CPPTRAJ: Trajectory Analysis. V16.00b OpenMP
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| Date/time: 06/02/16 16:32:02
| Available memory: 16.033 GB
INPUT: Reading input from '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]]
Reading '../../tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF
[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]]
Reading '../../tip3p/ff12sb/run2/traj.1.01' as Amber NetCDF
[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]]
Reading '../../tip3p/dacP-ff12sb/run1/traj.1.01' as Amber NetCDF
[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]]
Reading '../../tip3p/dacP-ff12sb/run2/traj.1.01' as Amber NetCDF
[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]]
Reading '../../tip3p/chen-garcia/run1/traj.1.01' as Amber NetCDF
[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]]
Reading '../../tip3p/chen-garcia/run2/traj.1.01' as Amber NetCDF
[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]]
Reading '../../tip3p/charmm36/run1/traj.1.01' as Amber NetCDF
[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]]
Reading '../../tip3p/charmm36/run2/traj.1.01' as Amber NetCDF
[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]]
Reading '../../opc/ff12sb/run1/traj.1.01' as Amber NetCDF
[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]]
Reading '../../opc/ff12sb/run2/traj.1.01' as Amber NetCDF
[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]]
Reading '../../opc/dacP-ff12sb/run1/traj.1.01' as Amber NetCDF
[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]]
Reading '../../opc/dacP-ff12sb/run2/traj.1.01' as Amber NetCDF
[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]
RMSD: (:1-2&!@H*), reference is first frame (:1-2&!@H*), mass-weighted.
Best-fit RMSD will be calculated, coords will be rotated and translated.
[cluster :1,2@C5',C4',C3',O3',P,C2 summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 5 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@C5',C4',C3',O3',P,C2]) best-fit
K-MEANS: Looking for 5 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 full.topo.hmr to "_DEFAULTCRD_"
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (6 total):
0: [tip3p-ff12sb] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent
1: [tip3p-dacP-ff12sb] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent
2: [tip3p-chen-garcia] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent
3: [tip3p-charmm36] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent
4: [opc-ff12sb] full.topo.hmr, 4368 atoms, 1086 res, box: Orthogonal, 1085 mol, 1073 solvent
5: [opc-dacP-ff12sb] full.topo.hmr, 4368 atoms, 1086 res, box: Orthogonal, 1085 mol, 1073 solvent
INPUT TRAJECTORIES (12 total):
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.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions):
0: [autoimage origin]
Anchor molecule is 1
1086 molecules are mobile.
1: [strip :WAT,Na+,Cl-]
Stripping 3236 atoms.
Stripped topology: 65 atoms, 2 res, box: Orthogonal, 1 mol
2: [rmsd :1-2&!@H= first mass]
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): 80.400 MB
----- traj.1.01 (1-50000, 1) -----
0%
----- traj.1.01 (1-50000, 1) -----
10%
.....................................................
ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions):
0: [autoimage origin]
Anchor molecule is 1
1086 molecules are mobile.
1: [strip :WAT,Na+,Cl-]
Stripping 3236 atoms.
Stripped topology: 65 atoms, 2 res, box: Orthogonal, 1 mol
2: [rmsd :1-2&!@H= first mass]
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) -----
20%
----- traj.1.01 (1-50000, 1) -----
30%
.....................................................
ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions):
0: [autoimage origin]
Anchor molecule is 1
1086 molecules are mobile.
1: [strip :WAT,Na+,Cl-]
Stripping 3236 atoms.
Stripped topology: 65 atoms, 2 res, box: Orthogonal, 1 mol
2: [rmsd :1-2&!@H= first mass]
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) -----
40%
----- traj.1.01 (1-50000, 1) -----
.....................................................
ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions):
0: [autoimage origin]
Anchor molecule is 1
1086 molecules are mobile.
1: [strip :WAT,Na+,Cl-]
Stripping 3236 atoms.
Stripped topology: 65 atoms, 2 res, box: Orthogonal, 1 mol
2: [rmsd :1-2&!@H= first mass]
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) -----
50%
----- traj.1.01 (1-50000, 1) -----
60%
.....................................................
ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions):
0: [autoimage origin]
Anchor molecule is 1
1084 molecules are mobile.
1: [strip :WAT,Na+,Cl-]
Stripping 4303 atoms.
Stripped topology: 65 atoms, 2 res, box: Orthogonal, 1 mol
2: [rmsd :1-2&!@H= first mass]
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) -----
70%
----- traj.1.01 (1-50000, 1) -----
80%
.....................................................
ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions):
0: [autoimage origin]
Anchor molecule is 1
1084 molecules are mobile.
1: [strip :WAT,Na+,Cl-]
Stripping 4303 atoms.
Stripped topology: 65 atoms, 2 res, box: Orthogonal, 1 mol
2: [rmsd :1-2&!@H= first mass]
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) -----
90%
----- traj.1.01 (1-50000, 1) -----
100% Complete.
Read 600000 frames and processed 600000 frames.
TIME: Avg. throughput= 51.4612 frames / second.
ACTION OUTPUT:
ANALYSIS: Performing 1 analyses:
0: [cluster :1,2@C5',C4',C3',O3',P,C2 summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 5 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@C5',C4',C3',O3',P,C2] corresponds to 11 atoms.
Calculating pair-wise distances.
Random_Number: seed is <= 0, using wallclock time as seed (1252180000)
Estimated pair-wise matrix memory usage: > 17.994 MB
Pair-wise matrix set up with sieve, 600000 frames, 3000 sieved frames.
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete.
Saving pair-wise distances to CpptrajPairDist
Memory used by pair-wise matrix and other cluster data: 20.994 MB
Round 0: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 0: 2995 points changed cluster assignment.
Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 1: 217 points changed cluster assignment.
Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 2: 350 points changed cluster assignment.
Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 3: 118 points changed cluster assignment.
Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 4: 38 points changed cluster assignment.
Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 5: 25 points changed cluster assignment.
Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 6: 16 points changed cluster assignment.
Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 7: 17 points changed cluster assignment.
Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 8: 20 points changed cluster assignment.
Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 9: 33 points changed cluster assignment.
Round 10: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 10: 32 points changed cluster assignment.
Round 11: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 11: 56 points changed cluster assignment.
Round 12: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 12: 61 points changed cluster assignment.
Round 13: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 13: 55 points changed cluster assignment.
Round 14: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 14: 61 points changed cluster assignment.
Round 15: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 15: 88 points changed cluster assignment.
Round 16: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 16: 130 points changed cluster assignment.
Round 17: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 17: 157 points changed cluster assignment.
Round 18: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 18: 94 points changed cluster assignment.
Round 19: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 19: 56 points changed cluster assignment.
Round 20: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 20: 20 points changed cluster assignment.
Round 21: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 21: 5 points changed cluster assignment.
Round 22: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 22: 6 points changed cluster assignment.
Round 23: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 23: 5 points changed cluster assignment.
Round 24: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 24: 1 points changed cluster assignment.
Round 25: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 25: 1 points changed cluster assignment.
Round 26: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
K-means round 26: No change. Skipping the rest of the iterations.
Restoring sieved frames.
Parallelizing calculation with 8 threads
0% 10% 20% 30% 40% 50% 60% 72% 80% 90% Complete.
#Clustering: 5 clusters 600000 frames
#Cluster 0 has average-distance-to-centroid 1.109172
#Cluster 1 has average-distance-to-centroid 0.778938
#Cluster 2 has average-distance-to-centroid 0.789160
#Cluster 3 has average-distance-to-centroid 1.351997
#Cluster 4 has average-distance-to-centroid 1.478364
#DBI: 1.212719
#pSF: 193138.279138
#Algorithm: Kmeans nclusters 5 maxit 100
#Representative frames: 132591 27557 219177 281823 392352
#Sieve value: 200 (random)
#Sieved frames: 275 439 557 629 653 849 867 994 1285 1320 1472 1502 1721 1966 2205 2389 2481 2551 2854 3200 3323 3386 3628 4004 4031 4151 4601 5198 5251 5313 5377 5521 5563 5605 5831 5929 6017 6042 6052 6287 6412 6434 7012 7070 7715 7765 7833 7855 7878 7997 8111 8754 8860 9019 9208 9831 9877 10112 10175 10176 10587 11013 11395 11624 11666 12316 12615 13574 13578 14230 14287 14324 14402 14696 14744 15100 15192 15233 15316 16074 16087 16187 16353 16384 16544 16551 16611 16868 17091 17285 17335 17383 17447 17676 17770 17793 17889 17895 17975 18173 18244 18319 18349 18449 18635 19074 19083 19367 19507 19782 19842 19944 19995 20007 20284 21056 21107 21297 21594 22131 22305 22598 22734 23099 23135 23400 23703 23783 23851 24221 24234 24313 24772 24862 24974 25073 25138 25225 25264 25294 25453 25530 25885 26433 26452 26490 26685 27272 27314 27557 27694 28382 28420 28489 28493 28527 28646 28845 28976 29000 29158 29272 29328 29419 29522 29823 30078 30082 30111 30642 30776 30837 30993 31155 31271 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499400 499431 499549 499767 499977 500246 500295 500639 500741 501116 501119 501839 501872 501875 502109 502768 502828 502873 502934 503217 503322 503364 503441 503645 504440 504496 504637 505473 505857 506114 506226 506592 507457 507783 508147 508276 508294 508355 508517 508617 509462 509576 509946 510421 510881 511063 511180 511238 511493 511587 511591 511640 511642 511819 512217 512423 512449 512575 512910 512995 513076 513542 513623 513696 514121 514143 514374 514377 514432 514844 515090 515229 515476 515491 515530 516165 516355 516465 516948 517021 517045 517199 517307 517428 517550 517660 517995 518290 518671 518680 518691 519557 519700 520272 520284 520667 520763 520821 520834 521008 522332 522430 522996 523164 523317 523345 523539 523672 524133 524275 524306 524528 524534 524852 524910 525157 525302 525327 525357 525705 525713 525856 526434 526455 526636 526691 526777 526785 527006 527207 528073 528245 528429 528543 528969 529909 529981 530175 530498 530685 531015 531086 531397 531820 531886 531916 531942 531945 532025 532052 532502 532616 532667 533176 533292 533394 533461 533700 533715 533865 534343 534389 534730 535026 535421 535547 535609 535965 536105 536132 536258 536509 536670 536717 536821 536834 537304 537612 538002 538107 538208 538230 538477 538508 538518 539362 539422 539537 539605 540129 540143 540326 540828 540991 541054 541257 541411 541665 542051 542333 542466 542680 542716 542847 543062 543429 543525 543630 543645 543652 544319 544409 544536 544728 545294 545554 545908 545975 545985 546247 546518 546950 546961 547163 547184 547209 547603 547609 548402 548530 548661 549288 549539 549555 549577 549728 549879 549947 550107 550217 550641 550654 550795 550824 550873 550966 551027 551028 551075 551489 551602 551900 552492 552656 553123 553306 553929 554236 554511 554566 554590 554713 554807 555255 555336 555569 555794 555854 556435 556494 556652 556705 556748 556782 557037 557239 557351 557507 557602 557613 557672 557704 557935 558067 558170 558412 558593 558995 559244 559314 559328 559467 559629 559667 559826 559910 560198 560882 560954 561079 561441 561476 561814 562896 563119 563677 563697 563805 564150 564285 564361 564507 564623 564714 564922 565274 565426 565514 565595 565639 566109 566231 566302 566429 566546 566724 566836 567153 567649 567752 567788 567960 568387 568390 568438 568549 568682 568921 569246 569361 569810 570506 570593 570784 570883 571067 571447 571741 571763 571852 572545 572864 573007 573039 573052 573102 573712 573736 573882 574248 574578 574616 574837 574864 575168 575383 575586 575675 575776 575812 576392 576494 576605 576770 576782 577125 577540 577674 577729 577753 577991 578072 578323 578392 578415 578715 579312 579607 579723 579932 580042 580135 580314 580406 580684 580720 580896 580946 581007 581142 581266 581405 581996 582026 582148 582527 582548 582591 582645 583142 583307 583387 583542 583651 583816 583849 584054 584483 584659 584830 584902 584987 585003 585022 585102 585104 585353 585394 585458 585587 585656 585696 585996 586221 586723 587040 587084 587156 587390 587721 588026 588203 588609 588731 588842 588985 588992 589372 589424 589542 590054 590257 590547 590959 591175 591182 591617 591830 592158 592224 592559 592910 593148 593161 593192 593355 594244 594696 594765 594785 595594 595745 596778 597004 597438 597453 598065 598148 598301 598503 598563 598564 598587 598683 598754 599551 599636
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 'rep.c0.pdb' as PDB
Warning: No PDB space group specified.
Writing 'rep.c1.pdb' as PDB
Warning: No PDB space group specified.
Writing 'rep.c2.pdb' as PDB
Warning: No PDB space group specified.
Writing 'rep.c3.pdb' as PDB
Warning: No PDB space group specified.
Writing 'rep.c4.pdb' as PDB
Warning: No PDB space group specified.
Cluster timing data:
TIME: Cluster Init. : 0.3439 s ( 0.07%)
TIME: Pairwise Calc.: 7.2560 s ( 1.47%)
TIME: Clustering : 1.4538 s ( 0.29%)
TIME: Cluster Post. : 484.3846 s ( 98.17%)
TIME: Total: 493.4383 s
TIME: Analyses took 493.4438 seconds.
DATASETS (3 total):
RMSD_00006 "RMSD_00006" (double, rms), size is 600000
_DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 600000 (482.400 MB) Box Coords, 65 atoms
Cnum_00008 "Cnum_00008" (integer), size is 600000
RUN TIMING:
TIME: Init : 0.0017 s ( 0.00%)
TIME: Trajectory Process : 11659.2762 s ( 95.86%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 493.4438 s ( 4.06%)
TIME: Data File Write : 0.0001 s ( 0.00%)
TIME: Other : 9.6210 s ( 0.00%)
TIME: Run Total 12162.3428 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 12203.2618 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.