Sure - you can ask cpptraj to compute an RDF (radial distribution
function) between (i) mask and (ii) Na+. Next, integrate that RDF up to
the specified distance ((using xmgrace for example)) to get the desired
ion count.
As for the second question, ions should be imaged too. If you have
doubts output the imaged trajectory and visualize it in vmd.
George
Mary Varughese wrote:
> Hi
>
> I have some ions related doubts
>
> *Is it possible to count Na+ ions with in the 3.6 A distance of atoms
> specified with in a mask?
>
> *In the below command does ions also get imaged along with water (I want to
> do grid analysis of Na+ ions)
>
> center :1-12 mass origin
> image origin center familiar
> center :1-24 mass origin
> image origin center familiar
>
>
> Thanking you
>
>
> mary
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Dr. George M. Giambasu
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NJ 08854, USA giambasu.rutgers.edu
www.rci.rutgers.edu/~giambasu
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Received on Wed Jul 26 2017 - 07:00:03 PDT
