[AMBER] clustering trajectories based on RMSD cut-off

From: Sorin Draga via AMBER <amber.ambermd.org>
Date: Mon, 17 Oct 2022 04:49:42 -0400

Hello everyone,

I would like to cluster a trajectory output strictly based on a RMSD
cutoff, without defining the number of output clusters (in other words, I
would like the clustering algorithm to output whatever number of clusters
it sees fit) and later adjust this based on the above rmsd cutoff.
I have looked at the clustering tutorials and manual but I cannot find a
suitable solution to this.

Would *dme [<mask] *coupled with* [nofit] * be a solution in this case?

Thank you and please excuse my ignorance on the matter.

Kind regards,

Sorin
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Received on Mon Oct 17 2022 - 02:00:02 PDT
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