[gmx-users] coordination number of ion: rdf integration

[Qiao Baofu]

2007/3/16, andrea spitaleri <spitaleri.andrea at hsr.it>:
>
> Qiao Baofu wrote:
> >
> > When integrating, it is for the sphere: 4*PI*integral[/pho*r^{2}*dr].
> fine. this is clear, where rho = N/V and N = number of particles (7 ions
> in this case)
> and V is the total Volume.


N is the total number of the atoms to be calculated (the 2nd group in the
input of g_rdf) in your system.


> Therefore, the efficient volume is (10x10x10). this may give you N=6.
>
> why the efficient volume should be 10x10x10? I cannot figure out how did
> you retrieve this conclusion.



When calculatin the rdf, half of the shortest box length is used to
determine how long distance will be calculated. You can see that from the
code of gmx_rdf.c.


Thanks for your help anyway,
>
> Regards
>
> Andrea
>
> --
> -------------------------------
> Andrea Spitaleri PhD
> Dulbecco Telethon Institute
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
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> http://biomolecularnmr.ihsr.dom/
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-- 
Sincerely yours,
**********************************************
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
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