CPPTRAJ: Trajectory Analysis. V15.00 OpenMP
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| Date/time: 11/16/15  23:39:09
| Available memory: 124166 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 kdist 20 sievetoframe 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
	DBSCAN:
		Only calculating Kdist graph for K=20
	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 0.0029 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: 700.0249 s
TIME: Avg. throughput= 857.1124 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 kdist 20 sievetoframe 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.
	Calculating pair-wise distances.
Random_Number: seed is <= 0, using wallclock time as seed (673750000)
	Estimated pair-wise matrix memory usage: > 17.1605 MB
	Pair-wise matrix set up with sieve, 600000 frames, 3000 sieved frames.
 0% 10% 21% 30% 41% 50% 60% 70% 81% 91% Complete.
	Saving pair-wise distances to CpptrajPairDist
	Memory used by pair-wise matrix and other cluster data: 20.0216 MB
	DBSCAN: Calculating Kdist(20), output to Kdist.20.dat
	No clusters found.
	Cluster timing data:
TIME:	  Cluster Init. : 0.0014 s (0.16%)
TIME:	  Pairwise Calc.: 0.3643 s (40.69%)
TIME:	  Clustering    : 0.5288 s (59.06%)
TIME:	  Cluster Post. : 0.0000 s (0.00%)
TIME:	Total: 0.8954 s

TIME: Analyses took 0.8963 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
	sievetoframe "sievetoframe" (integer), size is 0

DATAFILES:
  test.dat (Standard Data File):  RMSD_00000
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 716.7173 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.