I don't understand the reply but I will try to do and understand.
Thanking you
Mary
Sent from: Lenovo S90-A
On Jul 26, 2017 9:03 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> If you use the 'normdensity' keyword and specify bulk density (with
> 'density <#>' with units of molecules/Ang^3) the isovalue of 1 will be
> bulk.
>
> Hope this helps,
>
> -Dan
>
> On Wed, Jul 26, 2017 at 10:55 AM, maryvj1985 <maryvj1985.gmail.com> wrote:
> >
> > 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
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > 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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>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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Received on Wed Jul 26 2017 - 12:00:03 PDT
