Hello Tom,
Thank you, but could you pleas clarify what you mean by volume element
around each z value? rdf in amber is measuring average distribution
function in volume elements which are like spherical shells, and so z is
not constant. I saw figure 4 but I couldn't find the method you used to
obtain that figure.
Thanks,
Hadi
On Fri, Sep 14, 2018 at 9:49 PM Tom Kurtzman <simpleliquid.gmail.com> wrote:
> That works well for fluctuating surfaces and very inhomogeneous surfaces.
> You can also do something much simpler as we did (and I'm sure others have
> done) where you do some averaging in a volume element around each z value
> and divide by the bulk density.
>
> See figure 4 in JCP 137, 044101 (2012).
>
> Tom
>
> On Fri, Sep 14, 2018 at 9:36 PM Tom Kurtzman <simpleliquid.gmail.com>
> wrote:
>
> >
> > I always liked what Brooks and Karplus did:
> >
> > Brooks, C. L.; Karplus, M. J. Mol. Biol. 1989, 208, 159
> >
> > Tom
> >
> > On Fri, Sep 14, 2018 at 4:29 PM Hadi Rahmaninejad <ha.rahmaani.gmail.com
> >
> > wrote:
> >
> >> Dear Amber Users,
> >>
> >> I am using "rdf" to calculate the density of water around an especial
> >> atom.
> >> As you know, it is "radial" and so it is calculating radial distribution
> >> function which is an average on x,y and z dimension. However, because I
> am
> >> interested in calculating density of water on a surface as a function of
> >> distance to it (say z dimension), I have to obtain rdf in just one
> >> dimension(z). I highly appreciate any help if any of you who know a way
> to
> >> do it,
> >>
> >> Thank you in advance,
> >> Hadi
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> >>
> >
> >
> > --
> > ************************************************
> > Tom Kurtzman, Ph.D.
> > Associate Professor
> > Department of Chemistry
> > Lehman College, CUNY
> > 250 Bedford Park Blvd. West
> > Bronx, New York 10468
> > 718-960-8832
> > http://www.lehman.edu/faculty/tkurtzman/
> > <http://www.lehman.edu/faculty/tkurtzman/index.html>
> > ************************************************
> >
>
>
> --
> ************************************************
> Tom Kurtzman, Ph.D.
> Associate Professor
> Department of Chemistry
> Lehman College, CUNY
> 250 Bedford Park Blvd. West
> Bronx, New York 10468
> 718-960-8832
> http://www.lehman.edu/faculty/tkurtzman/
> <http://www.lehman.edu/faculty/tkurtzman/index.html>
> ************************************************
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Received on Sun Sep 16 2018 - 18:00:02 PDT
