Hi Andrea,

I have a program to look at the coordination number and other things
for cations and oxygen ligands. Maybe that could help... If you want,
I can send it to you.

Best,

Tsjerk

On 3/16/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
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...)?

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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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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