Date: Fri, 11 Apr 2014 12:33:49 -0600
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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-- ------------------------- 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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(image/jpeg attachment: Wat-Cl.jpg)
