CPPTRAJ: Trajectory Analysis. V15.00 OpenMP
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| Date/time: 11/16/15  23:41:41
| Available memory: 120508 MB

INPUT: Reading Input from file pt-clust.in
  [parm ../../tip3p/ff12sb/run1/build/full.topo.hmr [tip3p-ff12sb]]
	Reading '../../tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology
  [parm ../../tip3p/dacP-ff12sb/run1/build/full.topo.hmr [tip3p-dacP-ff12sb]]
	Reading '../../tip3p/dacP-ff12sb/run1/build/full.topo.hmr' as Amber Topology
  [parm ../../tip3p/chen-garcia/run1/build/full.topo.hmr [tip3p-chen-garcia]]
	Reading '../../tip3p/chen-garcia/run1/build/full.topo.hmr' as Amber Topology
  [parm ../../tip3p/charmm36/run1/build/full.topo.hmr [tip3p-charmm36]]
	Reading '../../tip3p/charmm36/run1/build/full.topo.hmr' as Amber Topology
	CHAMBER topology: 1: CHARMM 361       *  \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File ///
  [parm ../../opc/ff12sb/run1/build/full.topo.hmr [opc-ff12sb]]
	Reading '../../opc/ff12sb/run1/build/full.topo.hmr' as Amber Topology
  [parm ../../opc/dacP-ff12sb/run1/build/full.topo.hmr [opc-dacP-ff12sb]]
	Reading '../../opc/dacP-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]]
  [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]]
  [trajin ../../tip3p/dacP-ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/dacP-ff12sb/run1/traj.1.02,../../tip3p/dacP-ff12sb/run1/traj.1.03,../../tip3p/dacP-ff12sb/run1/traj.1.04,../../tip3p/dacP-ff12sb/run1/traj.1.05,../../tip3p/dacP-ff12sb/run1/traj.1.06,../../tip3p/dacP-ff12sb/run1/traj.1.07,../../tip3p/dacP-ff12sb/run1/traj.1.08,../../tip3p/dacP-ff12sb/run1/traj.1.09,../../tip3p/dacP-ff12sb/run1/traj.1.10,../../tip3p/dacP-ff12sb/run1/traj.1.11,../../tip3p/dacP-ff12sb/run1/traj.1.12,../../tip3p/dacP-ff12sb/run1/traj.1.13,../../tip3p/dacP-ff12sb/run1/traj.1.14,../../tip3p/dacP-ff12sb/run1/traj.1.15,../../tip3p/dacP-ff12sb/run1/traj.1.16,../../tip3p/dacP-ff12sb/run1/traj.1.17,../../tip3p/dacP-ff12sb/run1/traj.1.18 parm [tip3p-dacP-ff12sb]]
  [trajin ../../tip3p/dacP-ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/dacP-ff12sb/run2/traj.1.02,../../tip3p/dacP-ff12sb/run2/traj.1.03,../../tip3p/dacP-ff12sb/run2/traj.1.04,../../tip3p/dacP-ff12sb/run2/traj.1.05,../../tip3p/dacP-ff12sb/run2/traj.1.06,../../tip3p/dacP-ff12sb/run2/traj.1.07,../../tip3p/dacP-ff12sb/run2/traj.1.08,../../tip3p/dacP-ff12sb/run2/traj.1.09,../../tip3p/dacP-ff12sb/run2/traj.1.10,../../tip3p/dacP-ff12sb/run2/traj.1.11,../../tip3p/dacP-ff12sb/run2/traj.1.12,../../tip3p/dacP-ff12sb/run2/traj.1.13,../../tip3p/dacP-ff12sb/run2/traj.1.14,../../tip3p/dacP-ff12sb/run2/traj.1.15,../../tip3p/dacP-ff12sb/run2/traj.1.16,../../tip3p/dacP-ff12sb/run2/traj.1.17,../../tip3p/dacP-ff12sb/run2/traj.1.18 parm [tip3p-dacP-ff12sb] ]
  [trajin ../../tip3p/chen-garcia/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/chen-garcia/run1/traj.1.02,../../tip3p/chen-garcia/run1/traj.1.03,../../tip3p/chen-garcia/run1/traj.1.04,../../tip3p/chen-garcia/run1/traj.1.05,../../tip3p/chen-garcia/run1/traj.1.06,../../tip3p/chen-garcia/run1/traj.1.07,../../tip3p/chen-garcia/run1/traj.1.08,../../tip3p/chen-garcia/run1/traj.1.09,../../tip3p/chen-garcia/run1/traj.1.10,../../tip3p/chen-garcia/run1/traj.1.11,../../tip3p/chen-garcia/run1/traj.1.12,../../tip3p/chen-garcia/run1/traj.1.13,../../tip3p/chen-garcia/run1/traj.1.14,../../tip3p/chen-garcia/run1/traj.1.15,../../tip3p/chen-garcia/run1/traj.1.16,../../tip3p/chen-garcia/run1/traj.1.17,../../tip3p/chen-garcia/run1/traj.1.18 parm [tip3p-chen-garcia]]
  [trajin ../../tip3p/chen-garcia/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/chen-garcia/run2/traj.1.02,../../tip3p/chen-garcia/run2/traj.1.03,../../tip3p/chen-garcia/run2/traj.1.04,../../tip3p/chen-garcia/run2/traj.1.05,../../tip3p/chen-garcia/run2/traj.1.06,../../tip3p/chen-garcia/run2/traj.1.07,../../tip3p/chen-garcia/run2/traj.1.08,../../tip3p/chen-garcia/run2/traj.1.09,../../tip3p/chen-garcia/run2/traj.1.10,../../tip3p/chen-garcia/run2/traj.1.11,../../tip3p/chen-garcia/run2/traj.1.12,../../tip3p/chen-garcia/run2/traj.1.13,../../tip3p/chen-garcia/run2/traj.1.14,../../tip3p/chen-garcia/run2/traj.1.15,../../tip3p/chen-garcia/run2/traj.1.16,../../tip3p/chen-garcia/run2/traj.1.17,../../tip3p/chen-garcia/run2/traj.1.18 parm [tip3p-chen-garcia]]
  [trajin ../../tip3p/charmm36/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/charmm36/run1/traj.1.02,../../tip3p/charmm36/run1/traj.1.03,../../tip3p/charmm36/run1/traj.1.04,../../tip3p/charmm36/run1/traj.1.05,../../tip3p/charmm36/run1/traj.1.06,../../tip3p/charmm36/run1/traj.1.07,../../tip3p/charmm36/run1/traj.1.08,../../tip3p/charmm36/run1/traj.1.09,../../tip3p/charmm36/run1/traj.1.10,../../tip3p/charmm36/run1/traj.1.11,../../tip3p/charmm36/run1/traj.1.12,../../tip3p/charmm36/run1/traj.1.13,../../tip3p/charmm36/run1/traj.1.14,../../tip3p/charmm36/run1/traj.1.15,../../tip3p/charmm36/run1/traj.1.16,../../tip3p/charmm36/run1/traj.1.17,../../tip3p/charmm36/run1/traj.1.18 parm [tip3p-charmm36]]
  [trajin ../../tip3p/charmm36/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/charmm36/run2/traj.1.02,../../tip3p/charmm36/run2/traj.1.03,../../tip3p/charmm36/run2/traj.1.04,../../tip3p/charmm36/run2/traj.1.05,../../tip3p/charmm36/run2/traj.1.06,../../tip3p/charmm36/run2/traj.1.07,../../tip3p/charmm36/run2/traj.1.08,../../tip3p/charmm36/run2/traj.1.09,../../tip3p/charmm36/run2/traj.1.10,../../tip3p/charmm36/run2/traj.1.11,../../tip3p/charmm36/run2/traj.1.12,../../tip3p/charmm36/run2/traj.1.13,../../tip3p/charmm36/run2/traj.1.14,../../tip3p/charmm36/run2/traj.1.15,../../tip3p/charmm36/run2/traj.1.16,../../tip3p/charmm36/run2/traj.1.17,../../tip3p/charmm36/run2/traj.1.18 parm [tip3p-charmm36]]
  [trajin ../../opc/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../opc/ff12sb/run1/traj.1.02,../../opc/ff12sb/run1/traj.1.03,../../opc/ff12sb/run1/traj.1.04,../../opc/ff12sb/run1/traj.1.05,../../opc/ff12sb/run1/traj.1.06,../../opc/ff12sb/run1/traj.1.07,../../opc/ff12sb/run1/traj.1.08,../../opc/ff12sb/run1/traj.1.09,../../opc/ff12sb/run1/traj.1.10,../../opc/ff12sb/run1/traj.1.11,../../opc/ff12sb/run1/traj.1.12,../../opc/ff12sb/run1/traj.1.13,../../opc/ff12sb/run1/traj.1.14,../../opc/ff12sb/run1/traj.1.15,../../opc/ff12sb/run1/traj.1.16,../../opc/ff12sb/run1/traj.1.17,../../opc/ff12sb/run1/traj.1.18 parm [opc-ff12sb]]
  [trajin ../../opc/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../opc/ff12sb/run2/traj.1.02,../../opc/ff12sb/run2/traj.1.03,../../opc/ff12sb/run2/traj.1.04,../../opc/ff12sb/run2/traj.1.05,../../opc/ff12sb/run2/traj.1.06,../../opc/ff12sb/run2/traj.1.07,../../opc/ff12sb/run2/traj.1.08,../../opc/ff12sb/run2/traj.1.09,../../opc/ff12sb/run2/traj.1.10,../../opc/ff12sb/run2/traj.1.11,../../opc/ff12sb/run2/traj.1.12,../../opc/ff12sb/run2/traj.1.13,../../opc/ff12sb/run2/traj.1.14,../../opc/ff12sb/run2/traj.1.15,../../opc/ff12sb/run2/traj.1.16,../../opc/ff12sb/run2/traj.1.17,../../opc/ff12sb/run2/traj.1.18 parm [opc-ff12sb]]
  [trajin ../../opc/dacP-ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../opc/dacP-ff12sb/run1/traj.1.02,../../opc/dacP-ff12sb/run1/traj.1.03,../../opc/dacP-ff12sb/run1/traj.1.04,../../opc/dacP-ff12sb/run1/traj.1.05,../../opc/dacP-ff12sb/run1/traj.1.06,../../opc/dacP-ff12sb/run1/traj.1.07,../../opc/dacP-ff12sb/run1/traj.1.08,../../opc/dacP-ff12sb/run1/traj.1.09,../../opc/dacP-ff12sb/run1/traj.1.10,../../opc/dacP-ff12sb/run1/traj.1.11,../../opc/dacP-ff12sb/run1/traj.1.12,../../opc/dacP-ff12sb/run1/traj.1.13,../../opc/dacP-ff12sb/run1/traj.1.14,../../opc/dacP-ff12sb/run1/traj.1.15,../../opc/dacP-ff12sb/run1/traj.1.16,../../opc/dacP-ff12sb/run1/traj.1.17,../../opc/dacP-ff12sb/run1/traj.1.18 parm [opc-dacP-ff12sb]]
  [trajin ../../opc/dacP-ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../opc/dacP-ff12sb/run2/traj.1.02,../../opc/dacP-ff12sb/run2/traj.1.03,../../opc/dacP-ff12sb/run2/traj.1.04,../../opc/dacP-ff12sb/run2/traj.1.05,../../opc/dacP-ff12sb/run2/traj.1.06,../../opc/dacP-ff12sb/run2/traj.1.07,../../opc/dacP-ff12sb/run2/traj.1.08,../../opc/dacP-ff12sb/run2/traj.1.09,../../opc/dacP-ff12sb/run2/traj.1.10,../../opc/dacP-ff12sb/run2/traj.1.11,../../opc/dacP-ff12sb/run2/traj.1.12,../../opc/dacP-ff12sb/run2/traj.1.13,../../opc/dacP-ff12sb/run2/traj.1.14,../../opc/dacP-ff12sb/run2/traj.1.15,../../opc/dacP-ff12sb/run2/traj.1.16,../../opc/dacP-ff12sb/run2/traj.1.17,../../opc/dacP-ff12sb/run2/traj.1.18 parm [opc-dacP-ff12sb]]
  [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*), with fitting, mass-weighted.
  [cluster :1,2&!@H= summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 8 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000,250000,300000,350000,400000,450000,500000,550000,600000]
    CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1,2&!@H=]) best-fit
	K-MEANS: Looking for 8 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 150000 200000 250000 300000 350000 400000 450000 500000 550000 600000
	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 [tip3p-ff12sb] to "_DEFAULTCRD_"
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES:
 0: [tip3p-ff12sb] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 100000 frames
 1: [tip3p-dacP-ff12sb] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 100000 frames
 2: [tip3p-chen-garcia] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 100000 frames
 3: [tip3p-charmm36] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 100000 frames
 4: [opc-ff12sb] 'full.topo.hmr', 4368 atoms, 1086 res, box: Orthogonal, 1085 mol, 1073 solvent, 100000 frames
 5: [opc-dacP-ff12sb] 'full.topo.hmr', 4368 atoms, 1086 res, box: Orthogonal, 1085 mol, 1073 solvent, 100000 frames

INPUT TRAJECTORIES:
 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
 2: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
	Looking for frames at 298.41 K
 3: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
	Looking for frames at 298.41 K
 4: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
	Looking for frames at 298.41 K
 5: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
	Looking for frames at 298.41 K
 6: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
	Looking for frames at 298.41 K
 7: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
	Looking for frames at 298.41 K
 8: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
	Looking for frames at 298.41 K
 9: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
	Looking for frames at 298.41 K
 10: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000)
	Looking for frames at 298.41 K
 11: 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 600000 frames.
TIME: Run Initialization took 0.0027 seconds.

BEGIN TRAJECTORY PROCESSING:
	REMD: OPENING 18 REMD TRAJECTORIES
.....................................................
ACTION SETUP FOR PARM '[tip3p-ff12sb]' (4 actions):
  0: [autoimage origin]
	Anchor molecule is 1
	1086 molecules are mobile.
  1: [strip :WAT,Na+,Cl-]
	Stripping 3236 atoms.
	Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol
  2: [rmsd :1-2&!@H= first mass out test.dat]
	Target mask: [:1-2&!@H*](41)
	Reference mask: [:1-2&!@H*](41)
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): 77 MB
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

	REMD: OPENING 18 REMD TRAJECTORIES
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

	REMD: OPENING 18 REMD TRAJECTORIES
.....................................................
ACTION SETUP FOR PARM '[tip3p-dacP-ff12sb]' (4 actions):
  0: [autoimage origin]
	Anchor molecule is 1
	1086 molecules are mobile.
  1: [strip :WAT,Na+,Cl-]
	Stripping 3236 atoms.
	Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol
  2: [rmsd :1-2&!@H= first mass out test.dat]
	Target mask: [:1-2&!@H*](41)
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_]
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

	REMD: OPENING 18 REMD TRAJECTORIES
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

	REMD: OPENING 18 REMD TRAJECTORIES
.....................................................
ACTION SETUP FOR PARM '[tip3p-chen-garcia]' (4 actions):
  0: [autoimage origin]
	Anchor molecule is 1
	1086 molecules are mobile.
  1: [strip :WAT,Na+,Cl-]
	Stripping 3236 atoms.
	Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol
  2: [rmsd :1-2&!@H= first mass out test.dat]
	Target mask: [:1-2&!@H*](41)
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_]
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

	REMD: OPENING 18 REMD TRAJECTORIES
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

	REMD: OPENING 18 REMD TRAJECTORIES
.....................................................
ACTION SETUP FOR PARM '[tip3p-charmm36]' (4 actions):
  0: [autoimage origin]
	Anchor molecule is 1
	1086 molecules are mobile.
  1: [strip :WAT,Na+,Cl-]
	Stripping 3236 atoms.
	Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol
  2: [rmsd :1-2&!@H= first mass out test.dat]
	Target mask: [:1-2&!@H*](41)
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_]
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

	REMD: OPENING 18 REMD TRAJECTORIES
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

	REMD: OPENING 18 REMD TRAJECTORIES
.....................................................
ACTION SETUP FOR PARM '[opc-ff12sb]' (4 actions):
  0: [autoimage origin]
	Anchor molecule is 1
	1084 molecules are mobile.
  1: [strip :WAT,Na+,Cl-]
	Stripping 4303 atoms.
	Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol
  2: [rmsd :1-2&!@H= first mass out test.dat]
	Target mask: [:1-2&!@H*](41)
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_]
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

	REMD: OPENING 18 REMD TRAJECTORIES
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

	REMD: OPENING 18 REMD TRAJECTORIES
.....................................................
ACTION SETUP FOR PARM '[opc-dacP-ff12sb]' (4 actions):
  0: [autoimage origin]
	Anchor molecule is 1
	1084 molecules are mobile.
  1: [strip :WAT,Na+,Cl-]
	Stripping 4303 atoms.
	Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol
  2: [rmsd :1-2&!@H= first mass out test.dat]
	Target mask: [:1-2&!@H*](41)
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_]
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

	REMD: OPENING 18 REMD TRAJECTORIES
----- traj.1.01 (1-50000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 600000 frames and processed 600000 frames.
TIME: Trajectory processing: 691.0251 s
TIME: Avg. throughput= 868.2753 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 8 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000,250000,300000,350000,400000,450000,500000,550000,600000]
	Starting clustering.
	Mask [:1,2&!@H*] corresponds to 41 atoms.
	Loading pair-wise distances from CpptrajPairDist
Warning: ClusterMatrix CpptrajPairDist contains sieved data.
	Loaded CpptrajPairDist: 600000 original rows, 3000 actual rows, 4498500 elements, sieve=-200
	Memory used by pair-wise matrix and other cluster data: 20.0216 MB
	Round 0:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 0: 2992 points changed cluster assignment.
	Round 1:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 1: 255 points changed cluster assignment.
	Round 2:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 2: 74 points changed cluster assignment.
	Round 3:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 3: 60 points changed cluster assignment.
	Round 4:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 4: 77 points changed cluster assignment.
	Round 5:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 5: 82 points changed cluster assignment.
	Round 6:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 6: 117 points changed cluster assignment.
	Round 7:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 7: 130 points changed cluster assignment.
	Round 8:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 8: 87 points changed cluster assignment.
	Round 9:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 9: 139 points changed cluster assignment.
	Round 10:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 10: 241 points changed cluster assignment.
	Round 11:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 11: 149 points changed cluster assignment.
	Round 12:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 12: 57 points changed cluster assignment.
	Round 13:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 13: 12 points changed cluster assignment.
	Round 14:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 14: 2 points changed cluster assignment.
	Round 15:  0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	K-means round 15: No change. Skipping the rest of the iterations.
	Restoring sieved frames.
	Parallelizing calculation with 24 threads
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete.
#Clustering: 8 clusters 600000 frames
#Cluster 0 has average-distance-to-centroid 0.931203
#Cluster 1 has average-distance-to-centroid 1.164336
#Cluster 2 has average-distance-to-centroid 0.807526
#Cluster 3 has average-distance-to-centroid 1.068730
#Cluster 4 has average-distance-to-centroid 1.069448
#Cluster 5 has average-distance-to-centroid 1.393435
#Cluster 6 has average-distance-to-centroid 1.629931
#Cluster 7 has average-distance-to-centroid 1.658022
#DBI: 1.390300
#pSF: 163628.505157
#Algorithm: Kmeans nclusters 8 maxit 100
#Representative frames: 45510 30441 218667 355709 512177 413934 207750 162915
#Sieve value: 200 (random)
#Sieved frames: 180 525 646 822 870 876 1052 1252 1670 2211 2398 2407 2424 3596 4313 4367 4469 4710 4760 4970 5192 5263 5367 5659 5677 5929 5933 6248 6546 6716 6718 6864 7045 7115 7145 7243 7295 7310 7337 7864 8118 8267 8276 8544 8579 8819 8878 9274 9278 9868 9942 10323 10405 10421 10515 10630 10815 10968 11293 11569 11579 11611 11900 12100 12246 12374 12413 12466 12606 12608 12922 12972 12973 13364 13699 13892 13990 14317 14406 14445 14880 15002 15443 15556 15658 15711 15900 15992 16288 16876 17147 17576 17761 17947 18169 18464 18818 18831 19051 19072 19259 19474 19588 19797 19895 19944 20168 20473 20625 20666 20693 20730 20833 20877 21053 21151 21172 21417 21731 22339 22482 22513 22995 23887 23986 24260 25141 25422 25727 25893 26164 26408 26577 26766 26776 26777 26810 26843 26951 26956 27085 27275 27380 27454 27570 27809 28059 28223 28367 28562 28642 28715 28853 29112 29270 29366 29446 29893 30049 30401 30417 30433 30441 30451 30827 31291 31384 31493 31511 31695 31911 32120 32464 32490 32780 32948 33076 33374 33723 34165 34262 34608 34626 35091 35118 35260 35357 35535 35691 35786 36081 36427 36798 36913 36934 37009 37138 37201 37219 37231 37254 37663 37680 37738 38060 38293 38299 38555 38963 39158 39230 39690 39763 40076 40110 40225 40541 41250 41403 41637 41695 41705 41896 41955 42056 42066 42330 42441 42983 43109 43288 43491 43582 43803 44296 44346 44736 44808 45036 45054 45112 45310 45510 45606 46030 46451 46587 47205 47206 47505 47633 47636 47662 47746 48039 48082 48452 48888 48903 48943 48999 49001 49224 49787 49802 49972 50055 50214 50256 50278 50730 50863 51204 51451 51960 52159 52287 52575 52622 52822 53004 53168 53280 53463 53470 53591 53645 53658 54128 54441 54970 55417 55640 56165 56193 56263 56525 56706 57034 57094 57190 57383 57396 57425 57696 57742 57884 58146 58217 58722 58815 59185 59279 59410 60128 60148 60190 60565 60660 60741 60798 61386 61493 61594 61757 61776 62276 62346 62523 62801 63274 63344 63410 63566 63669 63842 63947 63969 64241 64448 64497 64892 64961 65267 65376 65501 65715 65979 66262 66884 67101 67173 67539 67767 67810 67853 67944 68214 68315 69119 69130 69434 69500 69584 69589 69923 70291 70714 70835 70887 70937 71006 71031 71032 71177 71507 71681 71701 72303 72940 72958 73191 73248 73331 73394 73661 73838 73880 73950 74189 75458 75692 75738 76340 76462 76466 76481 77113 77863 78131 78679 78702 78974 78988 79003 79021 79481 79634 80216 80299 80411 80968 81042 81049 81411 81783 82021 82229 82801 82817 82963 83141 83407 83477 83603 83845 83890 84909 85271 85414 85425 85499 85756 85880 85967 86164 86220 86642 86685 87066 87099 87159 87195 87276 87413 87441 87504 87556 87583 87649 87807 88129 88170 88273 88340 89216 89254 89393 89708 89760 90208 90212 90285 90383 90469 90709 90774 90892 90896 91437 91786 91826 91840 91845 91874 92089 92190 92695 92729 92775 92817 92885 93260 93469 93603 94034 94196 94203 94384 94449 94491 94539 94554 94855 94948 95100 95146 95421 95541 95550 95772 96034 96097 96170 96414 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441539 441600 441860 442253 442296 442614 442915 443129 443779 443786 443827 444082 444118 444160 444235 444371 444714 444799 444848 445021 445119 445164 445527 445712 445720 445819 445984 446119 446476 446733 446863 446906 447186 447602 448052 448221 448304 448371 448447 448491 448903 449066 449185 449318 449380 449507 449592 449939 450186 450337 450573 450581 450928 451282 451487 451625 451823 451868 451881 452268 452585 452591 452794 452817 453400 453817 453823 453928 453933 454127 454595 455071 455407 455861 456469 456487 456724 456725 456905 456955 457374 457680 458065 458438 458636 458732 458980 459485 459555 459878 459916 460175 460178 460438 460625 460627 460761 461214 461760 461823 462032 462191 462648 463003 463516 463825 463926 464065 464084 464103 464236 464519 464711 465095 465172 465235 465334 465467 465733 465818 465884 466005 466335 466503 466541 466846 466848 466925 467643 467901 467985 468062 468189 468377 468528 468749 469133 469154 469182 469575 469744 469850 469899 470059 470330 470409 470452 470680 471271 471418 471568 471627 471671 471678 471735 472015 472874 473148 473238 473330 473461 473654 474005 474045 474348 474380 474477 474591 474981 475235 475347 475403 475712 476233 476812 477248 477460 477675 477880 478057 478227 478295 478603 478634 478698 479354 479490 479553 479592 479597 479844 479905 480044 480092 480104 480304 480685 481208 481371 482309 482370 482818 483176 483426 483530 483670 483853 484015 484098 484315 484801 484948 485747 486041 486424 486958 487045 487170 487350 487435 487597 487721 488059 488105 488271 488275 488542 488593 489127 489142 489408 489655 490113 490156 490975 491212 491439 491489 491564 491574 491993 492023 492939 493093 493171 493177 493221 493423 493587 493709 493768 493811 494152 494340 494434 494617 494697 495343 495582 495622 495694 495780 496510 497276 497433 497454 497658 497906 498068 498377 498590 498694 498920 499060 499246 499503 499561 499578 499994 500407 500529 500765 500883 501026 501563 501623 501775 502361 502424 502623 502655 502795 503111 503249 503507 503693 503895 504513 504519 504550 504629 504647 504707 505121 505355 505364 505569 505641 505717 506859 507083 507136 507269 507330 507499 508146 508200 508909 508962 509125 509187 509299 510354 510417 510638 510769 511364 511384 511518 511536 511706 511808 511930 511957 512000 512114 512160 512177 512441 512623 512930 513119 513131 513191 513634 513691 514204 514411 514451 514540 514571 514675 514764 514772 514884 514914 514954 515088 515282 515603 516719 516863 517014 517236 517765 518123 518149 518380 518763 518799 519041 519108 519590 519618 519794 519848 519864 519872 520163 520173 520469 520697 520817 520877 521014 521166 521330 521630 522875 523052 523135 523199 523335 523538 523549 523721 524048 524445 524947 525082 525261 525285 525332 525375 525698 526173 526262 526275 526373 526619 526911 527262 527267 527282 527495 527529 527752 527859 528102 528404 528674 528947 529213 529232 529325 529446 530037 530303 530481 530496 531179 531246 531322 531369 531403 531715 532514 532692 532711 532780 532911 532979 533666 533669 533825 533936 533948 534822 535082 535164 535232 535347 535645 535993 536071 536462 536582 536760 536877 536970 537389 537447 537574 537823 537834 538012 538034 538474 538485 538490 538594 538708 538829 538929 539095 539414 539541 540476 541051 541076 541348 541351 541453 541506 541719 541773 542820 542973 543025 543502 543599 543972 544101 544343 544366 544498 544625 545714 545771 545852 546253 546456 546674 546790 546830 547140 547356 547697 547725 548199 548271 548315 548410 548635 549312 549349 549457 549560 549821 549933 549994 550458 550470 550687 550708 550981 551363 552132 552174 552232 552407 552738 552743 552786 553119 553199 553294 553333 553450 553561 553595 553610 553663 553705 553772 553800 554054 554275 554457 554495 554554 554624 554754 554888 555149 555427 555465 555876 555901 556335 556376 556594 556727 557386 557387 557618 557765 557797 558205 558240 558261 558404 558557 558798 558826 559036 559118 559172 559289 559634 560085 560505 560570 561031 561276 561718 561760 562187 562312 562437 562443 562596 562723 562791 562817 562926 562994 563004 563172 563414 563870 563917 564204 564423 564631 565282 565637 565823 565910 566187 566239 566583 566682 566792 566961 567649 567746 568035 568549 568625 568683 569244 569447 569529 569893 570048 570204 570309 570380 570521 570971 571052 571478 571805 571946 572452 573147 573246 573569 573591 573688 573778 574042 574094 574125 574260 574411 574532 574575 574636 574689 574698 574905 575080 575640 575659 575680 575873 576195 576290 576568 576765 576934 577034 577140 577199 577652 577935 578037 578074 578443 578531 578674 578694 578937 578971 579201 579545 579917 580179 580243 580337 580503 580841 581060 581071 581581 581626 581885 581886 582122 582540 582909 583774 583785 584308 584463 584948 585130 585188 585274 585602 585738 585752 585837 586017 586381 586392 586856 586915 587140 587413 587502 587631 587953 588406 588465 588582 588628 588731 588737 589035 589063 589217 589253 589687 589809 590002 590165 590176 590258 590436 590562 590721 591174 591816 591845 592069 592361 592824 592899 593058 593172 593327 593352 593371 593584 593614 593648 593758 593850 594507 595051 595154 595759 595950 595972 596320 596439 597038 597105 597350 597435 597669 598188 598274 598345 598427 598506 598814 598834 599041 599051 599466 599467 599869
Warning: split frame 600000 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 'ctraj.c7' as Amber NetCDF
	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.
	Writing 'rep.c6.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.c7.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. : 0.0048 s (0.00%)
TIME:	  Pairwise Calc.: 0.1391 s (0.00%)
TIME:	  Clustering    : 0.7075 s (0.01%)
TIME:	  Cluster Post. : 7544.5580 s (99.99%)
TIME:	Total: 7545.4106 s

TIME: Analyses took 7545.4121 seconds.

DATASETS:
  3 data sets:
	RMSD_00000 "RMSD_00000" (double, rms), size is 600000
	_DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 600000 (460.05 MB) Box Coords, 65 atoms
	Cnum_00002 "Cnum_00002" (integer), size is 600000

DATAFILES:
  test.dat (Standard Data File):  RMSD_00000
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 8251.5675 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.