Charges at atoms have to be summed using q/r for each point on the
isosurface. So the values at the surface are different from the values at
the atoms (smaller values). For example:
$ load c6h6.smol
$ isosurface molecular map mep
isosurface1 created with cutoff=0.0; number of isosurfaces = 1
isosurface full data range -0.2244125 to 0.079268284 with color scheme
spanning -0.1 to 0.1
$ print {1.1}.partialcharge.all
0.23929211
-0.23929211
-0.23929211
-0.23929211
-0.23929211
-0.23929211
-0.23929211
0.23929211
0.23929211
0.23929211
0.23929211
0.23929211
The atom charges range from -0.24 to 0.24, but the surface charges range
from -0.22 to 0.08. I think that's because the center of the ring gets a
substantial contribution from each of the 6 carbons and almost nothing from
the hydrogens (which are positive).
This is interesting -- using ESP charges instead of Mulliken charges from
that same file:
$ load c6h6.smol filter "ESPCHARGES"
$ isosurface molecular map mep
isosurface1 created with cutoff=0.0; number of isosurfaces = 1
isosurface full data range -0.13211405 to 0.046650272 with color scheme
spanning -0.1 to 0.1
$ print {1.1}.partialcharge.all
0.1415481
-0.14394641
-0.14394641
-0.1393379
-0.1393379
-0.1393379
-0.1393379
0.1405371
0.1405371
0.1405371
0.1405371
0.1415481
The ESP charges are less polarized.
Right now, Jmol 11 ignores any charges on atoms more than 8 angstroms away
from a given point, which doesn't mean much for small models. More
significantly, though, Jmol right now creates a "field" of potential around
the model and then uses that to map the surface. This isn't really necessary
-- you can just pick a surface point and sum all the q/d from all the atoms.
I've just rewritten the code for 12.0 and 12.1 to do that and will get that
in the next release.
Bob
On Mon, Sep 13, 2010 at 9:10 PM, Otis Rothenberger <osrot...@chemagic.com>wrote:
>
> The data range 0.41223556 to 0.6573585 seems to vary with the partial
> charges, but seems unrelated to the actual partial charges. The result
> below is for "range all" on the allyl cation and benzyl cation,
> respectively. In the snippet above, I was just trying out values other
> than "range all."
>
> full data range 0.41223556 to 0.6573585 with color scheme spanning
> 0.41223556 to 0.6573585
>
> data range 0.28645405 to 0.5315478 with color scheme spanning 0.28645405
> to 0.5315478
>
> All of this is part of my attempt to make Spartan charge numbers work
> well with Accelrys charge numbers. Can you give me any information on
> the origin of these numbers - calculated from my charges???
>
> Otis
>
> PS
> Thanks for the feedback on the array question.
>
> --
> Otis Rothenberger
> chemagic.com
>
>
>
>
>
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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
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