From owner-chemistry@ccl.net Mon Jul 31 01:21:01 2006 From: "=?iso-2022-jp?B?GyRCMTEwZiEhPy47VhsoQg==?= s-usui]|[cybernet.co.jp" To: CCL Subject: CCL: transition state optimization for ethylene Message-Id: <-32303-060730201208-13832-OIx7Prv3tRih/ECs50966w**server.ccl.net> X-Original-From: =?iso-2022-jp?B?GyRCMTEwZiEhPy47VhsoQg==?= Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-2022-jp" Date: Mon, 31 Jul 2006 09:11:57 +0900 MIME-Version: 1.0 Sent to CCL by: =?iso-2022-jp?B?GyRCMTEwZiEhPy47VhsoQg==?= [s-usui{=}cybernet.co.jp] Dear Daria Try CASSCF. This article will be helpful. $B!!(BJ. Mol. Struct. (THEOCHEM), 623, 167-178 (2003). Best Regards Shinji Usui -----Original Message----- > From: owner-chemistry##ccl.net [mailto:owner-chemistry##ccl.net] Sent: Saturday, July 29, 2006 8:41 AM To: Usui, Shinji Subject: CCL: transition state optimization for ethylene Sent to CCL by: "Daria Khvostichenko" [dkhvosti|,|uiuc.edu] Dear CCL subscribers, Does anybody know how to obtain a transition state structure for ethylene rotation about the double bond? I have tried QST2 and QST3 optimizations; they converge to the same structure, but frequency analysis of the output structure does not show any imaginary frequencies. Berny TS optimization does not converge (it runs into structures with two imaginary frequencies). When I used opt=(ts,noeigentest,calcfc,EF) it converged to the same structure as QST2 and QST3. I did calculations with ub3lyp/6-31g(d) and ub3lyp/6-311(d,p) methods; the results are more or less identical for both basis sets. Thank you in advance, Daria dkhvosti-.-uiuc.edu Daria Khvostichenko Postdoctoral Research Associate Department of Chemistry Roger Adams Laboratory, 23-5 600 S. Mathews ave., MC-712 University of Illinois Urbana, IL 61801 217-244-2102; 217-244-3186 (fax)http://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 Mon Jul 31 05:01:01 2006 From: "Jens Spanget-Larsen spanget^ruc.dk" To: CCL Subject: CCL:G: TDDFT in gaussian Message-Id: <-32304-060731045941-24417-dynlN/f5p6I2gsaqJ0DMZw++server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 31 Jul 2006 10:59:29 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget^^ruc.dk] Dear Agalya Govindasamy, maybe you already solved your problem. But nevertheless, for a closed shell species, it is easy to calculate the percentage contributions from the coefficients printed by a Gaussian TDDFT run. The coefficients refer to micro-configurations (not spin adapted). If you want the percentage contribution from the pertinent singlet configuration, you must square the printed coefficient and multiply it by 2 x 100. For instance, the contribution from the 129 -> 138 excitation in the first of your examples amounts to 0.45069^2 x 2 x 100 = 40.62%. In your second example, you get for the 130 -> 132 excitation 0.67417^2 x 2 x 100 = 90.90%. Please note that Gaussian by default prints only contributions larger than a certain treshold. There is an IOP input parameter that leads to printing also of smaller contributions, but I do not have it at hand. Good Luck! Jens >--< ------------------------------------------------------ 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://www.ruc.dk/~spanget ------------------------------------------------------ Agalya Govindasamy agalya81{}gmail.com wrote: > Sent to CCL by: "Agalya Govindasamy" [agalya81-x-gmail.com] > > Dear CCL users, > > I would like to know about calculating the precentage contribution of excitation coefficients given in the TDDFT output. > > For example, the following excitation shows mixture of transitions with different excitation coefficients. > > Excited State 31: Singlet-A 3.6351 eV 341.07 nm f=0.0001 > 119 ->132 0.11466 > 124 ->138 0.16417 > 124 ->140 -0.16712 > 129 ->138 0.45069 > 129 ->140 -0.3978 > 129 ->141 -0.12337 > 130 ->136 -0.10225 > > I have seen in some journals, that they have mentioned the coefficients as percentage. Here since there are many transitions, could anyone can please tell me how to calculate the percentage of the coefficients. > > This may be a stupid question. > > Does everyone divide the particular coefficient divided by the sum of all the coefficients and then multiplied by 100 to get the percentage value? > > If that is correct, then how to get percentage value of the coefficient for excitations like the following case > > Excited State 1: Singlet-A 1.5328 eV 808.90 nm f=0.0287 > 130 ->132 0.67417 > > can i mention it as 100%. > > Thankyou in adavnce > From owner-chemistry@ccl.net Mon Jul 31 10:17:00 2006 From: "Alex Popov alexei.a.popov(0)gmail.com" To: CCL Subject: CCL: PC GAMESS benchmarks on Intel Core2 Duo (Conroe) Message-Id: <-32305-060731084234-24053-5vtK4UBJXhKXe4XAf4tNUg||server.ccl.net> X-Original-From: "Alex Popov" Content-Type: multipart/alternative; boundary="----=_Part_46577_26814065.1154347378083" Date: Mon, 31 Jul 2006 16:02:58 +0400 MIME-Version: 1.0 Sent to CCL by: "Alex Popov" [alexei.a.popov++gmail.com] ------=_Part_46577_26814065.1154347378083 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCLers, I've run several QC benchmarks on Intel Conroe-based system using PC GAMESS. The results (which may be of interest to community) are available at: http://classic.chem.msu.su/gran/gamess/PC%20GAMESS%20Conroe%20performance.html I'm grateful to Dr. Alex Granovsky for providing me by the latest PC GAMESS binaries. Regards, Alexei Popov ------=_Part_46577_26814065.1154347378083 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear CCLers,

I've run several QC benchmarks on Intel Conroe-based system using PC GAMESS.
The results (which may be of interest to community) are available at:
 
I'm grateful to Dr. Alex Granovsky for providing me by the latest PC GAMESS binaries.
 
Regards,
Alexei Popov
------=_Part_46577_26814065.1154347378083-- From owner-chemistry@ccl.net Mon Jul 31 10:52:01 2006 From: "Alexei A Popov alexei.a.popov^gmail.com" To: CCL Subject: CCL: PC GAMESS benchmarks on Intel Core 2 Duo (Conroe) Message-Id: <-32306-060731094607-26670-aaDUj9UZEfjEkzLElTdzkQ~!~server.ccl.net> X-Original-From: "Alexei A Popov" Date: Mon, 31 Jul 2006 09:46:07 -0400 Sent to CCL by: "Alexei A Popov" [alexei.a.popov ~~ gmail.com] Dear CCLers, I've run several QC benchmarks on Intel Conroe-based system using PC GAMESS. The results (which may be of interest to community) are available at: http://classic.chem.msu.su/gran/gamess/PC%20GAMESS%20Conroe%20performance.html I'm grateful to Dr. Alex Granovsky for providing me by the latest PC GAMESS binaries. Regards, Alexei Popov From owner-chemistry@ccl.net Mon Jul 31 11:26:00 2006 From: "Jan Labanowski janl/a\speakeasy.net" To: CCL Subject: CCL: Computational Science & Engineering Online Web Site Message-Id: <-32307-060731102401-1057-BVMnNctzzPOJs3IIgpT32A+*+server.ccl.net> X-Original-From: "Jan Labanowski" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 31 Jul 2006 14:23:55 +0000 MIME-Version: 1.0 Sent to CCL by: "Jan Labanowski" [janl : speakeasy.net] Dear CCL Members, Please make sure that you pay a visit to a site of another supporter of CCL -- Computational Science & Engineering Online (CSE-Online) at: http://cse-online.net CSE-Online WILL HELP you in your research and teaching and may be an answer to many questions that appear on CCL: Where can I find the free software that does "this or that"... The CSE-Online 1.0 was just released with more than 30 application tools in various domains, such as Quantum Chemistry, Chemical Kinetics, Bio-Simulation, and Material Science as well as a number of general purpose tools to choose from. CSE-Online is a virtual desktop environment that can make network and grid computing transparent and practical. It is based on an innovative online, on demand, component-based software framework for distributed applications and data. Each application is treated as an independent tool. The framework allows you to select among many available tools to construct on demand a customizable large enterprise system or just a desktop environment that fits your particular needs. It also allows you to add your own tools to the environment and to COLLABORATE WITH OTHERS over the Grid. Getting started on CSE-Online is easy: 1. Go to the website: http://cse-online.net 2. Register for a free account 3. Download and install CSE-Online 4. Select applications from the catalog. The link to CSE is also available from the CCL Home page http://www.ccl.net Try CSE out, tell your friends, tell your boss... It may be something that you are looking for. Use it for collaboration and data exchange within your projects. CSE is Grid enabled and there is finally something real that comes out from the NSF Grid initiative for Computational Chemistry and we can now share the benefits of the Grid together with people who do Genomics or High Energy Physics. Again... Use it or loose it... Jan Labanowski CCL Admin From owner-chemistry@ccl.net Mon Jul 31 12:02:00 2006 From: "Roger Kevin Robinson r.robinson : imperial.ac.uk" To: CCL Subject: CCL: Polyrate 9.4.1 installation Message-Id: <-32308-060731115119-19929-QkydiDkdwd0P1TOfSW8Q2w]![server.ccl.net> X-Original-From: "Roger Kevin Robinson" Date: Mon, 31 Jul 2006 11:51:18 -0400 Sent to CCL by: "Roger Kevin Robinson" [r.robinson__imperial.ac.uk] hi, Has any one managed to install this software. Im having problems. The configure script seems to correctly create the Makefile in the src directory. When you run make from this directory. I get the message `ch4o.o' is up to date. anyone else had this problem ? thanks Roger From owner-chemistry@ccl.net Mon Jul 31 13:15:00 2006 From: "errol lewars elewars]~[trentu.ca" To: CCL Subject: CCL: transition state optimization for ethylene Message-Id: <-32309-060730134301-20534-ttOefHZc2ksTmgkYlb+H5w__server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 30 Jul 2006 12:40:50 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars{}trentu.ca] 2007 July 29 Hello, Because the TS is a singlet diradical, routine optimization methods, based on one-determinant wavefunctions, cannot be relied on. There are three approaches available: complete active space (CAS), generalized valence bond, and (still in the development stage) certain DFT methods. I suggest you check the literature for these three, as applied to ethene. If you are really stuck, I can send you more information. Regards, E. Lewars ==== Daria Khvostichenko dkhvosti%x%uiuc.edu wrote: >Sent to CCL by: "Daria Khvostichenko" [dkhvosti|,|uiuc.edu] >Dear CCL subscribers, > >Does anybody know how to obtain a transition state structure for ethylene rotation about the double bond? I have tried QST2 and QST3 optimizations; they converge to the same structure, but frequency analysis of the output structure does not show any imaginary frequencies. Berny TS optimization does not converge (it runs into structures with two imaginary frequencies). When I used opt=(ts,noeigentest,calcfc,EF) it converged to the same structure as QST2 and QST3. I did calculations with ub3lyp/6-31g(d) and ub3lyp/6-311(d,p) methods; the results are more or less identical for both basis sets. > >Thank you in advance, > >Daria > >dkhvosti-.-uiuc.edu > >Daria Khvostichenko >Postdoctoral Research Associate >Department of Chemistry >Roger Adams Laboratory, 23-5 >600 S. Mathews ave., MC-712 >University of Illinois >Urbana, IL 61801 >217-244-2102; 217-244-3186 (fax)> > > > > From owner-chemistry@ccl.net Mon Jul 31 13:50:00 2006 From: "Yunusa Umar uyunusa-x-kfupm.edu.sa" To: CCL Subject: CCL:G: Complexation energy Message-Id: <-32310-060729024958-1234-7q4kQbJAoDVmMy33BG3Rng[A]server.ccl.net> X-Original-From: "Yunusa Umar" Date: Mon, 31 Jul 2006 11:51:18 -0400 Sent to CCL by: "Yunusa Umar" [uyunusa[*]kfupm.edu.sa] Dear Members, I am trying to calculate the complexation energy of a silver complex = using Gaussian. Can anyone please explain to me what to be done, bearing = in mind that i am new user of Gaussian program.=20 Suggestions to any publications with detailed computational method of = calculating complexation energy will be highly appreciated. Thanks Yunusa Umar Chemistry Department KFUPM Dhahran 31261 KSA From owner-chemistry@ccl.net Mon Jul 31 14:34:00 2006 From: "Chunyi Sung juneyi1 ~ yahoo.com.tw" To: CCL Subject: CCL:G: Charges in ONIOM jobs Message-Id: <-32311-060731132036-27462-uP7lEtBqZDXMJ09U9u6PPA%x%server.ccl.net> X-Original-From: "Chunyi Sung" Date: Mon, 31 Jul 2006 13:20:36 -0400 Sent to CCL by: "Chunyi Sung" [juneyi1]-[yahoo.com.tw] Hi, I want to include charges for atoms in the outer layer in ONIOM jobs. I've tried to include the "qeq" keyword, but I actually don't know how it works. In Gaussian manual, it says "options are available to estimate charges at the initial point using the QEq algorithm...". Here are my questions: 1. So it means that charges are assigned to atoms initially, and they won't be updated during geometry optimization? 2. I couldn't find the qeq charges in the output file. Where are they stored? 3. Is there other (better) to include charges for atoms calculated by force field in ONIOM jobs? Thanks Chunyi From owner-chemistry@ccl.net Mon Jul 31 16:25:01 2006 From: "Wai-To Chan chan{=}curl.gkcl.yorku.ca" To: CCL Subject: CCL:G: transition state optimization for ethylene Message-Id: <-32312-060731161956-8959-lYbOOKSZP67eF+mz2IbF+A|server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Mon, 31 Jul 2006 16:23:24 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan%x%curl.gkcl.yorku.ca] <<<<<<<<<<<<<<<<<<<<<,, Because the TS is a singlet diradical, routine optimization methods, based on one-determinant wavefunctions, cannot be relied on. There are three approaches available: complete active space (CAS), generalized valence bond, and (still in the development stage) certain DFT methods. I suggest you check the literature for these three, as applied to ethene. If you are really stuck, I can send you more information. >>>>>>>>>>>>>>>>>>>>>>>>> Characterization of singlet diradicals using UHF-based methods and UDFT is not necessarily less reliable than the above methods provided that one understand their limitations. For curiosity I tried out a UDFT-BHandHLYP calculation of the ethylene twisting TS using Gaussian 98. One single imaginary frequency frequency (1226 cm-1) was obtained. Based on visualiazation of this frequency the TS appears to be correct but I did not verify the reaction pathway with IRC. A number of points should be noted if you want to follow the same procedure: In the first job step the 'guess=mix' option yields an UDFT solution for a singlet diradical with a spin contamination of 1.0021. Use of 'stable=opt' yield a lower energy solution with a rather similar spin contamination. In the geometry of the twisted structure I deliberately distorted the symmetry slightly from D2d to a lower symmetry. The distortion in the optimized structure from the D2d symmetry appears to be be very slight as far as I observed. It is possible that forcing the D2d symmetry on the TS will give you a second imaginary frequency. As discussed in a previous post there might exist a non-physical discontinuity in the transition from RDFT to UDFT solution in the potential energy pathway of the twisting of the closed-shell equilibrium structure. In that case the estimation of the barrier based on comparison of the UDFT energy of the twisted structure and the RDFT energy of the planar structure is not likely reliable. That would be like comparing the energy of two stationary points on two different theoretical PESs. Notwithstanding such shortcoming of the single-determinant method the use of a combination of UDFT and RDFT for the characterization of diradical PES still has its merits over CASSCF and GVB which recovers only a small fraction of the correlation energy. The input file is appended below. Wai-To Chan -------------------------------------------- %chk=c2h4d2d # ubhandhlyp/6-311G* guess=mix stable=opt ethene twisted 0 1 6 0.000000 0.000000 -0.661007 6 0.000000 0.000000 0.662007 1 0.917499 0.000000 -1.229914 1 -0.917499 0.000000 -1.229914 1 0. 0.917499 1.229914 1 0. -0.917499 1.229914 --Link1-- %chk=c2h4d2d # ubhandhlyp/6-311G* geom=check guess=check nosymm opt ethene twisted 0 1 --Link1-- %chk=c2h4d2d # ubhandhlyp/6-311G* geom=check guess=check nosymm freq ethene twisted 0 1 -------------------------------------------------------- From owner-chemistry@ccl.net Mon Jul 31 17:00:00 2006 From: "odmitr^^^UDel.Edu" To: CCL Subject: CCL:G: PbX2solids - I need to do NMR calcs, probably with ADF and NWchem input examples Message-Id: <-32313-060731163345-16887-a6J80qY9t0/CxAyrLbHK/g ~ server.ccl.net> X-Original-From: Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Mon, 31 Jul 2006 15:55:28 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: [odmitr#,#UDel.Edu] Hi everybody, I am starting entirely new for me project. I have to calculate NMR for lead- containing solids like PbO, PbX2 (X=Cl, Br, F and so on). I never did this kind of calculations and I know there is a problem in g03 with calculations of NMR shifts for transition metals because the available basis sets (LANL2DZ, CEP, SDD) are ECP basis sets which are incapable of giving the accurate electron densities at the nucleus which are necessary to calculate chemical shifts. I am going to learn ADF and NWchem programs. I would highly appreciate if you’ll share with me examples of inputs that can be related to the above project. Also I’ll be very much thankful for any related thoughts and suggestions (at least they’ll be acknowledged if not co-authored). Again, I am interested in approaches that will do NMR (GIAO) calculations, probably using all-electron basis sets and, probably, DFT and relativistic approximations. It looks like I’ll work with the given geometries and no optimization is necessary. Regards, Olga Dmitrenko From owner-chemistry@ccl.net Mon Jul 31 18:32:01 2006 From: "Ben Ellingson elling()t1.chem.umn.edu" To: CCL Subject: CCL: Polyrate 9.4.1 installation Message-Id: <-32314-060731171325-23658-Cy4+2zRZ8g945Kzv/5SbnA#server.ccl.net> X-Original-From: Ben Ellingson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Mon, 31 Jul 2006 15:22:35 -0500 Mime-Version: 1.0 (Apple Message framework v749.3) Sent to CCL by: Ben Ellingson [elling,+,t1.chem.umn.edu] The 'make' problem does appear to be a small bug, but the way the program was designed, it does not require a simple 'make' call from the src directory. If the Makefile has been created properly, then you may proceed directly to the testruns. The testrun scripts use the Makefile to compile anything that is needed. Or if you want to compile a certain executable outside of the testrun, for example the executable for the NH3 surface, you may type "gmake NH3S" from the src directory. You may also use your own surface by adding it to the Makefile. When using the interface programs like GAUSSRATE and MULTILEVELRATE, they create a new section at the bottom of the Makefile. The installation scripts for these programs then explicitly call 'gmake GRS' or 'gmake 'MLRS' to compile them. If the testrun scripts or the interface programs don't compile the code they need, then you have a problem. Otherwise, everything should be fine. Ben Ellingson University of Minnesota (POLYRATE Developer) > Date: Mon, 31 Jul 2006 12:02:52 -0400 > From: "Roger Kevin Robinson r.robinson : imperial.ac.uk" > > Reply-To: CCL Subscribers > To: "Dahlke, Erin Elizabeth " > Subject: CCL: Polyrate 9.4.1 installation > > Sent to CCL by: "Roger Kevin Robinson" [r.robinson__imperial.ac.uk] > hi, > > Has any one managed to install this software. Im having problems. > > The configure script seems to correctly create the Makefile in the > src directory. > > When you run make from this directory. I get the message > > `ch4o.o' is up to date. > > anyone else had this problem ? > > thanks Roger > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > From owner-chemistry@ccl.net Mon Jul 31 19:07:00 2006 From: "Ginovska, Bojana bojana.ginovska=pnl.gov" To: CCL Subject: CCL: Polyrate 9.4.1 installation Message-Id: <-32315-060731143824-15257-ebqeAdx7UkLVqJSI04dmLw^_^server.ccl.net> X-Original-From: "Ginovska, Bojana" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 31 Jul 2006 10:38:16 -0700 MIME-Version: 1.0 Sent to CCL by: "Ginovska, Bojana" [bojana.ginovska_+_pnl.gov] I have had the same problem. It seems the makefile only makes the very first target i.e. object file which happens to be `ch4o.o' and stops there. I would suggest making your own makefile. Bojana -----Original Message----- > From: owner-chemistry:+:ccl.net [mailto:owner-chemistry:+:ccl.net] Sent: Monday, July 31, 2006 9:03 AM To: Ginovska, Bojana Subject: CCL: Polyrate 9.4.1 installation Sent to CCL by: "Roger Kevin Robinson" [r.robinson__imperial.ac.uk] hi, Has any one managed to install this software. Im having problems. The configure script seems to correctly create the Makefile in the src directory. When you run make from this directory. I get the message `ch4o.o' is up to date. anyone else had this problem ? thanks Rogerhttp://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 Mon Jul 31 19:42:00 2006 From: "Mike Miller mill++pica.army.mil" To: CCL Subject: CCL:G: C70 nanotube Message-Id: <-32316-060731123005-15023-1R4IqcLSQ7t8nU1vHTpwLA * server.ccl.net> X-Original-From: "Mike Miller" Date: Mon, 31 Jul 2006 12:29:54 -0400 Sent to CCL by: "Mike Miller" [mill(0)pica.army.mil] Dear colleagues, I was provided the output of a semi-empirical PM3 optimization (z-matrix) of a C70 nanotube. I am now trying to run it using Gaussian 03 Rev.c.02, B3LYP/6-31g(d). It will not optimize, so I ran a single point energy calculation- same problems encountered; here is a summary: First calculation performed: T Opt B3LYP/6-31g(d) SCF=tight Results: Convergence criterion not met. E(RB+HF-LYP) = -2665.81029984 Convergence failure -- run terminated Second calculation performed: T B3LYP/6-31g(d) SCF=tight Results: Convergence criterion not met. E(RB+HF-LYP) = -2665.81029979 Convergence failure -- run terminated I don't know what the problem is, however, I see two ways to proceed... find a database of z-matrices of nanotubes and compare my z-matrix to that and go from there... or if there is something about the Gaussian program that I have to tweak in order to get the optimization to work. Any assistance would be appreciated. Mike From owner-chemistry@ccl.net Mon Jul 31 20:17:01 2006 From: "Ginovska, Bojana bojana.ginovska(-)pnl.gov" To: CCL Subject: CCL: Polyrate 9.4.1 installation Message-Id: <-32317-060731171709-26151-7s2glx0U4MVwqZfrWI7/Aw : server.ccl.net> X-Original-From: "Ginovska, Bojana" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 31 Jul 2006 14:17:05 -0700 MIME-Version: 1.0 Sent to CCL by: "Ginovska, Bojana" [bojana.ginovska]_[pnl.gov] What you need to do when running the make file is to specify a target you want created. For example you can do: >> make CH4OS And it is going to create the executable needed for the test run in polyrate9.4.1/testrun/ch4o The makefile does not have an all target that will create all the executables at ones, but if you want to do that you can specify a line in the makefile containing all the targets you want. >> all: CH4OS CLHBRS CMCS CWMCS >> make all Bear in mind that the executable files are not small, so you may be wasting your memory if you keep executable files that you do not need. Hope this helps. Bojana -----Original Message----- > From: owner-chemistry^-^ccl.net [mailto:owner-chemistry^-^ccl.net] Sent: Monday, July 31, 2006 9:03 AM To: Ginovska, Bojana Subject: CCL: Polyrate 9.4.1 installation Sent to CCL by: "Roger Kevin Robinson" [r.robinson__imperial.ac.uk] hi, Has any one managed to install this software. Im having problems. The configure script seems to correctly create the Makefile in the src directory. When you run make from this directory. I get the message `ch4o.o' is up to date. anyone else had this problem ? thanks Rogerhttp://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 Mon Jul 31 20:52:00 2006 From: "Jun Zhao jzhao#,#tamu.edu" To: CCL Subject: CCL: How to make a movie from the trajectory file at Cerius2? Message-Id: <-32318-060731172632-28626-aSv8VTT+9wmDMeJ9yNnvww*|*server.ccl.net> X-Original-From: "Jun Zhao" Date: Mon, 31 Jul 2006 17:26:32 -0400 Sent to CCL by: "Jun Zhao" [jzhao|-|tamu.edu] Does anyone know how to make a movie from the trajectory file? I got the trajectory file from the molecular dynamics simulation at Cerius 2. I want to make a short movie based on the trajectory file so that I can play it in the powerpoint presentation. Any suggestion is greatly appreciated. Jun Zhao Ph.D. Candidate Dept of Atmospheric Sciences Texas A&M University College Station, TX 77843 Office: (979) 458-0555 Fax: (979) 862-4466 From owner-chemistry@ccl.net Mon Jul 31 21:27:00 2006 From: "Mauricio Erben erben---quimica.unlp.edu.ar" To: CCL Subject: CCL: Radical cation Message-Id: <-32319-060731125639-20591-PfkhTbAtwIz5NqbE9j6DVw,server.ccl.net> X-Original-From: "Mauricio Erben" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 31 Jul 2006 12:55:37 -0300 MIME-Version: 1.0 Sent to CCL by: "Mauricio Erben" [erben*quimica.unlp.edu.ar] Dear CCL subscribers, In connection with radical-cation species, I would like to know about the possibility of calculating another cationic states distinct from the low-lying one. Are excited state or TDDFT methods applicable in these cases? Does anyone have some bibliography to suggest dealing with this and related issues? Thank you very much in advance, Mauricio Erben. ----- Original Message ----- > From: "adria gil mestres adria+/-klingon.uab.es" To: "Erben, Mauricio Federico " Sent: Thursday, July 27, 2006 10:17 AM Subject: CCL: Radical cation > Sent to CCL by: adria gil mestres [adria!=!klingon.uab.es] > Yes, it is ok doublet multiplicity and charge +1 for radical cations... > But if you do an unrestricted calculation you have to take into account > that the S square in the calculation has to be 0.75... then, be careful > with the value of S square in unrestricted calculations, specially if > you use MP2 methods, since this value could be higher than 0.75 and you > could have spin contamination. > > > En/na Agalya G agalya81 ~ gmail.com ha escrit: > > >Sent to CCL by: "Agalya G" [agalya81#%#gmail.com] > > > >How to model compounds with radical cation or anion? Is it ok, if i do unrestricted calculation with doblet multiplicity and charge +1 for radical cation?> > > From owner-chemistry@ccl.net Mon Jul 31 22:02:00 2006 From: "huanglei huanglei%%mail.utexas.edu" To: CCL Subject: CCL: How to make a movie from the trajectory file at Cerius2? Message-Id: <-32320-060731212705-19643-EwKUjciZ8L/gQzITxJLHxA-x-server.ccl.net> X-Original-From: "huanglei" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Mon, 31 Jul 2006 20:34:01 -0600 Mime-Version: 1.0 Sent to CCL by: "huanglei" [huanglei^mail.utexas.edu] Hi, Jun Generally I use vmd to generate a movie based on pdb file. You can write a program or use existing code to tranform the trajectory in other format into pdb. Good luck. Best regards, lei ======= 2006-07-31 18:58:25 ======= >Sent to CCL by: "Jun Zhao" [jzhao|-|tamu.edu] >Does anyone know how to make a movie from the trajectory file? I got the trajectory file from the molecular dynamics simulation at Cerius 2. I want to make a short movie based on the trajectory file so that I can play it in the powerpoint presentation. Any suggestion is greatly appreciated. > >Jun Zhao > >Ph.D. Candidate >Dept of Atmospheric Sciences >Texas A&M University >College Station, TX 77843 >Office: (979) 458-0555 >Fax: (979) 862-4466> >