Dear Daniel
>> the only thing I can think of is maybe you are using a trajectory with
periodic boundary conditions that has been rotated e.g. via an RMS fit,
which would cause imaging artifacts.
Yes you are right it was my mistake as I was analysing a RMS fitted traj.
Now I used nonimaged traj and allowed RDF to image by default and it works
fine.
Finally one thing, as now I am using a nonimaged traj with 'reference' , so
'radial' will consider the imaged or nonimaged referenced frame?
reference test.nc 10
trajin test.nc 10 10
radial rdf.dat 0.1 10 :WAT (:484,441,382,213>.100&.Cl-) volume
thanks
JIomm
On Fri, Apr 11, 2014 at 7:33 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I can't reproduce the behavior you are seeing. When I generate similar
> plots, I get a nice overlap between single RDFs and averaged RDF (see
> attached). I don't think this would be an averaging bug anyway - the
> fact that you get population at the lower distance bins means the
> underlying histogram had some data there. If you are absolutely
> certain none of those distances should be shorter than 2 Ang., the
> only thing I can think of is maybe you are using a trajectory with
> periodic boundary conditions that has been rotated e.g. via an RMS
> fit, which would cause imaging artifacts. What happens if you specify
> 'noimage' to the 'radial' command?
>
> -Dan
>
>
> On Thu, Apr 10, 2014 at 4:08 PM, newamber list <newamberlist.gmail.com>
> wrote:
> > Hi All
> >
> > I am getting some unusual rdf starting at zero distances of ion which is
> > wrong and I think could be an averaging problem. Here is a single frame
> > command. (and plot attached)
> >
> > reference test.nc 10
> >
> > trajin test.nc 10 10
> >
> > radial rdf.dat 0.1 10 :WAT (:484,441,382,213>.100&.Cl-) volume
> >
> >
> > Actually this should give me an average RDF for all the Cl- ions which
> are
> > 100 Ang. distance far from COM of :484,441,382,213. There should be no
> RDF
> > values below distance 2 or so. But when I test the same with some
> > individual Cl- ions (>100 Angs) with masks like this for individual
> ion:WAT
> > :3740, I don't get any such RDF near distance zero which is correct.
> >
> >
> > So I think there is some averaging bug?
> >
> >
> > Thanks
> >
> > Jiomm
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> 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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Received on Fri Apr 11 2014 - 12:30:02 PDT
