CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 06/02/16 17:18:22
| Available memory: 65.528 GB

INPUT: Reading input from 'pt-clust.in'
  [parm ../../tip3p/ff12sb/run1/build/full.topo.hmr [tip3p-ff12sb]]
	Reading '../../tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology
  [trajin ../../tip3p/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/ff12sb/run1/traj.1.02,../../tip3p/ff12sb/run1/traj.1.03,../../tip3p/ff12sb/run1/traj.1.04,../../tip3p/ff12sb/run1/traj.1.05,../../tip3p/ff12sb/run1/traj.1.06,../../tip3p/ff12sb/run1/traj.1.07,../../tip3p/ff12sb/run1/traj.1.08,../../tip3p/ff12sb/run1/traj.1.09,../../tip3p/ff12sb/run1/traj.1.10,../../tip3p/ff12sb/run1/traj.1.11,../../tip3p/ff12sb/run1/traj.1.12,../../tip3p/ff12sb/run1/traj.1.13,../../tip3p/ff12sb/run1/traj.1.14,../../tip3p/ff12sb/run1/traj.1.15,../../tip3p/ff12sb/run1/traj.1.16,../../tip3p/ff12sb/run1/traj.1.17,../../tip3p/ff12sb/run1/traj.1.18 parm [tip3p-ff12sb]]
	Reading '../../tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF
  [trajin ../../tip3p/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/ff12sb/run2/traj.1.02,../../tip3p/ff12sb/run2/traj.1.03,../../tip3p/ff12sb/run2/traj.1.04,../../tip3p/ff12sb/run2/traj.1.05,../../tip3p/ff12sb/run2/traj.1.06,../../tip3p/ff12sb/run2/traj.1.07,../../tip3p/ff12sb/run2/traj.1.08,../../tip3p/ff12sb/run2/traj.1.09,../../tip3p/ff12sb/run2/traj.1.10,../../tip3p/ff12sb/run2/traj.1.11,../../tip3p/ff12sb/run2/traj.1.12,../../tip3p/ff12sb/run2/traj.1.13,../../tip3p/ff12sb/run2/traj.1.14,../../tip3p/ff12sb/run2/traj.1.15,../../tip3p/ff12sb/run2/traj.1.16,../../tip3p/ff12sb/run2/traj.1.17,../../tip3p/ff12sb/run2/traj.1.18 parm [tip3p-ff12sb]]
	Reading '../../tip3p/ff12sb/run2/traj.1.01' as Amber NetCDF
  [autoimage origin]
    AUTOIMAGE: To origin based on center of mass, anchor is first molecule.
  [strip :WAT,Na+,Cl-]
    STRIP: Stripping atoms in mask [:WAT,Na+,Cl-]
  [rmsd :1-2&!@H= first mass out test.dat]
    RMSD: (:1-2&!@H*), reference is first frame (:1-2&!@H*), mass-weighted.
	Best-fit RMSD will be calculated, coords will be rotated and translated.
  [cluster :1,2@C5',C4',C3',O3',P,C2 summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 6 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000]
    CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1,2@C5',C4',C3',O3',P,C2]) best-fit
	K-MEANS: Looking for 6 clusters.
		Sequentially modify each point.
	Cluster to cluster distance will be based on cluster centroids.
	Initial clustering will be randomly sieved (with value 200).
	Previously calcd pair distances CpptrajPairDist will be used if found.
	Summary of cluster results will be written to clust-summary.dat
	Summary comparing parts of trajectory data for clusters will be written to split.dat
		Frames will be split at: 50000 100000
	Cluster trajectories will be written to ctraj, format Amber NetCDF
	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 full.topo.hmr to "_DEFAULTCRD_"
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):
 0: [tip3p-ff12sb] full.topo.hmr, 3300 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent

INPUT TRAJECTORIES (2 total):
 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
	Looking for frames at 298.41 K
 1: 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 100000 frames.

BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions):
  0: [autoimage origin]
	Anchor molecule is 1
	1086 molecules are mobile.
  1: [strip :WAT,Na+,Cl-]
	Stripping 3236 atoms.
	Stripped topology: 64 atoms, 2 res, box: Orthogonal, 1 mol
  2: [rmsd :1-2&!@H= first mass out test.dat]
	Target mask: [:1-2&!@H*](40)
	Reference mask: [:1-2&!@H*](40)
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.
  3: [createcrd _DEFAULTCRD_]
Warning: COORDS data sets do not store temperatures.
Warning: COORDS data sets do not store times.
	Estimated memory usage (100000 frames): 79.200 MB
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 
----- traj.1.01 (1-50000, 1) -----
50% 60% 70% 80% 90% 100% Complete.

Read 100000 frames and processed 100000 frames.
TIME: Avg. throughput= 49.8903 frames / second.

ACTION OUTPUT:

ANALYSIS: Performing 1 analyses:
  0: [cluster :1,2@C5',C4',C3',O3',P,C2 summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 6 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000]
	Starting clustering.
	Mask [:1,2@C5',C4',C3',O3',P,C2] corresponds to 11 atoms.
	Calculating pair-wise distances.
Random_Number: seed is <= 0, using wallclock time as seed (139680000)
	Estimated pair-wise matrix memory usage: > 499.064 kB
	Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames.
 0% 11% 20% 30% 41% 51% 61% 71% 81% 91% Complete.
	Saving pair-wise distances to CpptrajPairDist
	Memory used by pair-wise matrix and other cluster data: 999.160 kB
	Round 0:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 0: 494 points changed cluster assignment.
	Round 1:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 1: 13 points changed cluster assignment.
	Round 2:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 2: 3 points changed cluster assignment.
	Round 3:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 3: 5 points changed cluster assignment.
	Round 4:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 4: 3 points changed cluster assignment.
	Round 5:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 5: 8 points changed cluster assignment.
	Round 6:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 6: 2 points changed cluster assignment.
	Round 7:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 7: 1 points changed cluster assignment.
	Round 8:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 8: No change. Skipping the rest of the iterations.
	Restoring sieved frames.
	Parallelizing calculation with 8 threads
 0% 25% 25% 30% 44% 50% 63% 70% 82% 90% Complete.
#Clustering: 6 clusters 100000 frames
#Cluster 0 has average-distance-to-centroid 0.451052
#Cluster 1 has average-distance-to-centroid 0.705934
#Cluster 2 has average-distance-to-centroid 0.718971
#Cluster 3 has average-distance-to-centroid 1.113348
#Cluster 4 has average-distance-to-centroid 0.852456
#Cluster 5 has average-distance-to-centroid 1.279699
#DBI: 1.066293
#pSF: 45967.344378
#Algorithm: Kmeans nclusters 6 maxit 100
#Representative frames: 34293 622 52144 57011 45747 68974
#Sieve value: 200 (random)
#Sieved frames: 53 257 436 501 622 861 870 1239 1416 1487 1741 1984 2108 2719 3041 3221 3406 3884 4065 4172 4364 4419 4550 4633 5201 5317 5410 5552 5721 5848 5945 6494 6897 7029 7160 7274 7278 7397 7599 7660 7874 7875 8203 8212 8256 8368 8427 8631 8935 9104 9195 9371 9981 10175 10294 10304 10547 10612 11083 11228 11426 11431 11472 11679 11692 11777 11884 12020 12281 12307 12453 12500 12662 12748 12882 13323 13574 13694 13867 13980 14070 14145 14303 14400 14639 14699 14801 15874 16060 16452 16526 16581 16668 17332 17377 17391 17518 17594 17823 18066 18159 18568 18582 19149 19582 19807 19881 20120 20496 20599 20646 20832 20851 20872 21078 21366 21665 22011 22164 22350 22571 22628 23139 23170 23588 23786 23866 24020 24238 24410 24415 24491 24836 25215 25259 25407 25749 25853 25884 25936 26056 26065 26308 26385 26432 26559 27012 27307 27315 27772 27909 28487 28614 28904 28971 28981 29046 29186 29263 29333 29413 29539 29685 29928 30090 30342 30411 30673 30764 30908 30943 31393 32103 32131 32212 32248 32259 32267 32333 32373 32388 32428 32647 33204 33268 33302 33479 33645 33980 34196 34293 34444 35281 35454 35559 35747 36040 36283 36302 36543 36818 36956 37058 37060 37724 37911 38060 38301 38647 38662 38815 39024 39891 39928 39936 40057 40340 41109 41479 41480 41555 41943 42107 42740 43118 43405 43513 43862 44654 44863 45149 45421 45476 45611 45747 45769 46091 46182 46229 46481 46527 46772 47243 47436 47493 47612 47655 47711 47897 48549 48782 48919 49576 50007 50584 50699 51196 51359 51471 52029 52136 52144 52256 52397 52440 52860 52929 52990 53006 53060 53176 53319 53392 53548 53787 53857 54357 54445 54521 54680 54835 55303 55314 56084 56150 56709 56837 56897 57011 57043 58228 58290 58351 58565 58793 59568 59599 60155 60232 60340 60346 60448 61027 61143 61462 61517 61605 61965 62310 62345 62441 63229 63295 63319 63669 63890 63905 64032 64272 64393 64679 64716 64752 64814 65301 65330 65421 65630 66141 66267 66338 66402 66726 66749 66989 67067 67396 67698 67702 67761 67970 68059 68453 68974 68990 69090 69682 69770 70000 70231 70625 70735 70815 70877 70980 71149 71187 71253 71364 71577 71598 71943 72060 72450 72484 72906 72951 73198 73286 73317 73643 73659 73662 73683 73697 73719 73747 73772 73793 74010 74017 74067 74077 74091 74138 74149 74339 74386 74392 74510 74759 75047 75232 75279 75341 75346 75476 75497 75508 75689 76136 76229 76254 77208 77268 77524 77542 77559 77573 77769 77794 77958 78121 78212 78269 78471 78924 78963 79144 79364 79660 79878 79928 80492 80912 80984 81037 81063 81190 81624 81867 81939 81985 82539 82683 82861 83273 83277 83397 83759 84295 84320 84358 84814 85168 85430 85596 85599 85910 86799 87245 87272 87365 87454 87730 87954 88010 88363 88378 89251 89276 89370 89529 90201 90377 90443 90694 91067 91318 91649 92808 92954 93271 93443 94093 94349 94585 94605 94815 94852 95299 95471 95527 96201 96278 96304 96345 96874 97273 97360 98320 98497 98554 98769 98924 99073 99198 99285 99579 99650
Warning: split frame 100000 is out of bounds; ignoring.
	Writing 'ctraj.c0' as Amber NetCDF
	Writing 'ctraj.c1' as Amber NetCDF
	Writing 'ctraj.c2' as Amber NetCDF
	Writing 'ctraj.c3' as Amber NetCDF
	Writing 'ctraj.c4' as Amber NetCDF
	Writing 'ctraj.c5' as Amber NetCDF
	Writing 'rep.c0.pdb' as PDB
Warning: No PDB space group specified.
	Writing 'rep.c1.pdb' as PDB
Warning: No PDB space group specified.
	Writing 'rep.c2.pdb' as PDB
Warning: No PDB space group specified.
	Writing 'rep.c3.pdb' as PDB
Warning: No PDB space group specified.
	Writing 'rep.c4.pdb' as PDB
Warning: No PDB space group specified.
	Writing 'rep.c5.pdb' as PDB
Warning: No PDB space group specified.
	Cluster timing data:
TIME:	  Cluster Init. : 0.0374 s (  0.06%)
TIME:	  Pairwise Calc.: 0.4162 s (  0.64%)
TIME:	  Clustering    : 0.0465 s (  0.07%)
TIME:	  Cluster Post. : 64.3873 s ( 99.23%)
TIME:	Total: 64.8874 s

TIME: Analyses took 64.9125 seconds.

DATASETS (3 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 100000
	_DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100000 (79.200 MB) Box Coords, 64 atoms
	Cnum_00003 "Cnum_00003" (integer), size is 100000

DATAFILES (1 total):
  test.dat (Standard Data File):  RMSD_00001

RUN TIMING:
TIME:		Init               : 0.0000 s (  0.00%)
TIME:		Trajectory Process : 2004.3980 s ( 96.85%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 64.9125 s (  3.14%)
TIME:		Data File Write    : 0.2136 s (  0.01%)
TIME:		Other              : 0.0001 s (  0.00%)
TIME:	Run Total 2069.5243 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 2072.9673 seconds.
--------------------------------------------------------------------------------
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.