[gmx-users] clusters and rmsd

Patricia Soto soto at chem.rug.nl
Mon Aug 12 15:15:14 CEST 2002

Hello everybody,

I would like to know the exact definition used to calculate  the values
reported in the file cluster.log (output of g_cluster) that correspond
to columns 3 and 5:

  1    2    3       4     5      6   -> columns

cl. | #st rmsd | middle rmsd | cluster members

Are these values averages over rmsd values?
Do the definitions of these values depend on the cluster method?

Of course I have tried to get those definitions but I am getting a bit
strange numbers, so I want to be sure what gromacs is calculating.


Drs. Patricia Soto

Biofysische Chemie		 Telefoon: 31.50.3634329
Rijksuniversiteit Groningen	 Fax:      31.50.3634800
Nijenborgh 4 9747 AG Groningen	 email: P.Soto at chem.rug.nl
Nederland			 http://md.chem.rug.nl/~soto/soto.html

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