[gmx-users] atomic radius

[Oliver Beckstein]

Hi,
> David:
>       thank´s for replay. The center of my problem is RDF takes account the
> distance between the spheres (atoms) or the distance between centers of the
> spheres.

The rdf is calculated for the centers of atoms. There isn't a single
'atomic radius' but it rather depends on the circumstances. For ions in
water I found that the first peak g1 in the rdf g(X,Y) corresponds very
well to the Pauling radii: with R(Na+) = 0.095nm, R(Cl-) = 0.181 nm, eg
g1(Na+,Cl-) = 0.095 + 0.181 = 0.276 nm or g1(Na+,Na+) = 0.095 + 0.095 = 
0.19 nm. 

<late night rambling> In general, speaking of an 'atomic radius' or
'atomic volume' does not make a lot of sense as atoms are not hard
billiard balls with a well defined surface but rather diffuse and squidgy.
Though when we insist on treating these systems classically (instead of
quantum mechanically) we probably need these classical concepts... 
</late night rambling>

Oliver 

> So, I try to analyze the results using atomic radius.
>                                                       Thanks.
> 
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-- 
Oliver Beckstein * oliver at biop.ox.ac.uk
 http://sansom.biop.ox.ac.uk/oliver/