[gmx-users] coordination number per residue

Justin Lemkul jalemkul at vt.edu
Sun Feb 24 19:27:44 CET 2013

On 2/24/13 12:53 PM, benrezkallah djamila wrote:
> Hello everybody,
>   I am working on a system consisting of protein-ions in water box. I need
> to calculate the coordination number per residue for my protein, I have
> searched the gmx mailing list, and, I have not find the solution. please,
> can you help me with this, is anybody has a programm to look at the
> coordination number per residue?

I'm surprised there's nothing useful in the archive; there are hundreds of posts 
related to coordination number.  Even a simple Google search turns up a number 
of useful results within the first few links.

There is no automated way to break down coordination number per residue; that's 
your job to supply whatever tool you want to use (probably g_rdf) with a 
suitable reference group.  Luckily, creating such an index group is easy and 
iterative calls to g_rdf (or whatever else) are easily scripted.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list