Hello all,
I do the cluster analysis in a MD trajectory. And I have some problems with it.
1.How can I know the time scale of each cluster?
2. Here is the output file of the cluster analysis.
#Desired Clusters: 5
#Clustering Algorithm: AverageLink
#Distance Metric: RMS
#Matrix Calculation Time: 1236 seconds
#Total Calculation Time: 31714 seconds
#Cluster 0 has average-distance-to-centroid 2.837542
#Cluster 1 has average-distance-to-centroid 2.250712
#Cluster 2 has average-distance-to-centroid 1.753686
#Cluster 3 has average-distance-to-centroid 2.600417
#Cluster 4 has average-distance-to-centroid 2.933015
#DBI: 1.18191
#pSF: 4607.87695
#SSR/SST: 0.64839
What is the centroid? Is it the average structure?
And in the cluster pdb, I find that the cluster0 is very similar to
the initial structure and the cluster 4 is very different with the
initial structure.
But in the output it shows their distance is 2.8 and 2.9. They are
similar. Their structures are very different but the distances are
very similar. Why?
Thank you for your kind cooperation.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 05 2011 - 09:00:05 PDT
