[gmx-users] what is a "central structure"

[Mark Abraham]

On 30/12/2011 7:49 AM, Yun Shi wrote:
> Hello everyone,
>
> I am using g_cluster with gromos method to do some clustering, and by 
> default, -cl writes the central structure of each cluster obtained.
>
> So I wonder what 'central structure' mean? Assuming that I cluster 
> based on RMSD values relative to the starting conformation, 

With GROMACS, you can only cluster based on the matrix of 
inter-structure RMSD. Clustering based on the RMSD from some reference 
structure provides a nearly useless measure of similarity of two 
structures that each have the same RMSD to that reference structure, and 
that measure of similarity is needed to determine cluster membership.

> and that I then get a cluster with 3 structures (RMSD = 0.1, 0.2, 0.3 
> nm, respectively), should the structure with RMSD = 0.2 nm be the 
> "central structure"? What if there are 4 structures in this cluster, 
> with RMSD = 0.1, 0.2, 0.3, 0.4 nm, respectively?

The center of the cluster is the member of the structure with the 
smallest average RMSD to all other members of the structures. I have 
updated the documentation to include this.

Mark