CCL:G: molecular geometry visualization on GaussView
- From: "Gkourmpis, Thomas"
- Subject: CCL:G: molecular geometry visualization on GaussView
- Date: Wed, 20 Jul 2011 07:57:36 +0200
Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis :
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
> 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]
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.
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