AMBER: radial distribution by Ptraj

From: Esther Brugger <>
Date: Wed, 28 Nov 2007 06:35:49 -0800 (PST)

Dear Amber Users,
  I have some questions about the output files by using Radial command in Ptraj.
  I calculate the radial distribution function(RDF) between two ions in the solution. I used "radial" command in Ptraj. Then I plot the first and second columns in the file_standard.xmgr to get RDF. I am just wondering why the maxium of RDF value goes to 4 instead of 1. In the Amber manual, it shows: "root-filename_standard.xmgr" (which uses the more traditional RDF with a density input by the user). Do you think it is because of the density? I just don't know how to solve this problem. Any suggestions are very welcome. Thank you very much for your help!
  Best wishes,

Esther B.

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Received on Sun Dec 02 2007 - 06:07:06 PST
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