baaden at smplinux.de
Mon Nov 25 13:18:02 CET 2002
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.
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)
>>> 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
mailto:baaden at smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de
FAX/Voice +49 697912 39550 - Tel: +44 1865 275380 or +33 609 843217
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