VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jul 21 2016 - 18:11:24 CDT

On Thu, Jul 21, 2016 at 6:31 PM, Bennion, Brian <bennion1_at_llnl.gov> wrote:
> 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?

the progress output is not based on the number of clusters, but on how
much time has passed since the last output. the behavior you see is
intentional.

axel.

>
> Brian
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.