VMD-L Mailing List

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Thu Jul 21 2016 - 17:31:46 CDT

Hello,
I am performing clustering calculations on a number of large trajectories. In the output of one such calculation i found the following:

Aligning frames to CA atoms
selecting activesite residues
atomselect3
starting cluster calc with rmsd and cluster cutoff of 1.5 Ang
executing: measure cluster atomselect3 distfunc rmsd cutoff 1.5
Info) measure cluster: cluster 1 of 5: ( 20.00% complete). 7607 frames of 36901 left.
Info) measure cluster: cluster 2 of 5: ( 40.00% complete). 1542 frames of 36901 left.
Info) measure cluster: cluster 4 of 5: ( 80.00% complete). 394 frames of 36901 left.
{18003 6346 6585 6587 6591 6592.....

Cluster number 3 is missing or at least not reported. Has anyone else seen this behavior?

Brian