From owner-chemistry@ccl.net Wed Jul 20 08:58:00 2011 From: "Gkourmpis, Thomas Thomas.Gkourmpis.*|*.borealisgroup.com" To: CCL Subject: CCL:G: molecular geometry visualization on GaussView Message-Id: <-45114-110720015749-28867-x/DI9dy06er9F1Z7VOcGag*|*server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 20 Jul 2011 07:57:36 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis : borealisgroup.com] Hyunbok Hi Regarding your first question I would say that the differences you see are just rounding errors due to the way the software handles the geometry. Don't forget than no matter how you do the calculation Gaussian uses internal coordinates (by default at least unless you changed this), thus when these coordinates have to be translated into Cartesians some level of rounding errors for large numbers is expected. Personally I wouldn't be bother with differences of the order of 10-7 Å, as these are well within the uncertainty of the actual calculation. Regarding the second question Gaussian has two different ways of defining atomic bonds. One is via the distance between the two nuclei based on some internal tables that let the program know what to expect and how to interpret atoms at certain distance levels and second via the atomic connectivity defined by the user. If you setup the connectivity in GaussView when you prepare the job and save it to the input file (geom=connectivity) then GaussView will present these bonds as the type of bonds you set up despite the distance between the atoms. With respect to the actual distance the small differences have to do probably with the way the calculation is done. If these differences are really small I would not be alarmed about it. Obviously you know your system best, so I might be mistaken here. Regarding editing the bond from the chk file you can do this using the bond edit tools that GaussView has, although you will probably need to freeze the bond in the distance you require using modredundant coordinates and run a single point calculation to get the new energy. Ideally if the distance difference is only due to rounding errors from the coordinate system the energy differences should be really small. I hope this helps Thomas -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com^^^ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com^^^ccl.net] On Behalf Of Hyunbok Lee mutebeat*gmail.com Sent: Sunday, July 17, 2011 6:09 AM To: Gkourmpis, Thomas Subject: CCL:G: molecular geometry visualization on GaussView Sent to CCL by: "Hyunbok Lee" [mutebeat/./gmail.com] Dear all, I performed geometry optimization of a molecule with Gaussian 09. The output was visualized by GaussView 5.0 and I have two questions about it. 1. Cartesian coordinates varied with output file type, *.out or *.chk. Although the differences are very small, (~10^-7 A orders) it is possible? I think that they must have the exactly same geometry because both 'out' and 'chk' come from the same calculation. (An error was not found in my out file.) 2. How are 'bonds' determined in molecular geometry visualization on GaussView? Atomic bonds in the molecule were also not the same due to the above reason. What is the parameter whether two atoms bond or not? (atomic distance?) And can I modify the bond when I load 'chk' file? Thanks in advance. Hyunbok Leehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis Email and any files transmitted with it are confidential and intended solely for the use of the individual or the entity to whom it is addressed. If you have received this Email by error, please notify the sender and delete the material from any storage device. Borealis extends no warranties and makes no representations as to the accuracy or completeness of the information provided. It is the customer's responsibility to inspect and test our products and technical advice in order to satisfy itself as to the suitability of the products and technical advice for the customer's particular purpose.