Sorry for the long delay in replying - this got lost in my inbox over
the holidays:
On Tue, Dec 25, 2012 at 2:56 AM, Nihal Korkmaz <enihalkorkmaz.gmail.com> wrote:
> 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
The noise may just be the result of having less data to work with.
What I mean is, when you do something like:
radial :Cl- :WAT
you are getting the RDF of every Cl- to every WAT, so there's a lot of
data in there since :WAT makes up a very large fraction of your
system. However, when you do something like:
radial :23&!(.CA,C,N,O,H)
that's the RDF of Cl- to one specific residue. Even if Cl- tends to be
there a lot, that's still significantly less data than Cl- to every
WAT residue. Depending on how many frames you're using, it wouldn't
surprise me that this comes out a little noisy.
Hope this was helpful, sorry again that it's so late.
-Dan
>
> 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
> _______________________________________________
> AMBER mailing list
> 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) 585-9119 (Fax)
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Received on Mon Jan 21 2013 - 10:00:03 PST
