Dear Amber Users,
I have been looking carefully at the clustering tools in ptraj in particular the cluster validity testing using the davies bouldin index (DBI). If my set measure is RMSD then I am able to reproduce the DBI when I calculate it "by hand" using ptraj... i.e taking the RMSD of each centroid with the others and applying the DBI formula. However, when I take the set measure to be the DME then I am unable to reproduce the values that ptraj calculates. In this case ptraj doesn't have a DME command but it is easy enough to use the distance command and calculate this matrix by hand. My question is: how is ptraj calculating the DBI when the set measure is DME?
Thanks in advance, Geoffrey Wood
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Received on Tue May 04 2010 - 08:00:06 PDT
