[gmx-users] g_cluster: optimal cutoff

Xiaohu Hu x.hu1982 at googlemail.com
Fri Nov 5 17:29:58 CET 2010


I am also trying to do clustering analysis, but g_cluster version 4.5.1 
seems to have a bug. it does not crash but show strange std output like
# RMSD calculations left: -897758633
and the stopps after some time.

Which version do you guys use?



On 11/05/2010 06:57 AM, 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.
> Fabio

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