CPPTRAJ: Trajectory Analysis. V15.00 OpenMP
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| Date/time: 11/18/15  11:21:48
| Available memory: 88776.1 MB

INPUT: Reading Input from file pt-cluster.in
  [parm ../../build/full.topo.hmr [traj]]
	Reading '../../build/full.topo.hmr' as Amber Topology
  [trajin ../../traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,]
  [strip :WAT,Na+,Cl-]
    STRIP: Stripping atoms in mask [:WAT,Na+,Cl-]
  [rmsd :1,2,C6,C5,C4,O4,N3,C2,O2 first mass]
    RMSD: (:1,2,C6,C5,C4,O4,N3,C2,O2), reference is first frame (:1,2,C6,C5,C4,O4,N3,C2,O2), with fitting, mass-weighted.
  [cluster summary summary.dat repout rep repfmt pdb sieve 100 clusterfmt netcdf averagelinkage rms mass :1-2 clusters 6 cpopvtime cluster_pop.agr normframe]
Warning: No clustering algorithm specified; defaulting to 'hieragglo'
    CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1-2]), mass-weighted best-fit
	Hierarchical Agglomerative: 6 clusters, average-linkage.
	Initial clustering sieve value is 100 frames.
	Cluster pop vs time will be written to cluster_pop.agr (normalized by frame)
	Summary of cluster results will be written to summary.dat
	Cluster representatives will be written to separate trajectories,
		prefix (rep), format PDB
Warning: One or more analyses requested creation of default COORDS DataSet.
    CREATECRD: Saving coordinates from Top [traj] to "_DEFAULTCRD_"
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES:
 0: [traj] 'full.topo.hmr', 4370 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames

INPUT TRAJECTORIES:
 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
	Looking for frames at 298.41 K
  Coordinate processing will occur on 50000 frames.
TIME: Run Initialization took 0.0108 seconds.

BEGIN TRAJECTORY PROCESSING:
	REMD: OPENING 18 REMD TRAJECTORIES
.....................................................
ACTION SETUP FOR PARM '[traj]' (3 actions):
  0: [strip :WAT,Na+,Cl-]
	Stripping 4311 atoms.
	Stripped parm: 'full.topo.hmr', 59 atoms, 2 res, box: Orthogonal, 1 mol
  1: [rmsd :1,2,C6,C5,C4,O4,N3,C2,O2 first mass]
	Target mask: [:1,2,C6,C5,C4,O4,N3,C2,O2](59)
	Reference mask: [:1,2,C6,C5,C4,O4,N3,C2,O2](59)
Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning:  after the RMS-fit is performed.
  2: [createcrd _DEFAULTCRD_]
Warning: COORDS data sets do not store temperatures.
Warning: COORDS data sets do not store times.
	Estimated memory usage (50000 frames): 35 MB
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 50000 frames and processed 50000 frames.
TIME: Trajectory processing: 65.1375 s
TIME: Avg. throughput= 767.6073 frames / second.

ACTION OUTPUT:

ANALYSIS: Performing 1 analyses:
  0: [cluster summary summary.dat repout rep repfmt pdb sieve 100 clusterfmt netcdf averagelinkage rms mass :1-2 clusters 6 cpopvtime cluster_pop.agr normframe]
	Starting clustering.
	Mask [:1-2] corresponds to 59 atoms.
	Calculating pair-wise distances.
	Estimated pair-wise matrix memory usage: > 0.4759 MB
	Pair-wise matrix set up with sieve, 50000 frames, 500 sieved frames.
 0% 26% 35% 40% 44% 53% 61% 70% 87% 92% Complete.
	Memory used by pair-wise matrix and other cluster data: 0.7145 MB
	Starting Hierarchical Agglomerative Clustering:
	Progress: '+' = 10 iterations.
	500 initial clusters.
         0 +++++++++++++++++++++++++
       250 ++++++++++++++++++++++++
	Target # of clusters (6) met (6), clustering complete.
	Completed after 493 iterations, 6 clusters.
	Restoring sieved frames.
	Parallelizing calculation with 24 threads
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete.
#Clustering: 6 clusters 50000 frames
#Cluster 0 has average-distance-to-centroid 0.945012
#Cluster 1 has average-distance-to-centroid 1.439075
#Cluster 2 has average-distance-to-centroid 1.308197
#Cluster 3 has average-distance-to-centroid 1.311196
#Cluster 4 has average-distance-to-centroid 1.361212
#Cluster 5 has average-distance-to-centroid 1.478277
#DBI: 1.260601
#pSF: 14511.489254
#Algorithm: HierAgglo linkage average-linkage nclusters 6 epsilon 1.79769e+308
#Representative frames: 21901 9401 38501 42001 46501 31101
#Sieve value: 100
	Writing 'rep.c0.pdb' as PDB
Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1.
Warning: No PDB space group specified.
	Writing 'rep.c1.pdb' as PDB
Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1.
Warning: No PDB space group specified.
	Writing 'rep.c2.pdb' as PDB
Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1.
Warning: No PDB space group specified.
	Writing 'rep.c3.pdb' as PDB
Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1.
Warning: No PDB space group specified.
	Writing 'rep.c4.pdb' as PDB
Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1.
Warning: No PDB space group specified.
	Writing 'rep.c5.pdb' as PDB
Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1.
Warning: No PDB space group specified.
	Cluster timing data:
TIME:	  Cluster Init. : 0.0000 s (0.00%)
TIME:	  Pairwise Calc.: 0.1032 s (4.94%)
TIME:	  Clustering    : 1.2947 s (61.93%)
TIME:	  Cluster Post. : 0.6926 s (33.13%)
TIME:	Total: 2.0905 s

TIME: Analyses took 2.0905 seconds.

DATASETS:
  9 data sets:
	RMSD_00000 "RMSD_00000" (double, rms), size is 50000
	_DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 50000 (34.90 MB) Box Coords, 59 atoms
	Cnum_00002 "Cnum_00002" (integer), size is 50000
	Cnum_00002[Pop]:0 "Pop:0" (float), size is 50000
	Cnum_00002[Pop]:1 "Pop:1" (float), size is 50000
	Cnum_00002[Pop]:2 "Pop:2" (float), size is 50000
	Cnum_00002[Pop]:3 "Pop:3" (float), size is 50000
	Cnum_00002[Pop]:4 "Pop:4" (float), size is 50000
	Cnum_00002[Pop]:5 "Pop:5" (float), size is 50000

DATAFILES:
  cluster_pop.agr (Grace File):  Pop:0 Pop:1 Pop:2 Pop:3 Pop:4 Pop:5
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 69.2821 seconds.
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To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
  Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
  Theory Comput., 2013, 9 (7), pp 3084-3095.