From owner-chemistry@ccl.net Wed Sep 3 08:21:01 2008 From: "Mr shabbir shabbir^^nenu.edu.cn" To: CCL Subject: CCL:G: NBO ercentage bond order characters Message-Id: <-37703-080903081848-25360-baChLHvtvLK/L7BS2f6aEw|server.ccl.net> X-Original-From: "Mr shabbir" Date: Wed, 3 Sep 2008 08:18:44 -0400 Sent to CCL by: "Mr shabbir" [shabbir%%nenu.edu.cn] Dear all I want to calculate the Natural Bond Order: (total/covalent/ionic).I am using following keywords in gaussian03 route section pop=nboread gfinput iop(6/7=3) below the molecule specification line $nbo bndidx $end As a result I get Wiberg bond order and some other information but not the (total/covalent/ionic) orders. So any keyword that can give me percentage character of the bond. I would be highly grateful if some one tells me about it. We have also NBO 5 versions but that also I cant use. Regards Mr.Shabbir shabbir(a)nenu.edu.cn From owner-chemistry@ccl.net Wed Sep 3 09:11:00 2008 From: "Roberto Olivares-Amaya olivares(a)fas.harvard.edu" To: CCL Subject: CCL:G: Gaussian cube file in molekel Message-Id: <-37704-080902155836-28607-ATFRtM6U9SIKoNCZnEShYQ*_*server.ccl.net> X-Original-From: "Roberto Olivares-Amaya" Content-Type: multipart/alternative; boundary="----=_Part_456_15185885.1220381330082" Date: Tue, 2 Sep 2008 14:48:50 -0400 MIME-Version: 1.0 Sent to CCL by: "Roberto Olivares-Amaya" [olivares%fas.harvard.edu] ------=_Part_456_15185885.1220381330082 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi I'm trying to read a Gaussian cube file in molekel. In one of them, I have the electron ground state density and in the other, I have the HOMO. However, I can only visualize the molecule and not the surface around it. Does anyone have a quick guide to molekel where this can be covered? Also, I can get a molden file. Is that, in general, easier in molekel? Thanks for the help! ------=_Part_456_15185885.1220381330082 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi
I'm trying to read a Gaussian cube file in molekel. In one of them, I have the electron ground state density and in the other, I have the HOMO. However, I can only visualize the molecule and not the surface around it. Does anyone have a quick guide to molekel where this can be covered?
Also, I can get a molden file. Is that, in general, easier in molekel?

Thanks for the help!
------=_Part_456_15185885.1220381330082-- From owner-chemistry@ccl.net Wed Sep 3 12:16:01 2008 From: "Grigoriy Zhurko reg_zhurko(0)chemcraftprog.com" To: CCL Subject: CCL:G: Easy convergence of Diffuse functions Message-Id: <-37705-080903121451-630-t1IUmQLoq/k3C7ABacrNqQ#,#server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 3 Sep 2008 20:13:49 -0700 MIME-Version: 1.0 Sent to CCL by: Grigoriy Zhurko [reg_zhurko]=[chemcraftprog.com] Hello, > Sent to CCL by: "David Hose" [anthrax_brothers:hotmail.com] > Hi Ya, > The addition of diffuse functions to the basis set is well known to cause problems with the > convergence of the calculations. The most common fix is to use a better quality guess for the > initial wavefunction in the second calculation. > Assuming that you are using Gaussian, the simplest way is to optimise the geometry of the > molecule at say HF/6-31G* level of theory. Duplicate the resulting checkpoint point file. Then set > up the second (single point?) calculation, at say the HF/6-31+G* level of theory, with > Guess=Checkpoint included in the route selection, ensuring that the %chk points to the previous > calculation checkpoint file. On occasions, it is better if the previous calculation included a > frequency calculation as the superior hessian allows the subsequent calculation converge more > easily. > There are some other approaches that can be used for difficult cases, but the above method > typically works. Can this method be used with Gamess? > Regards, > Dave. Grigoriy Zhurko. From owner-chemistry@ccl.net Wed Sep 3 15:31:00 2008 From: "David Hose Anthrax_brothers-.-hotmail.com" To: CCL Subject: CCL:G: Easy convergence of Diffuse functions Message-Id: <-37706-080903153027-16863-p6VSVvLT90GC6USJeuFTGg|server.ccl.net> X-Original-From: "David Hose" Date: Wed, 3 Sep 2008 15:30:23 -0400 Sent to CCL by: "David Hose" [Anthrax_brothers:_:hotmail.com] Grigoriy, As I've never used GAMESS I can't answer that question. May be one of the GAMESS users on the list can? What I would say is if the wavefunction from the previous calculation can be passed on to the one that uses the larger basis set, then yes, this method should work. > From my previous experience with Spartan'04, I know that if the output file from the first calculation is used as the starting point of the second, the wavefunction information is passed on as the guess for the next calculation. Just transferring the atomic coordinates (i.e. via say a pdb file) wont work. I can't imagine that GAMESS wouldn't do something similar, I just don't know the mechanism of doing it. -- Regards, Dave. ------ Sent to CCL by: Grigoriy Zhurko [reg_zhurko]=[chemcraftprog.com] Hello, > Sent to CCL by: "David Hose" [anthrax_brothers:hotmail.com] > Hi Ya, > The addition of diffuse functions to the basis set is well known to cause problems with the > convergence of the calculations. The most common fix is to use a better quality guess for the > initial wavefunction in the second calculation. > Assuming that you are using Gaussian, the simplest way is to optimise the geometry of the > molecule at say HF/6-31G* level of theory. Duplicate the resulting checkpoint point file. Then set > up the second (single point?) calculation, at say the HF/6-31+G* level of theory, with > Guess=Checkpoint included in the route selection, ensuring that the %chk points to the previous > calculation checkpoint file. On occasions, it is better if the previous calculation included a > frequency calculation as the superior hessian allows the subsequent calculation converge more > easily. > There are some other approaches that can be used for difficult cases, but the above method > typically works. Can this method be used with Gamess? > Regards, > Dave. Grigoriy Zhurko. From owner-chemistry@ccl.net Wed Sep 3 22:21:01 2008 From: "naser eltaher Eltayeb nasertaha90~!~yahoo.co.uk" To: CCL Subject: CCL: Online course in computational chemistry Message-Id: <-37707-080903221026-25303-cWVE4cEN9j8JCtwmpdnkKw_-_server.ccl.net> X-Original-From: "naser eltaher Eltayeb" Date: Wed, 3 Sep 2008 22:10:22 -0400 Sent to CCL by: "naser eltaher Eltayeb" [nasertaha90/./yahoo.co.uk] Hi All Is there any institute of University offer online or distance learing course in couputational chemistry? Naser Eltaher Eltayeb