[gmx-users] Regarding gromos method in g_cluster

[bipin singh]

Hello All,

I was trying to do clustering on my MD trajectory using gromos method under
g_cluster module. I got one doubt regarding the output, as I used the
cutoff of 0.3nm for RMSD calculation, I was expecting that all the
snapshots which have RMSD less than or equal to 0.3nm will form the first
cluster and the rest of snapshots will form another cluster. But the output
gives a single cluster. Please let me know if I have not understood it
correctly.

I am appending the output below:

####################################################
Using gromos method for clustering
Using RMSD cutoff 0.3 nm
The RMSD ranges from 0.0602553 to 0.411066 nm
Average RMSD is 0.107366
Number of structures for matrix 12501
Energy of the matrix is 960.075 nm

Found 1 clusters

Writing middle structure for each cluster to clusters.pdb
Counted 0 transitions in total, max 0 between two specific clusters
######################################################

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Thanks and Regards,
Bipin Singh*