AMBER Archive (2009)

Subject: [AMBER] radial distribution function

From: Dharmik Meghana shankar (
Date: Sat Aug 01 2009 - 00:33:58 CDT

  I am the beginner for amber md software. I have calculated RDF using
ptraj command .I have got 3 different files ,each having 3 different
columns.I have been told that first column is for distance and second is
for RDF .But what is the meaning of third column?
   I plotted all the 3 files using 1 and 2nd column to see the difference
among them . Surprisingly .there was no difference in nature except
magnitude of variations. So it has become difficult to understand the
physical significance of standard , carnal, volume RDF as well as 3
columns in each file.
   Can anyone help me to sort out my problem?


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