule Message-Id: <-43232-101126092524-17103-TRiUE5FHM0T1ABrHYi2fSA##server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 26 Nov 2010 14:25:01 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl::st-andrews.ac.uk] The centre of charge of each Gaussian function is its origin, i.e. the nucleus if you have atom-centred basis functions. The Mulliken charge is the sum of those functions, multiplied with their occupation number. Shouldn't this sum have its centre on the nucleus as well? And the sum of all of them (over all atoms) gives the complete charge distribution. Where am I going wrong? Herbert Ulf Ekström ulfek(~)few.vu.nl wrote: > Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek],[few.vu.nl] > On Thu, Nov 25, 2010 at 9:56 AM, Herbert Fruchtl > herbert.fruchtl-.-st-andrews.ac.uk wrote: >> Sent to CCL by: Herbert Fruchtl [herbert.fruchtl*_*st-andrews.ac.uk] >> I don't have time to look at the maths of it, but I think the centre of >> charge of the electron density should be identical to the centre of the >> Mulliken charges, which would be easy to calculate (analogous to the centre >> of mass). > > This will not work, for example if you have a single centre basis set all > Mulliken charge would be on that center. What you should do is to compute > the dipole moment of the molecule and use that to work out the center > of charge. > > Sincerely, > Ulf Ekstrom> > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Fri Nov 26 10:37:00 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= ulfek_-_few.vu.nl" To: CCL Subject: CCL: Question on calculation of charge center of electrons in a molecule Message-Id: <-43233-101126103558-29709-ZpwEgrQkDr84s6IaJPc1SA]-[server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 26 Nov 2010 16:35:51 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek.:.few.vu.nl] On Fri, Nov 26, 2010 at 3:25 PM, Herbert Fruchtl herbert.fruchtl[#]st-andrews.ac.uk wrote: [..] > Where am I going > wrong? The density is not centered on the nucleus for a polarized atom. For example the density may be described by an s function with some small p component added. The center of this charge lies away from the nucleus. Plot this in 1d and you will be convinced. If your argument was true atoms could never be polarized, even in external fields. Perhaps you are confusing properties of each basis function product with properties of their sum? Sincerely, Ulf From owner-chemistry@ccl.net Fri Nov 26 13:41:00 2010 From: "Anselm Horn Anselm.Horn]*[chemie.uni-erlangen.de" To: CCL Subject: CCL: suggestions needed..... Message-Id: <-43234-101126074956-32440-lpRQCuaQAG0QhC413CUmYA#%#server.ccl.net> X-Original-From: Anselm Horn Content-Disposition: inline Content-Type: text/plain; charset="us-ascii" Date: Fri, 26 Nov 2010 13:49:21 +0100 MIME-Version: 1.0 Sent to CCL by: Anselm Horn [Anselm.Horn.-,-.chemie.uni-erlangen.de] Hi, maybe you want to have a look into the book of Comba, Hambley & Martin ("Molecular modeling of inorganic compounds", 3rd ed. 2009, Wiley-VCH) to obtain some suggestions about your topic of interest. Regards, Anselm Horn