Hi,
You have a different average density because your second mask has a
different number of atoms, so the number of things you expect in a
volume slice will necessarily be different (you can see this by the
vastly different number of 'distances' reported). Each plot is
measuring different things. The first is calculating the RDF from
every water atom to all chloride ions within 50 Ang. of residues 484
and 441. The second is calculating the RDF from every water to a
single chloride ion. They may be qualitatively similar, but you'll
have better statistics with the first one (and probably even better if
you just make the second mask ':Cl-').
-Dan
On Tue, Apr 8, 2014 at 8:12 PM, Jio M <jiomm.yahoo.com> wrote:
> Hi All
>
> I have generated two RDF plots with different masks (for a single frame) and the output shows that both are using different avg. density for rdf calculation.
> Please correct me if I am wrong how RDF is calculated here:
>
> RDF= density*[ Vol(R+dR) - Vol(R)]
> Avg. density = (#mask1*#mask2)/avg. volume.
>
> I am just wondering in this case how we can compare both plots because avg. density used is different in both the cases? I have pasted here both commands with main outputs.
>
> 1) radial dat1 0.1 10 :WAT (:484,441>.50&:Cl-) volume
>
> ACTION OUTPUT:
> RADIAL: 1 frames, 502721 distances.
> # in mask1= 230148, # in mask2 = 1015, # in common = 0
> Average volume is 2555636.055524 Ang^3.
> Average density is 91.405902 distances / Ang^3.
>
>
> 2) radial dat2 0.1 10 :WAT :514 volume # (514 is an Cl- ion)
>
> ACTION OUTPUT:
> RADIAL: 1 frames, 396 distances.
> # in mask1= 230148, # in mask2 = 1, # in common = 0
> Average volume is 2555636.055524 Ang^3.
> Average density is 0.090055 distances / Ang^3.
>
> 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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Received on Wed Apr 09 2014 - 07:30:04 PDT
