CCL:G: molecular geometry visualization on GaussView

 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
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