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

[spitaleri.andrea at hsr.it]

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)



********************************************************************
Sostieni la ricerca del San Raffaele con il 5permille!
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei
redditi ("Ricerca sanitaria") 
il codice fiscale della 
Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Se vuoi saperne di piu' scrivi a 5permille at hsr.it o vai sul sito
www.5xmille.org
-------------- next part --------------
A non-text attachment was scrubbed...
Name: spitaleri.andrea.vcf
Type: text/x-vcard
Size: 241 bytes
Desc: Card for <spitaleri.andrea at hsr.it>
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070316/42b8c731/attachment.vcf>