CPPTRAJ: Trajectory Analysis. V15.00 OpenMP
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| Date/time: 11/17/15 16:18:24
| Available memory: 119841 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 20 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= 20
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 0.0131 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: 740.2870 s
TIME: Avg. throughput= 810.4964 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 20 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.
237332 of 597000 sieved frames were discarded as noise.
#Clustering: 7 clusters 600000 frames
#Cluster 0 has average-distance-to-centroid 1.458640
#Cluster 1 has average-distance-to-centroid 0.794720
#Cluster 2 has average-distance-to-centroid 0.749707
#Cluster 3 has average-distance-to-centroid 0.754454
#Cluster 4 has average-distance-to-centroid 0.861708
#Cluster 5 has average-distance-to-centroid 0.678773
#Cluster 6 has average-distance-to-centroid 0.674049
#DBI: 1.268870
#pSF: 28297.024950
#Algorithm: DBSCAN minpoints 20 epsilon 1 sieveToCentroid 0
#NOISE_FRAMES: 52 359 360 9328 9380 12194 14942 17310 28372 28433 29090 29180 31174 31436 33632 39264 43831 45365 46039 46458 50265 51441 51734 55488 58292 61582 62246 65005 66893 69103 69421 70288 73217 73948 75446 75640 77380 85335 88508 91333 92527 94194 95020 95632 100453 101752 102392 105320 110326 111970 115218 115706 118358 123486 124330 124539 126134 126808 127649 130426 131248 131892 132190 137786 138653 140218 140534 140557 142923 147589 148221 148751 149115 149546 149985 155993 159708 160556 161253 168044 168236 168835 172120 175183 176879 183071 184094 184536 185288 188554 193423 194721 200208 200415 200757 201200 201826 202098 202845 203460 204379 204520 205102 205620 205810 206195 208750 208813 209476 210012 210018 211002 211520 211691 211827 212087 213033 213460 215535 215662 215739 217304 218539 218629 218666 219512 220035 220401 221051 222201 222566 223164 223309 224219 224959 225667 226830 230442 230614 231018 231262 232496 232511 232880 233346 233362 233941 233981 237314 240291 240864 240896 241078 241684 241793 242105 244531 245387 245983 246870 248449 248735 248926 249098 249146 249148 250640 251133 251540 251678 251832 252794 253122 253617 253635 254237 260032 260470 261342 262081 262299 263282 263342 264000 264450 264876 265332 266535 266804 269174 269251 269548 270035 270208 270211 270939 270957 271063 271070 273814 273832 275984 276185 276793 277344 279852 279961 279966 280003 281232 282154 282618 282956 285182 286259 286448 287502 288643 289184 289598 290030 290721 290844 290950 291414 291629 292755 293665 293696 293712 294514 294531 295324 295593 295878 296353 297100 297800 298048 299357 299465 300728 301250 301350 301523 301808 305835 305959 306786 306861 308314 308839 309047 311119 312872 314001 315906 316614 318949 319140 319158 319301 319997 320533 321434 321763 321919 322332 322692 324156 325559 325764 326042 326228 327086 327776 327850 327977 330615 331755 332352 332754 333396 333945 334128 334813 335517 336359 336447 337590 337974 338479 338627 338700 338836 339660 339807 340571 341928 341940 342044 342154 342608 343291 343870 345123 345747 348206 348518 348778 348860 349737 350916 351184 351695 351809 353104 353391 354127 354200 355738 357244 357332 357694 357998 358807 358847 359241 359266 360010 360735 360846 361271 361316 362305 362440 362534 362963 362981 363069 363830 363999 364109 364285 364364 364479 364854 365192 367022 367881 367917 368062 369126 370255 370298 371618 371925 372810 373666 374495 374851 375315 375330 377575 377947 378002 379203 380169 380908 381054 381557 381837 381929 381933 382518 382957 383589 383800 384363 384681 384851 386747 387877 388534 389428 390871 390919 391180 391684 392355 392837 393106 393410 394563 395745 395847 398070 398559 398653 398884 398958 399546 399590 400117 407064 407602 410214 412427 412866 413499 416565 416697 419153 422930 429072 430648 431148 431576 438687 439592 441430 442054 443453 445763 445862 447687 448538 448637 455167 457507 458312 458494 459537 462657 462658 463092 464785 467862 476217 476986 482194 485842 487708 489081 489864 490510 492624 493508 495688 497010 502312 503316 503423 504319 505718 508475 511238 512796 513833 515629 516737 516805 518419 518637 519969 520747 524992 526537 527605 527886 529296 529328 532044 532357 532359 533112 533428 533928 535108 536953 539791 539934 541379 545737 546230 546243 547119 547585 548390 549281 550285 551750 552926 554110 554144 554793 556088 560569 560871 563627 565422 567903 569007 572744 573117 573770 574286 578167 579255 588428 588469 589089 590899 592598 593869 596225 598016 598831 598930 599837
#Number_of_noise_frames: 520
#Representative frames: 8806 147569 572096 429041 101561 546595 341762
#Sieve value: 200 (random)
#Sieved frames: 52 56 125 176 180 359 360 491 576 938 1252 1332 1593 1654 1720 1737 2007 2251 2286 2315 2660 2865 3214 3271 3324 3327 3401 4072 4181 4246 4865 5325 5428 5480 6849 7023 7159 7437 7777 7853 8033 8357 8394 8638 8736 8806 8960 9328 9380 9508 9600 10233 10264 10358 11065 11072 11254 11375 11466 11619 11693 11790 12086 12102 12128 12194 12274 12463 12540 12830 13066 13122 13225 13489 13591 13944 14709 14925 14942 15050 15411 15518 15704 16184 16193 16754 17249 17295 17310 17493 17570 18151 18311 18351 18404 18718 18792 19528 19623 19780 20096 20142 20391 20531 20907 21459 21464 21733 21863 22053 22132 22342 22656 22772 22776 22782 22926 23040 23491 23499 23614 23775 23809 24440 24587 24696 24982 24999 25221 25257 25270 25434 25955 26327 26342 26612 26630 26758 26961 27274 27605 27906 28102 28372 28433 28520 28708 28957 29090 29148 29180 29294 29375 29466 29596 29803 29886 29965 30188 30445 31174 31313 31373 31406 31436 31988 32075 32519 33043 33163 33499 33632 33711 33889 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472184 472584 472704 472758 473109 473263 473409 473444 473602 473627 473660 473787 474405 475178 475208 475519 475844 475919 476217 476336 476685 476986 477254 477302 477733 477984 478298 478937 479037 479442 479708 480272 480630 481230 481275 481441 481840 481861 482194 482274 482313 482599 482778 483006 483097 483367 483552 483555 483906 484150 484325 484742 484851 485014 485352 485723 485842 485944 486107 486292 486696 486992 487083 487137 487183 487269 487558 487708 487716 487729 487793 487827 487961 488193 488244 488446 488718 488888 489081 489295 489370 489721 489864 490040 490091 490119 490510 490613 490773 490925 491081 491129 491221 491345 491510 491515 491603 491820 491995 492624 492750 493122 493204 493318 493508 493853 493970 494123 494286 495116 495267 495319 495383 495510 495682 495688 495869 496072 496190 496332 496655 496938 496970 497010 497019 497135 497570 498042 498439 498518 498843 499003 499137 499224 499350 499685 499718 499813 499956 500384 500457 500513 500938 501450 501492 501519 501693 501721 502175 502312 502442 502458 502694 502704 503316 503423 503596 504259 504319 504426 504663 505115 505159 505332 505385 505718 506036 506153 506501 506587 506748 506853 506856 507117 507546 507565 507747 507827 507993 508047 508051 508475 508757 509021 509106 509113 509191 509215 509216 509389 509643 509651 509693 509708 509951 510001 510526 510571 510659 510677 511086 511238 511366 511908 511924 512345 512796 512817 512888 512916 512945 513134 513675 513833 514445 514456 514516 514901 515197 515284 515324 515390 515502 515629 515662 516149 516374 516510 516622 516737 516805 516874 517057 517074 517501 517986 518125 518362 518419 518637 519175 519447 519751 519969 519983 520008 520271 520586 520661 520697 520747 520823 520886 521120 521153 521210 521466 522176 522381 522648 522835 522909 523392 523653 523833 524096 524187 524198 524228 524686 524692 524992 525726 525824 525888 526279 526537 526956 527400 527430 527464 527516 527605 527648 527886 529183 529296 529297 529313 529328 529573 529888 530157 530335 530749 531385 531483 531487 532044 532357 532359 532808 532814 532914 533072 533112 533326 533428 533770 533928 534095 534211 534523 534560 534726 535086 535108 536221 536594 536605 536886 536953 537323 537557 537744 538014 538244 538369 538529 538682 538935 538955 539007 539056 539076 539085 539181 539476 539791 539878 539934 539937 540363 541009 541029 541328 541347 541379 541679 541797 542220 542867 542941 542973 543010 543044 543761 544005 544219 544683 545418 545503 545737 545779 545836 546036 546062 546230 546243 546291 546595 547119 547585 547646 548034 548366 548390 548449 549281 549521 549723 549742 549765 550050 550240 550263 550285 550379 550430 550767 551214 551397 551431 551446 551485 551736 551750 551820 551908 551942 552032 552916 552926 552947 553225 553597 553742 554110 554144 554793 554912 555058 555063 555267 555268 555609 556088 556280 556645 556952 557323 557478 557595 557858 558916 559181 559638 560016 560407 560458 560551 560569 560871 561121 561153 561226 561479 561822 561838 561861 561899 561939 562441 562609 562697 563140 563149 563169 563364 563559 563627 563637 564030 564086 564148 564208 564331 564665 564705 564791 564990 565129 565286 565422 565840 566171 566257 566404 567047 567048 567541 567903 567908 568172 568334 568399 568758 569007 569135 569159 569891 570025 570205 570226 570547 570564 570688 570920 571386 571655 572096 572141 572149 572607 572655 572744 572910 572957 573117 573258 573484 573763 573770 573821 574046 574075 574286 574293 574483 574551 574600 574919 574946 574947 575206 575208 575601 576126 576580 576672 577240 577241 577382 577462 577598 577969 578051 578149 578167 578495 579024 579058 579062 579255 579477 579848 579952 581089 581283 581801 582243 582686 582974 583001 583161 583167 583760 583780 583849 583915 584118 584530 584631 585152 585274 585699 586117 586262 586321 586325 586485 586651 586653 586846 586931 587097 587263 587360 587392 587401 587409 587843 588166 588365 588375 588428 588469 588691 588976 588994 589089 589213 589573 589619 589709 589736 589865 590021 590022 590137 590192 590560 590669 590681 590899 592223 592228 592539 592598 593330 593566 593573 593847 593869 594094 594202 594998 595168 595256 595496 595729 595780 595791 596171 596225 596559 597121 597201 597275 597395 597590 598016 598049 598091 598546 598610 598765 598797 598831 598930 598966 599013 599143 599366 599810 599837
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 '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.
Cluster timing data:
TIME: Cluster Init. : 0.0153 s (0.00%)
TIME: Pairwise Calc.: 0.1293 s (0.00%)
TIME: Clustering : 0.0986 s (0.00%)
TIME: Cluster Post. : 7331.8409 s (100.00%)
TIME: Total: 7332.0876 s
TIME: Analyses took 7332.0982 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: 8088.6200 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.