[gmx-users] g_cluster

[Daniele Avancini]

Hi all,

I'm trying to perform a cluster analysis on my MD simulation using
g_cluster. I'm analysing a simulation of a 11 base pair DNA sequence 10 ns
long with 5000 frames.
I have no problem using the program, i runs perfectly using the 'gromos'
method.

I have 2 questions, one of which is more advice than a proper question.

1. The out.pdb file produced by g_cluster contains one structure for each
cluster identified using a specific cutoff. Is the structure chosen for
each cluster a real frame (e.g. the closest to the centroid of the cluster)
or an average structure? and if it is the average is it a representative
structure?

2. Depending on the -cutoff applied I obtain (of course) different
clusters. If i read correctly the default cutoff is 0.1 nm but i can't find
much in the literature about this applied to DNA. What would it be a good
cutoff for this experiment or what parameter should i consider to make my
decision?

Thanks in advance,
Daniele