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