CPPTRAJ: Trajectory Analysis. V15.00 OpenMP
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| Date/time: 11/18/15  09:47:22
| Available memory: 121627 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 dbscan minpoints 4 epsilon 1.0 sievetoframe sieve 200 random loadpairdist 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
	DBSCAN:
		Minimum pts to form cluster= 4
		Cluster distance criterion= 1.000
		Sieved frames will only be added back if they are within
		  1.000 of a frame in an existing cluster.
		  (This option is more accurate and will identify sieved
		  frames as noise but is slower.)
	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 0.0241 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: 722.9490 s
TIME: Avg. throughput= 829.9340 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 dbscan minpoints 4 epsilon 1.0 sievetoframe sieve 200 random loadpairdist 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
	Starting DBSCAN Clustering:
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
	Restoring sieved frames.
	Restoring sieved frames if within 1.000 of frame in nearest cluster.
	Parallelizing calculation with 24 threads
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete.
	160607 of 597000 sieved frames were discarded as noise.
#Clustering: 9 clusters 600000 frames
#Cluster 0 has average-distance-to-centroid 1.549786
#Cluster 1 has average-distance-to-centroid 0.769897
#Cluster 2 has average-distance-to-centroid 0.693098
#Cluster 3 has average-distance-to-centroid 0.992656
#Cluster 4 has average-distance-to-centroid 0.922620
#Cluster 5 has average-distance-to-centroid 0.831964
#Cluster 6 has average-distance-to-centroid 0.844343
#Cluster 7 has average-distance-to-centroid 0.917942
#Cluster 8 has average-distance-to-centroid 0.908238
#DBI: 1.099820
#pSF: 9981.183317
#Algorithm: DBSCAN minpoints 4 epsilon 1 sieveToCentroid 0
#NOISE_FRAMES: 26 3637 5503 6174 7149 7677 19620 19831 19997 24017 25033 33185 39639 40249 50405 54379 61899 62768 64252 69293 72186 100643 108950 119053 119645 135681 159709 162268 162944 171835 177397 178048 182540 183729 188311 199645 201346 203363 203390 206067 210233 211570 212203 213169 214457 214792 215673 215691 216179 216189 220335 224653 224661 227090 227528 229890 230653 237018 239251 239926 241303 241330 242627 248594 248945 249682 250168 252949 253397 253537 253561 253747 255325 257714 258526 259343 260322 261030 261659 262420 262939 263900 264567 264868 264984 266047 266346 266593 266778 267265 267652 271384 271628 273751 276087 277580 278246 278366 279591 280929 282018 284430 284932 286107 288296 288647 291959 291989 293666 293796 295004 296981 298164 300929 301219 303831 304021 304132 305282 305614 306766 306820 308496 310223 311053 311778 312513 312551 313032 313280 314011 315983 319707 320395 320942 321887 322216 323377 324989 326511 328278 330745 331883 332973 334356 338709 339929 341383 342885 343161 345400 345503 346157 346694 347074 347375 348128 348634 349746 349813 350284 350297 350737 351289 356092 357950 358413 361041 366269 367617 367835 368038 369456 369858 372075 372684 373807 374747 375586 377418 377576 378082 381061 381899 382727 383573 384120 385073 385235 387680 389828 394005 395435 396589 397503 398220 398453 398693 399434 403089 406201 407208 411007 417726 429398 431993 432133 432536 434317 438606 438871 447488 448638 451398 453875 456723 460953 473104 492955 502688 502717 503418 504064 506855 512244 518255 519085 522313 523414 528151 528181 532012 538852 541371 541782 552560 553117 555173 557158 569112 569224 576102 577046 577732 578228 581249 588789
#Number_of_noise_frames: 247
#Representative frames: 42663 488006 321252 366275 210190 336415 427920 210538 279154
#Sieve value: 200 (random)
#Sieved frames: 26 224 445 458 600 698 710 769 939 1469 1476 1628 2286 2425 2604 2641 2733 2768 2813 2936 3037 3457 3500 3637 3857 3918 3942 4004 4164 4195 4285 4456 5146 5434 5503 5571 5832 5846 5867 5962 6060 6174 6416 6500 6564 6640 6772 7149 7408 7599 7677 7716 7835 8394 8530 8648 8953 9223 9447 9618 9828 9940 10363 10479 10745 10805 10808 10830 11296 11603 11900 12031 12130 12161 12172 12276 12572 12653 12697 12704 12804 13037 13060 13144 13549 13562 13587 13658 14427 14438 14752 15063 15269 15371 15643 15764 16826 16845 17163 17329 17467 17514 17550 18459 18474 18539 19101 19215 19259 19296 19457 19620 19661 19753 19792 19831 19906 19997 20130 20570 20806 20828 21037 21244 21456 21859 21962 22100 22235 22756 22860 23024 23061 23171 23530 23597 23938 24017 24183 24192 24483 25033 25088 25808 26178 26228 26240 26247 26305 26878 27017 27167 27460 27539 27756 27895 27970 28072 28211 28280 28539 28557 28759 29096 29374 29619 29628 29873 30176 30444 30512 30597 30692 31199 31356 31608 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500344 500814 501092 501175 501281 501741 502055 502688 502717 503336 503418 503513 503520 503790 504064 504252 504480 504758 505231 505341 506217 506320 506396 506483 506614 506704 506805 506855 507085 507340 507463 507601 507801 507864 507889 508003 508732 508742 508870 509164 509396 509428 509549 509740 509743 509903 510013 510298 510321 510393 510467 510501 511026 511851 512060 512244 512257 512372 512495 512551 513072 513340 513766 513890 514121 514321 514764 514970 515052 515603 515876 515890 515924 516109 516118 516169 516514 517143 517494 517769 517935 518007 518255 518859 519085 519190 519211 519840 519990 520247 520644 520679 520812 520873 520888 520890 521419 521520 521850 521944 521972 522228 522300 522313 522833 522836 523340 523399 523414 523995 524003 524021 524508 525299 525409 525535 525768 525777 525822 526032 526093 526227 526521 527027 527188 527290 527409 527847 528011 528118 528128 528151 528181 528566 528619 528785 529462 530224 530280 530283 530598 530727 531058 531343 531542 531822 531939 532012 532023 532672 532698 532947 533002 533120 533218 533323 533841 533923 534003 534025 534039 534079 534172 534248 534339 534529 534948 534994 535059 535273 535508 535777 536160 536541 536696 536729 536980 537136 537368 538018 538135 538146 538148 538209 538330 538775 538776 538852 538861 539124 539220 539384 539475 539495 539535 539688 539814 539929 539940 540173 540412 540740 540985 541003 541072 541106 541234 541371 541436 541613 541782 541815 542106 542147 542200 542410 542515 542565 542662 543121 543232 543260 543326 543595 543606 543630 543645 543787 543970 544210 544239 544305 544806 545520 545844 546073 546320 546617 546903 547062 547078 547127 547149 547342 547446 547542 547956 548085 548208 548250 548289 548369 548383 548460 548500 549448 549602 549620 549634 549679 550008 550060 550602 550844 550896 550953 551119 551697 552003 552079 552180 552560 552853 553117 553450 555173 555351 555429 556151 556329 556367 556391 556475 556683 556952 557158 557948 558089 558182 558251 558627 559124 559306 559372 559424 559807 560011 560184 560218 560883 561209 561255 561535 561606 561843 562191 562228 562659 562705 562911 562921 563096 563162 563232 563378 563479 563553 564077 564402 564482 564496 564510 564661 565168 565435 565582 565763 565775 566251 566394 566456 567134 567196 567223 567242 567244 567445 567504 567748 568042 568191 568286 568603 568737 569112 569148 569224 569440 570098 570189 570277 570396 570716 571205 571522 571968 572027 572075 572674 572922 572989 573799 574075 574078 574222 574675 574810 574860 574978 575214 575470 575480 575528 575810 575935 576091 576102 576220 576339 576368 576509 576540 576623 576786 576813 576856 576872 577046 577732 577762 577771 578228 578543 578945 579101 579228 579530 579550 581058 581065 581249 581353 581410 582116 582286 582293 582410 582492 582601 582634 582673 583558 583598 583752 583828 583860 584016 584603 585090 585427 585461 585528 585633 585701 585720 586045 586046 586209 586368 586376 586780 587603 587872 588130 588131 588213 588247 588433 588636 588789 588998 589433 589608 590163 590698 590704 590815 590988 591122 591271 591414 591460 591467 591643 592908 592968 593032 593324 593467 593754 593770 593774 593775 593784 593829 594014 594081 594117 594353 594763 594852 594912 595625 595689 597033 597520 597559 598018 598084 598114 598387 598761 599060 599086 599142 599224 599334 599385 599777
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 'ctraj.c8' 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.
	Writing 'rep.c8.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. : 0.0460 s (0.00%)
TIME:	  Pairwise Calc.: 0.5951 s (0.01%)
TIME:	  Clustering    : 0.1136 s (0.00%)
TIME:	  Cluster Post. : 5994.3098 s (99.99%)
TIME:	Total: 5995.0693 s

TIME: Analyses took 5995.0924 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: 6736.0609 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.