On 05/11/10 10:57, Fabio Affinito wrote:
On 10/31/2010 08:20 PM, Valeria Losasso wrote:
Dear all,
for my cluster analysis I am using the g_cluster tool with the gromos method.
The problem is that I have to compare the results for system of different
lengths, and of course the result of the cluster analysis changes according to
the cutoff chosen. So what will be a great choice in this case?
I was thinking about different possibilities, namely: i) choosing - as it is
quite frequent in the literature - an arbitrary cutoff (like the default 0.1),
but using the same for different systems would be probably not suitable...
ii) looking for every case at the RMSD distribution and choosing the minimum
value between the two peaks - in this case the cutoff would vary for every
system; iii) choosing for every system the cutoff that allows to have in the
largest cluster the 50% of the structures, and also in this case the cutoff
would be different for the different cases...
Any hint?
Thanks a lot,
Valeria
Option ii) is the right one.
I tend to think that ii) is the most correct, but there could be reasons
to choose i) or iii) as well. It very much depends on your problem and
what you want to obtain -I don't think there is an absolutely "right" or
"wrong" one in this set.
m.
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