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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> ************************************************
> 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 Fri Sep 14 2018 - 19:00:02 PDT
