[gmx-users] g_cluster: optimal cutoff

Fabio Affinito f.affinito at cineca.it
Fri Nov 5 11:57:26 CET 2010

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.


Fabio Affinito, PhD
SuperComputing Applications and Innovation Department - SCAI
Via Magnanelli, 6/3
40033 Casalecchio di Reno (Bologna) ITALY
+39/051/6171794 (Phone)

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