The 'center2' keyword was added (along with some others) in update 12 to
AmberTools 13: http://ambermd.org/bugfixesat.html
It works like 'center1' but for the second mask.
-Dan
On Mon, Mar 17, 2014 at 5:16 PM, Jio M <jiomm.yahoo.com> wrote:
> Hi Daniel
>
> >>to calculate using the center of mass of atoms in the
> >>second mask you would need to specify 'center2'
>
>
> I think the manual miss this thing (center2), it just says one can use
> center1 (for mask1?) or one can do for both?
>
> thanks
>
>
>
>
> On Monday, March 17, 2014 7:46 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> 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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> _______________________________________________
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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 - 17:00:03 PDT
