Hi, what version of cpptraj are you using? Bugfix 10 in particular
fixed the normalization in the 'intrdf' plot.
-Dan
On Mon, Apr 7, 2014 at 8:33 PM, Jio M <jiomm.yahoo.com> wrote:
> Hi All
>
> I am using radial function to plot RDF of K ions around center of mass of O atoms. I have around 2100 K+ ions and octahedron box (149.1524703 149.1524703 149.1524703)
>
> radial temp.dat 0.1 95 :K+ :1-389.O volume intrdf temp_int.dat
>
>
> I should get almost exact number of K+ in my box after integrating. I have following queries:
>
> 1) The integral values goes upto 1076448 which is too high. Also what should be max bin size in this case to get expected number of ions? I have chosen 95 because the RDF plot shows fall at 95 Angstroms (also it confuses me as box size dimension goes upto 149 Angstroms and I should see a fall around 140 or so)
>
> 2) Also I have one more query regarding 'volume' key word used here. In manual it says
>
> ".. if the volume keyword is specified the density is determined from the average volume of the system over all Frames."
>
> So in this case does this mean density is a 'number density' which is = (total number of K+ ions in a box / avg. volume of box)
>
> 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
