Hi,
You can use the 'rdf' command in cpptraj to calculate a radial
distribution function of ions from the DNA. For the normalization to
make sense (i.e. for a value of 1 to be "bulk") you'll have to adjust
the reference density from its default of 0.033456 mols/Ang^3 (which
corresponds to 1 g/mL, the reference density for water) to something
appropriate to your ion concentration. You can get the raw counts with
the 'rawrdf' keyword, but keep in mind those are the actual raw
counts. they are not averaged over frames.
Note that as of version 6.11.0 there is a CUDA version of the RDF
calculation in cpptraj, which can be significantly faster.
-Dan
On Tue, Oct 18, 2022 at 6:27 AM angad sharma via AMBER
<amber.ambermd.org> wrote:
>
> Dear amber users,
> I want to calculate the number of ions with respect to distance from the
> DNA. I have a system consisting of many ions, I want a plot of,* ion
> concentration vs distance* from dna.
> Is there any way to do this in cpptraj ? , where we can increment the
> distance from DNA in step wise say 1Å and corresponding this distance from
> DNA we can get the number ions present and this must continue till bulk
> reaches over the entire trajectory.
>
> *-------------------------------------------------*
> *With Regards*
> *Angad Sharma*
>
> *Research Scholar*
> *School of Computational & Integrative Sciences*
>
> *Jawaharlal Nehru University*
> *New Delhi 110067, (INDIA)*
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Received on Wed Oct 19 2022 - 12:00:04 PDT
