[gmx-users] g_cluster

[Marc Baaden]

Hi Dallas,

from your email I guess that you misinterpreted the role of g_cluster.
It has nothing to do with aggregation, but with "measuring the similarity"
of structures in a simulation. Similar structures are said to belong to
the same "cluster".

The criterium is typically RMSD deviation of the structures.

g_cluster -h

gives you a good description and one of many references, where you can read
more about this type of analysis: Daura et al. (Angew. Chem. Int. Ed. 1999,
38, pp 236-240)

Cheers,
Marc

>>> Dallas Warren said:
 >> Anyone with experience using g_cluster on the list?
 >> 
 >> I am trying to use it to generate data on the aggregation of molecules in 
 >> my simulations.  Either I am expecting it to do what it can (I was 
 >> expecting it to output the number of clusters/aggregates per frame for the 
 >> simulation) or I am doing something wrong in using it.
-- 
 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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