Thank you very much for the reply.
I will try this option.
Are you familiar with grid analysis of Na+ ions in a simulation.
I have done a grid analysis. But I don't understand what range if isovalue should I specify. Like in the case of water analysis you say 2 times bulk water density.
My system has 0.3 M NaCl added.
Mary
Sent from: Lenovo S90-A
On Jul 26, 2017 7:16 PM, George Giambasu <giambasu.gmail.com> wrote:
>
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Dr. George M. Giambasu
> Rutgers, The State University of New Jersey
> 174 Frelinghuysen Road, Room 308E Piscataway,
> NJ 08854, USA giambasu.rutgers.edu
> www.rci.rutgers.edu/~giambasu
> Office: 1-848-445-5223 Cell: 1-612-644-8285
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
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Received on Wed Jul 26 2017 - 08:00:03 PDT
