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

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Mar 16 08:54:40 CET 2007

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.



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)
> ********************************************************************
> Sostieni la ricerca del San Raffaele con il 5permille!
> 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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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

More information about the gromacs.org_gmx-users mailing list