It does some normalization but the problem is that the output has a lot
of noise. It looks as if it is not handling it correctly... From the
same trajectory Cl- around WAT ends up with a smooth rdf curve but when
I do
radial 10c1Na4d 0.05 16 0.05 16 :Cl- :23&!(.CA,C,N,O,H) volume or
radial 10c1Na4d 0.05 16 0.05 16 :Cl- :56-74 volume
to see the distribution of Cl- around specific regions of the protein,
the plot looks pretty scattered.
Any suggestions?
Thanks,
Nihal
On 12/12/2012 12:50 PM, Daniel Roe wrote:
> Hi,
>
> On Sun, Dec 9, 2012 at 9:08 PM, Nihal Korkmaz <enihalkorkmaz.gmail.com> wrote:
>> However I need the /volume vs radius/ data to be able to obtain the
>> actual g(r). Any suggestions will be greatly appreciated.
> Hi,
>
> As far as I know ptraj should already normalize g(r) properly based on
> the particle density (from density <density> keyword or determined
> from average volume) and volume of each bin. Is this not happening
> correctly in your case?
>
> -Dan
>
>
>> Thanks,
>> Nihal
>>
>> --
>> Nihal Korkmaz
>>
>> Research & Teaching Assistant
>> UW-Madison, Biophysics Program
>> Member of Qiang Cui Lab
>> 1101 University Ave, Rm. 8359
>> Madison, WI 53706
>> Phone: 608-265-3644,
>> Email: korkmaz.wisc.edu
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
E. Nihal Korkmaz
Research & Teaching Assistant
UW-Madison, Biophysics Program
Member of Qiang Cui Lab
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone: 608-265-3644,
Email: korkmaz.wisc.edu
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Received on Tue Dec 25 2012 - 02:00:02 PST
