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
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