<br><div><span class="gmail_quote">2007/3/26, syma <<a href="mailto:syma.khalid@bioch.ox.ac.uk">syma.khalid@bioch.ox.ac.uk</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br><br>I am attempting to calculate the rdfs of the various components of my system<br>wrt to DNA phosphate groups. However, I was wondering how I can normalise so<br>I can compare the various rdfs? Ideally I would like to have the g(r)
<br>normalised in the range 0-1.</blockquote><div><br>In fact, there is not flag to control the normalised range. But you can take the range, 0-1, of rdf.xvg. <br>The caluclated neighbour number at dr is normalised by the ideal case at dr (average density times the volume at dr) . For the ideal condition, the density at the short range is the same as the average density. Therefore, ......
<br> </div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">I have read on the user list that I should get three columns in the *.xvg<br>
output, the distance, the normalised data and the raw data, I only get two<br>columns.</blockquote><div><br>The default rdf.xvg will give only two columns, r and g(r)<br> </div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks in advance for any help.<br><br>-Syma<br><br>***************************************************<br><br>Dr Syma Khalid<br>Department of Biochemistry,<br>University of Oxford<br>South Parks Road,<br>Oxford<br>OX1 3QU
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