Greetings all,

I have 30 frames taken from MD simulations that I am trying to cluster. I get a dendrogram using the rmsd tool, however I am finding it very difficult to interpret. What I would like is a similar clustering to gold whereby each member of a cluster is within x nm of each other (probably 0.2 nm in my case). As far as I can tell the dendrogram gives distances from average positions, which leads to some bizare behavior when looking within clusters. e.g. 0.23 nm to the top (common ancestor?) of the cluster but 0.73 rmsd between the two members.

I was wondering if there is a script out there that clusters by rmsd?

All the best,

Tom