ptraj rdf output

From: Prabal Maiti <>
Date: Fri 20 Sep 2002 16:24:35 -0700 (PDT)

Dear Amber users:
I tried to calculate radial distribution function between water and Na+
and Na+ and DNA (this may not be so well defined). For each of this I
get two output, one with _standard extension and another with volume
Both has two columns of output apart from the 1st column with
distance(bin). Can someone explain me what are these numbers in these 2
columns. Also I would have exptected the g(r) eventually goes to 1 if it
is proporely normalized. But the numbers in 2nd and 3rd columns are
different than that.

Can someome please explain me these numbers,

>From the code I see that _standarrd is Allen & Tildesley style histogram
    fprintf(outFile, "%8.3f %8.3f %8.3f\n",
            ((double) i + 0.5) * radialInfo->spacing,
            hist, occupancy);
In this case hist should apporach 1 at large distance which is not
the case. it ranges from 0.8 to 5. What
exactly is the occupnacy means. IS it the number of molecules within
a given distnace?

Here is my ptraj input
trajin md_prod_final.trj.gz 590 690 1
radial rdf_DNA-WAT 0.05 8.0 :WAT :1-196
radial rdf_DNA-NA 0.05 8.0 :Na+ :1-196


Prabal K Maiti                   
Beckman Institute (139-74)             
California Institute of Technology         Tel:626-395-8151 (O)
400 South Wilson Avenue                       :626-744-1363 (H)                    
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Received on Fri Sep 20 2002 - 16:24:35 PDT
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