<br><br><div><span class="gmail_quote">2007/3/16, <a href="mailto:spitaleri.andrea@hsr.it">spitaleri.andrea@hsr.it</a> <<a href="mailto:spitaleri.andrea@hsr.it">spitaleri.andrea@hsr.it</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 all,<br>I am struggling with the rdf. I have 7 structural ions in my protein and<br>I'd like to monitor the coordination number around them (ion - protein)<br>during my MD. I have read papers about it and:<br><a href="http://www.gromacs.org/pipermail/gmx-users/2006-November/024911.html">
http://www.gromacs.org/pipermail/gmx-users/2006-November/024911.html</a><br>and<br><a href="http://www.gromacs.org/pipermail/gmx-users/2006-November/024694.html">http://www.gromacs.org/pipermail/gmx-users/2006-November/024694.html
</a><br>and<br><a href="http://www.gromacs.org/pipermail/gmx-users/2003-August/006621.html">http://www.gromacs.org/pipermail/gmx-users/2003-August/006621.html</a><br>and trying to get my conclusions.<br>If I use xmgrace to visualize
rdf.xvg and I integrate from 0 to the<br>first minimum (trapezoid method) I get 6 wich matches the number of<br>rdf_cn.xvg (obtained by the -cn option) and mainly matches the right<br>coordination number around my ion.<br>
However if I try to use the method explained in:<br><a href="http://www.gromacs.org/pipermail/gmx-users/2006-November/024911.html">http://www.gromacs.org/pipermail/gmx-users/2006-November/024911.html</a><br>I get a total different results (
0.013) using V = (12x11x10)nm3 and N=7.<br>What am I doing wrong? Did I misunderstand something (probably yes...)?</blockquote><div><br>Something that may be helpful. <br><br>When integrating, it is for the sphere: 4*PI*integral[/pho*r^{2}*dr]. Therefore, the efficient volume is (10x10x10). this may give you N=6.
<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 for any clarification.<br><br>Regards,<br><br>andrea<br><br>Andrea Spitaleri PhD
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