On Wed, Sep 28, 2011 at 2:55 PM, jenheta da silva <[email protected]> wrote:
> Hello Bob and Jmol community,
>
> I would like to report a (minor) bug related to the original topic of this
> post.
> If one uses the model kit to add, let's say, a double bond to a molecule,
> the reported
> data from a UFF minimization will show the wrong number of atoms.
>
I think what you mean is "the wrong numbers for the atoms" not "the wrong
number of atoms" -- there are still the proper number of atoms.
In Jmol after you delete atoms, you will see gaps in the atom numbering. The
numbers should be thought of as labels that identify
atoms based on "atomno" so, for example,
select atomno=17
will work just fine in your case.
So it's not a bug.
Bob Hanson
> For instance, using benzene as a test case, adding 3 doubles to the ring
> and
> performing a minimization (with zero steps) will result in :
>
> logLevel = 6
> Initial E = 337.322 kJ/mol criterion = 0.001000 max steps = 0
> Universal Force Field -- Rappe, A. K., et. al.; J. Am. Chem. Soc. (1992)
> 114(25) p. 10024-10035
> Jmol Minimization Version 12.1.51_dev 2011-06-29 11:15
>
> S T E E P E S T D E S C E N T
>
> ATOM X Y Z TYPE GRADX GRADY GRADZ
> ---------BONDED ATOMS--------
>
> -----------------------------------------------------------------------------------------------
> 1 3.885 17.722 24.599 C_R 0.000 0.000 0.000 2 6
> 17
> 2 3.499 18.381 25.768 C_R 0.000 0.000 0.000 1
> 3 15
> 3 2.560 19.410 25.710 C_R 0.000 0.000 0.000 2
> 4 16
> 4 1.986 19.767 24.490 C_R 0.000 0.000 0.000 3
> 5 13
> 5 2.363 19.102 23.319 C_R 0.000 0.000 0.000 4 6
> 14
> 6 3.300 18.061 23.365 C_R 0.000 0.000 0.000 1 5
> 7
> 7 3.703 17.403 22.103 H_ 0.000 0.000 0.000 6
> 13 1.237 20.571 24.449 H_ 0.000 0.000 0.000 4
> 14 1.921 19.398 22.356 H_ 0.000 0.000 0.000 5
> 15 3.936 18.088 26.734 H_ 0.000 0.000 0.000 2
> 16 2.271 19.942 26.629 H_ 0.000 0.000 0.000 3
> 17 4.651 16.933 24.643 H_ 0.000 0.000 0.000 1
>
> Apparently, changing a bond affects the total number of atoms.
> Unfortunately, this bug is also being propagated into the reported bond,
> angle, torsion, out-of-plane data of the log data as well.
>
> Jen
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2dcopy1
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