CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 05/29/16 22:45:44
| Available memory: 16.142 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&!@H= summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 7 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000]
    CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1,2&!@H=]) best-fit
	K-MEANS: Looking for 7 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, 3299 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: 63 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): 78.000 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= 87.5510 frames / second.

ACTION OUTPUT:

ANALYSIS: Performing 1 analyses:
  0: [cluster :1,2&!@H= summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 7 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000]
	Starting clustering.
	Mask [:1,2&!@H*] corresponds to 40 atoms.
	Calculating pair-wise distances.
Random_Number: seed is <= 0, using wallclock time as seed (150820000)
	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% 90% 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: 493 points changed cluster assignment.
	Round 1:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 1: 20 points changed cluster assignment.
	Round 2:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 2: 14 points changed cluster assignment.
	Round 3:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 3: 18 points changed cluster assignment.
	Round 4:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 4: 15 points changed cluster assignment.
	Round 5:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 5: 20 points changed cluster assignment.
	Round 6:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 6: 29 points changed cluster assignment.
	Round 7:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 7: 13 points changed cluster assignment.
	Round 8:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 8: 7 points changed cluster assignment.
	Round 9:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 9: 5 points changed cluster assignment.
	Round 10:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 10: 3 points changed cluster assignment.
	Round 11:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 11: No change. Skipping the rest of the iterations.
	Restoring sieved frames.
	Parallelizing calculation with 8 threads
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete.
#Clustering: 7 clusters 100000 frames
#Cluster 0 has average-distance-to-centroid 0.968467
#Cluster 1 has average-distance-to-centroid 1.168749
#Cluster 2 has average-distance-to-centroid 1.129489
#Cluster 3 has average-distance-to-centroid 1.404662
#Cluster 4 has average-distance-to-centroid 1.580331
#Cluster 5 has average-distance-to-centroid 1.638150
#Cluster 6 has average-distance-to-centroid 1.495716
#DBI: 1.462604
#pSF: 19254.279731
#Algorithm: Kmeans nclusters 7 maxit 100
#Representative frames: 51525 62348 61124 11839 83191 56906 19996
#Sieve value: 200 (random)
#Sieved frames: 59 327 616 647 771 872 900 1239 1363 1602 1710 1978 2160 2631 2694 2702 3590 3712 3905 4004 4990 5109 5136 5326 5347 5373 5520 5521 5689 5876 5897 6120 6481 6623 7039 7403 7772 7859 7868 7927 8081 8158 8195 8269 8294 8299 8326 8344 8903 9019 9767 9938 10358 10455 10674 10747 10975 11159 11161 11441 11582 11839 11932 12142 12503 12554 12987 13012 13086 13298 13380 13411 13689 13705 13722 14207 14312 14428 14587 14594 14972 15019 15462 15619 16138 16199 17021 17116 17252 17360 17506 17852 17947 18119 18380 18846 18991 19185 19227 19290 19762 19996 20557 20877 21049 21248 21255 21264 21283 21630 21806 21969 22276 22623 22765 22846 22932 22985 23070 23898 23960 24171 24404 24448 24522 24670 24915 25129 25246 25303 25381 25611 25624 25838 26259 26593 26613 26771 27029 27108 27193 27418 27447 27693 27871 27926 27931 28009 28055 28400 28423 28612 28643 28822 28846 28849 29376 30294 30414 30416 30584 30613 30835 30955 30981 31103 31216 31483 31917 31959 32004 32023 32146 32237 32772 32973 33323 33610 33663 33672 33863 34599 34990 35140 35209 35609 35947 36152 36201 36301 36585 36850 36874 36930 36953 37012 37157 37315 37347 37570 37640 37647 37743 37811 37819 38002 38447 39038 39132 39830 40020 40076 40343 40478 40575 40925 41258 41569 42093 42094 42601 43111 43118 43444 43628 43653 43717 43733 43837 44131 44363 44689 44733 44749 45027 45466 45543 45553 45734 45803 45924 45952 46060 46255 46668 46739 46864 47200 47277 47333 47523 48168 48224 48764 48850 48879 49079 49183 49330 49550 49559 49729 49947 50028 50418 50937 51032 51168 51233 51265 51525 51704 51718 52308 52341 52388 52984 53039 53690 53734 53796 53840 53861 54060 54459 54710 54786 55161 55311 55357 55485 55561 55799 55831 55852 55875 56318 56351 56454 56889 56906 57151 57438 57493 57655 57975 58710 58876 59102 59501 59803 59968 60292 60383 60566 60911 61124 61262 61522 61828 61969 62348 62409 62416 62661 62689 62695 62801 63238 63329 63683 63785 64140 64195 64453 64597 64673 64812 64831 65184 65482 65549 65658 65985 66072 66197 66302 66307 66579 66658 66858 66952 67028 67924 68056 68157 68915 69010 69153 69360 69653 69702 69749 69959 70019 70054 70311 70358 70655 70934 71315 71537 71816 72440 72561 72573 72610 72735 72789 72923 73142 73154 73325 73345 73523 73721 73788 73794 74020 74294 74385 74537 74677 74811 74834 74856 74923 75502 75835 75846 75934 76212 76313 76502 77140 77656 77764 77878 78937 79042 79340 79472 80162 80187 80597 80678 80722 80954 80978 81972 82035 82443 82475 82720 83068 83191 83292 83351 83358 83415 84133 84413 84581 84692 84762 84856 84996 85079 85319 85771 85849 86139 86186 86685 86832 86946 87002 87014 87157 87426 87625 87722 87780 87989 88028 88079 88867 88868 89067 89112 89485 90281 90382 90720 91007 91080 91550 91617 92399 92404 92550 92724 93023 93367 93469 93492 93763 93951 94100 94163 94210 94353 94462 95695 95822 95944 96196 96389 97397 97957 98020 98359 98579 98872 98942 99125 99217 99570 99717 99894
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 'ctraj.c6' 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.
	Writing 'rep.c6.pdb' as PDB
Warning: No PDB space group specified.
	Cluster timing data:
TIME:	  Cluster Init. : 0.3252 s (  0.56%)
TIME:	  Pairwise Calc.: 0.0548 s (  0.09%)
TIME:	  Clustering    : 0.1162 s (  0.20%)
TIME:	  Cluster Post. : 57.6979 s ( 99.15%)
TIME:	Total: 58.1940 s

TIME: Analyses took 58.1940 seconds.

DATASETS (3 total):
	RMSD_00001 "RMSD_00001" (double, rms), size is 100000
	_DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100000 (78.000 MB) Box Coords, 63 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 : 1142.1920 s ( 95.14%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 58.1940 s (  4.85%)
TIME:		Data File Write    : 0.1350 s (  0.01%)
TIME:		Other              : 0.0002 s (  0.00%)
TIME:	Run Total 1200.5212 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 1201.3716 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.