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)
********************************************************************
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 [EMAIL PROTECTED] o vai sul sito
www.5xmille.org
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
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
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
