AMBER Archive (2007)

Subject: AMBER: radial distribution by Ptraj

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Wed Nov 28 2007 - 08:35:49 CST

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

Esther B.

       
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