[gmx-users] g_cluster -dm option

santhu kumar mesanthu at gmail.com
Thu Sep 29 22:25:34 CEST 2011


I am using g_cluster to cluster trajectories.
The exact command I am using is : g_cluster -s protein.pdb -f all.trr -n
index.ndx -o rmsd-clust.xpm -method gromos -cutoff 0.07 -wcl 250. This
command gives me 145 clusters.

This command writes out a rmsd-clust.xpm, which is the RMSD distance matrix.
Since the trajectory is quite huge, i want to perform the RMSD matrix
computation only once.
If I want to change options of clustering, I have tried giving the computed
matrix as input to another run but the results are quite different.

For example : g_cluster -s ubqs.pdb -f all.trr -n index.ndx -dm
rmsd-clust.xpm -method gromos -cutoff 0.07 -wcl 250 would then give only 3

Can somebody please advice me on how to avoid recomputing the RMSD distance
matrix for each change in clustering option??

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