[gmx-users] g_clustsize not recognize the -mol option and ignore the index file

Eudes Fileti fileti at ufabc.edu.br
Wed Sep 29 18:24:37 CEST 2010

Hello everybody,
I'm using g_clustsize to analyze clusters formed in my solution.
However I noticed that not would get consistent results using the
complete trajectory (containing both solvent and solute). To see
the aggregation, using g_clustsize, I had to convert my trajectory
to a file containing only the solute molecules. That's because -mol
option considered all the molecules in the box (ignoring the index file)
and as a result I always got a single cluster with all the solvent+solute

Is there a more efficient way to do this? Is this a bug in the program?
I've been reading all information on this tool from the gmx-list and I
could see some difficulties in dealing with it the way it is.

Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
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