[gmx-users] coordination number of ion: rdf integration

[Tsjerk Wassenaar]

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, spitaleri.andrea at hsr.it <spitaleri.andrea at hsr.it> 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
F: +31-30-2537623