[gmx-users] g_cluster: optimal cutoff

devicerandom devicerandom at gmail.com
Sun Apr 10 01:09:07 CEST 2011

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.



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