[AMBER] number of ions (integral) too much in RDF plot

From: Jio M <jiomm.yahoo.com>
Date: Mon, 7 Apr 2014 19:33:01 -0700 (PDT)

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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Received on Mon Apr 07 2014 - 20:00:02 PDT
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