AMBER Archive (2009)

Subject: [AMBER] Is the integral value from RDF the same as average number of atoms?

From: Gustaf Olsson ( ((
Date: Wed Nov 18 2009 - 15:56:31 CST

In the output file that is produced by running a radial analysis using PTRAJ you find three columns with values. From what I have gathered the first column is the r-value (bin spaceing/ distnace), I don't know the correct term, sorry. The second column is the g(r) value, the odds of finding a solven atom at this distance from the analysed solute atom. Correct me if I'm wrong.

Now to the question, the values in the third column. The way I had this explained to me is that these values are integral values of g(r) up to the given r-value and that this integral value is equal to the average number of solvent atoms at this distance around the solute atoms analysed in the system. Is this correct? If not, does anyone know how these values are calculated?

I appologise for my English and are greatfull for any feedback on this subject.

Best regards
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