CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 06/02/16 17:17:43
| Available memory: 65.871 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 5 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 5 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= 49.3860 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 5 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 (140980000)
	Estimated pair-wise matrix memory usage: > 499.064 kB
	Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames.
 0% 10% 21% 30% 40% 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: 495 points changed cluster assignment.
	Round 1:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 1: 17 points changed cluster assignment.
	Round 2:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 2: 1 points changed cluster assignment.
	Round 3:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 3: 1 points changed cluster assignment.
	Round 4:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 4: 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: 5 clusters 100000 frames
#Cluster 0 has average-distance-to-centroid 0.468583
#Cluster 1 has average-distance-to-centroid 0.710809
#Cluster 2 has average-distance-to-centroid 0.792819
#Cluster 3 has average-distance-to-centroid 1.119989
#Cluster 4 has average-distance-to-centroid 1.367934
#DBI: 0.981573
#pSF: 50864.687022
#Algorithm: Kmeans nclusters 5 maxit 100
#Representative frames: 34246 82987 8556 41359 70031
#Sieve value: 200 (random)
#Sieved frames: 148 217 232 469 593 683 767 851 981 1157 1447 1656 1765 1837 2032 2563 2692 2908 3147 3452 3588 3593 3619 3714 3893 4456 4499 4519 5042 5842 6211 6226 6355 6545 6576 6650 6859 7076 7223 7244 7277 7495 7588 8184 8307 8556 8723 8766 8785 8829 9033 9127 9209 9333 9468 9513 9662 9695 10685 12029 12060 12303 12439 12457 12621 12640 12894 13010 13105 13343 13363 13530 13605 13979 14848 15069 15191 15235 15561 15789 15951 16127 16143 16172 16880 17122 17231 17517 17579 17693 17840 17906 17993 18382 18402 18432 18587 19165 19511 19530 19878 20117 20447 20490 20515 20672 20836 20945 21334 21951 22462 22646 23067 23635 23733 23780 23932 23999 24198 24210 24357 24678 24754 24756 25258 25753 25831 25876 26005 26043 26143 26144 26340 26381 26681 26688 26728 26846 27045 27444 27448 27565 27685 27757 27830 27896 28058 28277 28694 28744 28782 29110 29296 29653 29897 29948 30153 30334 30495 30536 30549 30726 30935 31182 31477 31528 31716 31926 32152 32348 32480 32627 32956 33116 33557 33647 33650 33656 33822 34246 34409 34492 34955 35320 35764 37206 37377 37435 37465 37866 38500 38520 38618 38702 38814 38817 39124 39401 39457 39824 39873 40179 40281 40472 40557 40729 41061 41161 41213 41230 41359 41459 41828 41837 41861 41870 42265 42506 42528 42909 43233 43402 43518 44304 44371 44451 44769 44841 44865 44889 45233 45415 45529 45702 45717 45743 45804 46288 46343 46567 46592 46681 46825 47017 47400 47638 47840 47988 48128 48532 48880 49150 49276 49446 49617 50086 50672 50713 50730 50740 51415 51688 51844 51866 51944 51956 52068 52142 52219 52652 52684 52743 52883 52984 53264 53421 53577 53820 54320 54792 55141 55387 56579 56753 56985 57230 57566 57885 58058 58106 58108 58475 58488 58749 58796 58818 59151 59362 59496 59562 59582 60301 60476 60728 60745 61114 61261 61275 61289 61555 61851 62063 62112 62171 62527 62670 63166 63565 63629 63675 64072 64263 64574 64827 64952 65207 65263 65620 65759 66161 66222 66307 66316 66356 66401 66584 66696 66807 67165 67286 67495 68108 68200 68242 68456 68527 68588 68715 68721 68767 69100 69263 69488 69530 69631 69773 70031 70278 70380 70537 70817 70963 70983 71201 71321 71468 71703 71709 72104 72221 72441 72474 72587 72631 73637 73720 73752 73920 74010 74066 74244 74534 75145 75445 75468 76567 76798 77082 77157 77433 77442 77550 77712 77819 78369 78776 78782 79952 80051 81054 81125 81234 81295 81467 81747 82256 82524 82801 82878 82895 82987 83361 83377 83420 83531 83712 83837 84134 84173 84815 84880 84941 85080 85373 85656 86148 86429 86753 87143 87336 87361 87732 87757 88063 88089 88101 88310 88344 88466 88518 88650 88733 89181 89576 89674 89787 89879 89905 89958 90000 90159 90269 90271 90401 90894 90924 91469 91985 92531 92631 92659 92766 92896 92976 93270 93733 93823 93942 94203 94239 94340 94488 94679 95671 95687 95888 96007 96297 96300 96440 96615 96865 96991 97170 97190 97390 97474 97523 97606 97839 97888 97930 98216 98349 98483 99335 99733 99869 99879 99983
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 '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.
	Cluster timing data:
TIME:	  Cluster Init. : 0.0262 s (  0.04%)
TIME:	  Pairwise Calc.: 0.3687 s (  0.55%)
TIME:	  Clustering    : 0.0234 s (  0.03%)
TIME:	  Cluster Post. : 66.7847 s ( 99.38%)
TIME:	Total: 67.2031 s

TIME: Analyses took 67.2249 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 : 2024.8663 s ( 96.78%)
TIME:		Action Post        : 0.0000 s (  0.00%)
TIME:		Analysis           : 67.2249 s (  3.21%)
TIME:		Data File Write    : 0.1564 s (  0.01%)
TIME:		Other              : 0.0001 s (  0.00%)
TIME:	Run Total 2092.2478 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 2114.2126 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.