I may be be missing some small point here : i want to calculate RDF of
Na+ ions around a nucleic acid backbone (which is a COUNT of the particle
as a function of distance) , i have used the following command :
radial rdf_na_bin_50_2.dat 0.2 10 :2.P,OP?,O?P .Na+ volume center1
radial rdf_na_bin_50_3.dat 0.2 10 :3.P,OP?,O?P .Na+ volume center1
radial rdf_na_bin_50_4.dat 0.2 10 :4.P,OP?,O?P .Na+ volume center1
Mask 1 has 3 atoms(in all cases); mask 2 i.e. total number of sodium ions
in my system is 17. Total system volume is : 205471.233980 Ang^3 . But on
the RDF plot, the value of y axis, is going till 25 which can't be possible
if the max ions is 17. I am confused about the normalization process?
Command used by me seems to be on a wrong track..surely..Can you please
suggest me a way as to how RDF of ions can be calculated using cpptraj
Thanks
Asmita
On Mon, Feb 4, 2013 at 10:07 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Feb 04, 2013, Asmita Gupta wrote:
> >
> > If i don't use the volume keyword, i have to mention some value using
> the
> > density keyword, as RDF has to be calculated for Na+; not for waters. How
> > to calculate this value...is it by using the regular
> (Density=mass/volume)
> > method??
>
> "density" in this context means number density, not mass density.
>
> ...dac
>
>
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Received on Tue Feb 05 2013 - 09:30:02 PST
