CPPTRAJ: Trajectory Analysis. V15.00 OpenMP
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| Date/time: 11/16/15 23:16:03
| Available memory: 124109 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 7 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 7 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 0.0100 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: 744.4095 s
TIME: Avg. throughput= 806.0079 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 7 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 (704330000)
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% 80% 91% Complete.
Saving pair-wise distances to CpptrajPairDist
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: 2993 points changed cluster assignment.
Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 1: 414 points changed cluster assignment.
Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 2: 200 points changed cluster assignment.
Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 3: 111 points changed cluster assignment.
Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 4: 101 points changed cluster assignment.
Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 5: 93 points changed cluster assignment.
Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 6: 85 points changed cluster assignment.
Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 7: 84 points changed cluster assignment.
Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 8: 38 points changed cluster assignment.
Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 9: 11 points changed cluster assignment.
Round 10: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 10: 12 points changed cluster assignment.
Round 11: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 11: 3 points changed cluster assignment.
Round 12: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 12: 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: 7 clusters 600000 frames
#Cluster 0 has average-distance-to-centroid 1.285048
#Cluster 1 has average-distance-to-centroid 0.958208
#Cluster 2 has average-distance-to-centroid 0.905283
#Cluster 3 has average-distance-to-centroid 1.130966
#Cluster 4 has average-distance-to-centroid 1.349975
#Cluster 5 has average-distance-to-centroid 1.641538
#Cluster 6 has average-distance-to-centroid 1.672274
#DBI: 1.425757
#pSF: 160257.998342
#Algorithm: Kmeans nclusters 7 maxit 100
#Representative frames: 178560 214810 49969 431154 349276 278940 90163
#Sieve value: 200 (random)
#Sieved frames: 62 89 321 471 740 809 1079 1521 1918 2039 2167 2598 2786 2888 3107 3317 3408 3511 3535 3864 4380 4966 5169 5309 5392 5459 5803 5966 6092 6192 6411 6449 6488 6733 7413 7799 8104 8286 8298 8499 8538 8548 8797 8860 9076 9237 9423 9445 9446 9696 9741 10194 10273 10377 10474 10596 10633 10657 10724 10838 11074 11349 11468 11614 11819 11824 12135 12408 12813 12814 13120 13393 13450 13580 13649 13795 13936 13978 13988 14315 14630 14685 14861 15300 15719 16115 16620 16710 17309 17317 17786 18580 18781 19025 19224 19225 19268 19511 20203 20677 20890 20968 21165 21310 21610 22276 22496 22575 22671 23426 23671 24395 24447 24448 24655 25371 25697 25711 25794 25928 25962 25992 26016 26036 26047 26140 26748 27152 27181 27191 27220 27573 27585 27671 28035 28158 28448 28757 29246 29285 29555 29608 29720 29749 29820 30219 30406 30605 30606 30734 30854 30916 31144 31380 31506 31740 31743 31751 31783 31927 32029 32118 32170 32336 32694 32789 32941 33306 33903 34170 34560 34904 35082 35267 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533250 533598 533704 533720 533730 533976 534078 534239 534244 534435 534595 534624 534667 534798 534894 535007 535055 535294 535295 535384 535408 535417 535703 535747 535841 535904 536006 536156 536246 536332 536742 536752 537438 537643 537661 537905 537957 538249 538280 538294 538985 539165 539199 539425 539430 539695 539762 539890 540418 541040 541153 541473 541556 541622 541641 541697 541819 541975 542098 542150 542758 542778 543493 543539 543665 543731 543975 544255 544423 545421 545559 545623 545900 545939 545966 546045 546465 546561 546646 547220 547439 547657 547879 547897 548145 548195 548249 548259 548742 548953 548974 549151 549309 549351 549533 549573 549978 550228 550651 551120 551612 551786 551855 552369 553147 553215 553314 553353 553402 553494 553575 553751 553792 553807 553966 554174 554319 554359 554465 554676 554695 554897 555059 555882 556451 556470 556615 556710 556778 556941 557311 557443 557661 557699 557825 557905 557941 557965 558014 558430 558489 558516 558565 558640 558720 559031 559766 560001 560230 560327 560558 560851 561094 561221 561352 561436 561736 561749 561769 561792 561931 561960 562112 562202 562258 562628 562719 562774 562779 563187 563746 563935 564088 564356 564762 565173 565225 565400 565532 565584 565723 565728 566111 566214 566393 566573 566834 566856 566887 567004 567019 567171 567477 567543 567627 567681 567743 567831 568038 568190 568270 568350 568429 568616 568630 568734 569229 569419 569574 569592 569660 570370 570404 570428 570644 570694 570700 570843 570978 571269 571805 571891 571959 572079 572454 572572 572705 572818 573145 573331 573479 573741 573939 574278 574339 574731 575116 575151 575274 575408 575586 575742 575796 575975 576110 576308 576514 576581 576767 576951 576994 577062 577155 577249 577352 577761 577811 577861 578047 578224 578231 578300 578409 578647 578788 578832 579184 579194 579935 580159 580889 581556 581615 581818 582169 582307 582563 582733 582745 583007 583108 583125 583273 583494 583688 583924 584282 584588 584922 585324 585530 585876 586118 586641 586672 587106 587209 587512 588488 588839 589147 589381 590005 590216 590513 590545 590820 590834 591018 591265 591430 591897 592276 592341 592705 592725 592756 592926 593080 593217 593672 593855 593941 594327 594543 594666 594716 594825 594992 595131 595144 595186 595269 595441 595586 595796 597089 597394 598015 598020 598196 598263 598551 598591 598612 599002 599281 599324 599329 599473 599631 599892
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. : 0.0084 s (0.00%)
TIME: Pairwise Calc.: 0.3766 s (0.01%)
TIME: Clustering : 0.5948 s (0.01%)
TIME: Cluster Post. : 6623.2948 s (99.99%)
TIME: Total: 6624.2781 s
TIME: Analyses took 6624.2877 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: 7383.5628 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.