From owner-chemistry@ccl.net Tue Dec 27 00:07:00 2005 From: "Zhijian Wu zhijw^^^hotmail.com" To: CCL Subject: CCL:G: spin-orbit coupling effect Message-Id: <-30396-051226184216-8735-fV4R8CxEwlVrfle3iJseDw(0)server.ccl.net> X-Original-From: "Zhijian Wu" Content-Type: text/html; format=flowed Date: Mon, 26 Dec 2005 18:42:09 -0500 Mime-Version: 1.0 Sent to CCL by: "Zhijian Wu" [zhijw[A]hotmail.com]
Hi, CCLers,
 
Does anybody know how to calculate the spin-orbit coupling effect separately using G03? I am trying to do calculations on molecules containing 5d transition metals. Initially, I use LANL2DZ or CEP-121G basis set, but in these two basis sets, the spin-orbit coupling effect was averaged out. I am now trying to use SDDALL basis set, in which spin-orbit coupling is considered explicitly. But I do not know how to separate the spin-orbit coupling effect from this basis set, and I even do not know if it is possible to do such a thing by use of G03.
 
I appreciate for your help.
 
Thank you very much and Happy new year!
 
Zhijian WU
 
Changchun Institute of Applied Chemistry
From owner-chemistry@ccl.net Tue Dec 27 00:41:01 2005 From: ". Rajendran raji .. anal.chem.tohoku.ac.jp" To: CCL Subject: CCL:G: base stacking and TDDFT calculations Message-Id: <-30397-051227000952-13576-Jr6CyWA3auJTH+yejs2pbw###server.ccl.net> X-Original-From: ". Rajendran" Sent to CCL by: ". Rajendran" [raji#,#anal.chem.tohoku.ac.jp] Dear CCL members, Presently I am working on the base stacking and TDDFT calculations. For this, a Trimer containing my Ligand and two flanking bases (5Gua-Lig-Gua3)were generated from canonical B-form X-ray crystallographic data by mutating adenine to my Ligand and removing the sugar and phosphate units. In the geometry optimization, using g03, with B3LYP/6-311+G(d) one of the guanine base is moving out (some distortion, not so close, not so far, but sufficiently far from the stacking interaction with the Ligand) from the timer geometry and the optimization was failure with error termination. So can you please tell me what I have to do to solve this problem? 2) Can some one tell me how to calculate only 10 Highest occupied MOs and 10 lowest vacant Mos in the population calculations(in ground state calculation)? Because if I use Pop=full, it will calculate all the possible orbitals and is taking very long time for big systems. 3) How to use the SCF BasicFunction cutoff? For big systems SCF=Tight is time consuming and some times getting convergence problem. I have tried SCF=Sleazy but its only for Single point calculations, so I got error message. In some methods/programmes SCF BFCut 1e-14 option will solve this problem, so may I use this option in the route section () and is it available in g03? Looking forward for your kind information. Thank you very much in advance. You can write to raji/at/anal.chem.tohoku.ac.jp My Belated Christmas wishes and Wish you very happy new year 2006. Raji. From owner-chemistry@ccl.net Tue Dec 27 10:06:00 2005 From: "Kalju Kahn kalju/a\chem.ucsb.edu" To: CCL Subject: CCL:G: base stacking and TDDFT calculations Message-Id: <-30398-051227054017-3428-0ty7gEKGZISni6/EAg+nZw]|[server.ccl.net> X-Original-From: Kalju Kahn Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 27 Dec 2005 01:31:22 -0800 MIME-Version: 1.0 Sent to CCL by: Kalju Kahn [kalju#%#chem.ucsb.edu] Dear Rajendran, I am not sure that B3LYP can reproduce base-stacking geometries. There are three major forces (dispersion attraction, short-range repulsion, and electrostatic interaction) behind stacking. DFT methods that you are using do not describe dispersion interactions. For a recent paper in this topic, see Jiri & Hobza in Physical Chemistry Chemical Physics (2005), 7, 1624-1626. Happy Holidays, Kalju ------------------- > Sent to CCL by: ". Rajendran" [raji#,#anal.chem.tohoku.ac.jp] > Dear CCL members, > Presently I am working on the base stacking and TDDFT calculations. > For this, a Trimer containing my Ligand and two flanking bases > (5Gua-Lig-Gua3)were generated from canonical B-form X-ray > crystallographic data by > mutating adenine to my Ligand and removing the sugar and phosphate > units. In the geometry optimization, using g03, with B3LYP/6-311+G(d) > one of the guanine base is moving out (some distortion, not so close, > not so far, but sufficiently far from the stacking interaction with the > Ligand) from the timer geometry and the optimization was failure with > error termination. So can you please tell me what I have to do to solve > this problem? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara From owner-chemistry@ccl.net Tue Dec 27 16:03:00 2005 From: "Oleg Yazyev oleg.yazyev=epfl.ch" To: CCL Subject: CCL:G: Calculation of total magnetic moment Message-Id: <-30399-051227123323-29005-IKduzLrAmbSC3YB+RqJBOw|server.ccl.net> X-Original-From: Oleg Yazyev Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15 Date: Tue, 27 Dec 2005 17:35:24 +0100 MIME-Version: 1.0 Sent to CCL by: Oleg Yazyev [oleg.yazyev*o*epfl.ch] Dear Delwar, As well as many other codes which originate from chemistry, Gaussian03 assumes fixed _total_ magnetic moment (due to electron spins) which is defined by the spin multiplicity. This means that only integer magnetic moments of proper parity can be used. This is true for the most of cases considering isolated finite systems (molecules), and for the silicon cluster doped with single transition metal ion this should be fine too. In this case you should perform a set of calculation with reasonable spin multiplicities and choose one which has the lowest total energy. If you are aware of itinerant ferromagnetism (magnetic metals) or non-collinear magnetism (magnetic solids or clusters of transition metal atoms), you should try codes which originate from condensed matter physics. Good examples are plane wave codes (CPMD, PWSCF, Vasp, etc.) and localized AO codes (SIESTA, etc.). However, calculations involving exact exchange (i.e. hybrid functionals like B3LYP) may be more expensive (if implemented) than with Gaussian. DHhyc> Dear CCLers, DHhyc> I am interested to calculate total magnetic moment of DHhyc> transition metal droped medium size silicon cluster. I did my DHhyc> calculation on G03 at B3LYP/6-311+G*. However, G03 has no DHhyc> option to calculate total magnetic moment. DHhyc> My questions is: DHhyc> Is there any freee software or program for DHhyc> calculating total magnetic moment using the optimized geometry DHhyc> from G03? DHhyc> I therefore request you to help me sending your comments and advice. DHhyc> Thank you in advance. DHhyc> With regards, DHhyc> Sincerely yours, DHhyc> Delwar Hossain DHhyc> Mississippi State University -- Best regards, Oleg ______________________________________________________ Oleg Yazyev Ecole Polytechnique Fédérale de Lausanne (EPFL) Institut des Sciences et Ingénierie Chimiques CH-1015 Lausanne (Switzerland) Tel.: +41 21 693 9881 E-mail: oleg.yazyev . epfl.ch WWW: http://icmbcu001.epfl.ch/yazyev/index.html _______________________________________________________ From owner-chemistry@ccl.net Tue Dec 27 19:59:00 2005 From: "wbx wangbx!=!dicp.ac.cn" To: CCL Subject: CCL: [CCL]how to install polyrate? Message-Id: <-30400-051227195446-24473-kUVK9JsSt7gUrbvj1Qs8pg[a]server.ccl.net> X-Original-From: "wbx" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="gb2312" Date: Wed, 28 Dec 2005 08:54:52 +0800 Mime-Version: 1.0 Sent to CCL by: "wbx" [wangbx^_^dicp.ac.cn] Dear all CCLer£¬ recently i want to use the polyrate9.1 program to compute the reaction rate. but i meet some problems. first, i follow the polyrate manual to install it in the linux. in the second step i did not find the .docdir in the doc directory and .exedir in the exe directory. why? second, in the step 3, when i type set_machine.jc to run under C shell, it shows that there is no this commond. i guess it is because i didn't install fortran. right? third, if i want to install it in the windows, how should i do? i would like to use windows. thanks a lot!! With best regards, sincerely, Bingxing Wang 2005-12-27 email: wangbx__dicp.ac.cn From owner-chemistry@ccl.net Tue Dec 27 20:34:00 2005 From: "wbx wangbx[#]dicp.ac.cn" To: CCL Subject: CCL: how to install polyrate? Message-Id: <-30401-051227195201-17111-dzlbczKdcG3nj5kHKhpg/Q . server.ccl.net> X-Original-From: "wbx" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="gb2312" Date: Wed, 28 Dec 2005 08:51:52 +0800 Mime-Version: 1.0 Sent to CCL by: "wbx" [wangbx**dicp.ac.cn] Dear all CCLer£¬ recently i want to use the polyrate9.1 program to compute the reaction rate. but i meet some problems. first, i follow the polyrate manual to install it in the linux. in the second step i did not find the .docdir in the doc directory and .exedir in the exe directory. why? second, in the step 3, when i type set_machine.jc to run under C shell, it shows that there is no this commond. i guess it is because i didn't install fortran. right? third, if i want to install it in the windows, how should i do? i would like to use windows. thanks a lot!! With best regards, sincerely, Bingxing Wang 2005-12-27 email: wangbx_+_dicp.ac.cn