\-/  
  -/-   PTRAJ: a utility for processing trajectory files
  /-\  
  \-/   Version: "AMBER 11.0 integrated" (4/2010)
  -/-   Executable is: "/home/droe/Amber/amber11/bin/ptraj"
  /-\   Running on 1 processor(s)
  \-/   Residue labels:

 ACE  ALA  ALA  ALA  ALA  ALA  ALA  ALA  ALA  ALA 
 ALA  NHE 

 PRMTOP does not contain %FLAG RADIUS_SET

PTRAJ: Processing input from file test0.in

PTRAJ: prnlev 0
  PRNLEV: value is now 0

PTRAJ: trajin /home/droe/ALA10/NETCDFtraj/rem.nc 
  Checking coordinates: /home/droe/ALA10/NETCDFtraj/rem.nc
NETCDF file:

PTRAJ: cluster out testcluster representative pdb average pdb averagelinkage clusters 12 rms sieve 10 @CA
MASK = @CA
Mask [@CA] represents 10 atoms
[No output trajectory specified (trajout)]
  /home/droe/ALA10/NETCDFtraj/rem.nc: 50000 frames.

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 50000 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (/home/droe/ALA10/NETCDFtraj/rem.nc) is a NetCDF AMBER trajectory with 50000 sets

NO OUTPUT COORDINATE FILE WAS SPECIFIED

ACTIONS
  1>  CLUSTERING.

      Clusters will be assigned and output to files with the prefix "testcluster".
      The clustering algorithm is AverageLink using RMS as the distance metric.
      Cluster-to-cluster distance is measured by its centroid.
      The cluster count is set to 12.
      Clustering will be performed in two passes (sieve method).
      Sieved frames in the first pass will be selected every 10 frames starting from frame 1.
      The atom selection for best fit is :2-11@CA
      Output of type 'all' will be written to a file of type: 'Amber trajectory'
      Output of type 'representative' will be written to a file of type: 'PDB'
      Output of type 'average' will be written to a file of type: 'PDB'

 1% ............ 25% ............ 50% ............ 75% ............ 100% 


  The first pass through the trajectory is complete.
  Calculating the PairwiseDistances
  Writing Pairwise Distances to file "PairwiseDistances".
  Clustering using the average linkage algorithm.
  Aligning the most representative frames from each clusters to cluster 1.
  Sieve was active.  Preparing for the second pass.
  Dumping out current clusters to file EndFirstPass.txt.
  Clustering elapsed time: 7331 seconds
  Computing centroids and expanding clusters.
  Ready for the second pass through the trajectories...
 1% ............ 25% ............ 50% ............ 75% ............ 100% 


PTRAJ: Successfully read in 50000 sets and processed 50000 sets.

Dumping accumulated results (if any)


PTRAJ CLUSTER:  Clustering elapsed time: 7359 seconds
  Printing distribution of distances to file testcluster.txt
    Distribution of Distances
  [   0.282,   0.701] --   0.02% (  2150 out of 12497500)
  [   0.701,   1.121] --   0.17% ( 21710 out of 12497500)
  [   1.121,   1.541] --   0.56% ( 70332 out of 12497500)
  [   1.541,   1.960] --   1.41% (175987 out of 12497500)
  [   1.960,   2.380] --   3.16% (395047 out of 12497500)
  [   2.380,   2.800] --   6.78% (847794 out of 12497500)
  [   2.800,   3.220] --  13.19% (1647933 out of 12497500)
  [   3.220,   3.639] --  20.94% (2617138 out of 12497500)
  [   3.639,   4.059] --  22.66% (2831999 out of 12497500)
  [   4.059,   4.479] --  15.75% (1968118 out of 12497500)
  [   4.479,   4.899] --   8.42% (1052096 out of 12497500)
  [   4.899,   5.318] --   3.94% (492846 out of 12497500)
  [   5.318,   5.738] --   1.72% (215031 out of 12497500)
  [   5.738,   6.158] --   0.74% ( 92262 out of 12497500)
  [   6.158,   6.577] --   0.32% ( 39821 out of 12497500)
  [   6.577,   6.997] --   0.14% ( 17158 out of 12497500)
  [   6.997,   7.417] --   0.06% (  6898 out of 12497500)
  [   7.417,   7.837] --   0.02% (  2392 out of 12497500)
  [   7.837,   8.256] --   0.01% (   699 out of 12497500)
  [   8.256,   8.676] --   0.00% (    89 out of 12497500)