# Re: [AMBER] rdf in one dimmension

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 17 Sep 2018 07:22:57 -0400

Hi,

Try looking at the ‘density’ command, which can calculate density along a
single axis.

-Dan

wrote:

> 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,
>
> 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,
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> 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>
> > ************************************************
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Sep 17 2018 - 04:30:02 PDT
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