[gmx-users] gmx cluster -binary flag to get the "centroid" as the member that has max neighbours < cutoff ?

Christopher Neale chris.neale at alum.utoronto.ca
Tue May 9 06:47:06 CEST 2017

Dear users:

I have a bunch of trajectories of the same system. I want to cluster them together (using gmx cluster gromos algorithm), identify the centroids, and then use gmx rms to evaluate the RMSD to the centroid of the top N clusters in each trajectory. The reason I want to do this is to be able to estimate the statistical error on the population in each cluster.

The difficulty is that gmx cluster lists the "middle" structure in the cluster as the one with the smallest average RMSD to all members of the cluster. What I want is the cluster member with an RMSD <= cutoff to all cluster members.

I could do it by developing the clusters with gmx cluster, then testing all members in an all-to-all RMSD evaluation with many runs through gmx rms to find the structure that is a direct neighbour (given the cutoff) of all cluster members.

That seems tedious. The -binary flag to gmx cluster seems to do what I want. It's behavious is defined but there is no other documentation. Is this whas the -binary flag is for?

Any better ideas?

Thank you,

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