Hi,
On Mon, Mar 17, 2014 at 1:18 PM, Jio M <jiomm.yahoo.com> wrote:
> 1) Is this making spherical shells, (n1 to n) depending on 'dr' chosen
> (here 0.1), around each N atom and finally averaging each shell
> coressponding to each N (average all n1 for all Ns, average of n2 for all
> Ns and so on....)?
>
Yes; with the volume keyword the expected density is calculated from the
average box size and number of distances calculated (otherwise you can
specify the expected density).
>
> 2) Also does the spherical shell cross the original box as well? Which I
> think yes as I have some N atoms at one corner of the box so the rdf should
> cross the boundry.
>
Yes; imaging is performed unless 'noimage' is specified.
> 3) Is there any function any one knows that helps for linear molecules.
> eg. if I use
> radial rdf_Cl 0.1 10 :Cl- :1-339 volume (Note not considering N atoms in
> mask2)
> then it will consider center of mass of 1-339 resdiues and make spherical
> shells around center of mass, which would not be a good representation. So
> is there something cylindrical distribution function in cpptraj?
>
There is no cylindrical distribution function at this time. Note the
command you specified actually calculates the average RDF over every atom
in the second mask; to calculate using the center of mass of atoms in the
second mask you would need to specify 'center2'.
Hope this helps,
-Dan
>
>
> thanks
> Jiom
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Mar 17 2014 - 13:00:02 PDT
