[gmx-users] Re: G_cluster

[Anton Feenstra]

Joseph Pichler wrote:
>     Anton,
> Thank you for the instructions you sent me pertaining to g_cluster, g_covar
> and g_anaeig.  I ran the g_cluster command at the default full-linkage
> method and received only one cluster.  I know that several clusters of
> conformations of the atoms I selected and placed in the index file must
> exist.  What types of parameters, options, etc, must be used in order to
> receive more than just one cluster.  Will the theory used whether it be
> Jarivs Patrick, Monte Carlo, diagonalization, or Gromos affect the number of
> clusters outputted in the cluster.log file?  What types of commands or
> options at the command prompt were used etc? Please if you have any time or
> desire to help me it would be greatly appreciated.

The manual describes (shortly) which parameters affect which methods. For
the rest, as I mentioned before, it depends tremendously on your system and
the actual dynamics you are looking at. Simply try any of the available
methods, with any sensible-seeming combinations of parameters.
I have actually only used it once for a small peptide, and also needed some
time and a lot of trial and error before my results looked good. Therefore,
also, it is necessary to check afterwards if, and how, the clusters identified
are separated from each other. There is some info on this in the cluster.log
file, but you can also get impressions from the 2d or 3d projections (using
g_anaeig) of the cluster members.

P.S. I really want to keep these discussions on the gmx-users list. That way
others can also learn from my replies, and your questions, but also others
(possibly more knowledgable) can answer you.

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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