2007/3/16, [EMAIL PROTECTED] <[EMAIL PROTECTED]>:
Hi all,
I am struggling with the rdf. I have 7 structural ions in my protein and
I'd like to monitor the coordination number around them (ion - protein)
during my MD. I have read papers about it and:
http://www.gromacs.org/pipermail/gmx-users/2006-November/024911.html
and
http://www.gromacs.org/pipermail/gmx-users/2006-November/024694.html
and
http://www.gromacs.org/pipermail/gmx-users/2003-August/006621.html
and trying to get my conclusions.
If I use xmgrace to visualize rdf.xvg and I integrate from 0 to the
first minimum (trapezoid method) I get 6 wich matches the number of
rdf_cn.xvg (obtained by the -cn option) and mainly matches the right
coordination number around my ion.
However if I try to use the method explained in:
http://www.gromacs.org/pipermail/gmx-users/2006-November/024911.html
I get a total different results (0.013) using V = (12x11x10)nm3 and N=7.
What am I doing wrong? Did I misunderstand something (probably yes...)?
Something that may be helpful.
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.
Thanks for any clarification.
Regards,
andrea
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
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Sincerely yours,
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Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
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