CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 16:00:42 | Available memory: 16.032 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&!@H= 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 50000,100000,150000,200000,250000,300000,350000,400000,450000,499733,549733,599733] CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1,2&!@H=]) 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 499733 549733 599733 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, 3299 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent 1: [tip3p-dacP-ff12sb] full.topo.hmr, 3299 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent 2: [tip3p-chen-garcia] full.topo.hmr, 3299 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent 3: [tip3p-charmm36] full.topo.hmr, 3299 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent 4: [opc-ff12sb] full.topo.hmr, 4374 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent 5: [opc-dacP-ff12sb] full.topo.hmr, 4374 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 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 49733 of 49733) 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 599733 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: 63 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](39) Reference mask: [:1-2&!@H*](39) 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): 78.000 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: 63 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](39) 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: 63 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](39) 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) ----- 50% ..................................................... 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: 63 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](39) 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) ----- ----- traj.1.01 (1-50000, 1) ----- 60% ..................................................... 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 4311 atoms. Stripped topology: 63 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](39) 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 (1-49733, 1) ----- 80% ..................................................... 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 4311 atoms. Stripped topology: 63 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](39) 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 599733 frames and processed 599733 frames. TIME: Avg. throughput= 49.8463 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 5 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000,250000,300000,350000,400000,450000,499733,549733,599733] Starting clustering. Mask [:1,2&!@H*] corresponds to 39 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (1261350000) Estimated pair-wise matrix memory usage: > 17.982 MB Pair-wise matrix set up with sieve, 599733 frames, 2999 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: 20.981 MB Round 0: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 0: 2994 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 229 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 232 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 121 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 67 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 31 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 10 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 9 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 10 points changed cluster assignment. Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 9: 9 points changed cluster assignment. Round 10: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 10: 1 points changed cluster assignment. Round 11: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 11: No change. Skipping the rest of the iterations. Restoring sieved frames. Parallelizing calculation with 8 threads 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete. #Clustering: 5 clusters 599733 frames #Cluster 0 has average-distance-to-centroid 0.741917 #Cluster 1 has average-distance-to-centroid 1.052344 #Cluster 2 has average-distance-to-centroid 1.155263 #Cluster 3 has average-distance-to-centroid 1.633339 #Cluster 4 has average-distance-to-centroid 1.576177 #DBI: 1.213778 #pSF: 275112.889822 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 535396 194964 531721 521638 516501 #Sieve value: 200 (random) #Sieved frames: 45 109 115 137 492 553 1072 1129 1490 1549 1879 1913 1936 2131 2160 2198 2279 2468 2527 2655 3008 3315 3717 4023 4266 4628 4783 4936 5050 5244 5395 5465 5652 5752 6163 6188 6656 6730 6830 7274 7624 7752 7922 8035 8363 8440 8675 8744 8947 9139 9210 9260 9650 9764 9793 9813 9833 9926 10158 10209 10318 10674 10837 10910 10920 11983 12210 12216 12731 12805 13244 13249 13355 13658 13759 13839 14192 14427 14737 14747 14816 15073 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539412 539580 539841 540123 540594 540640 541028 541041 541583 541630 542166 542235 542549 542840 542841 543495 543866 543890 543980 544193 545005 545032 545047 545055 545375 545593 545598 545713 545850 546250 546367 546840 547006 547093 547359 547451 547495 547574 547590 548317 548968 549326 549571 549604 549665 549729 549990 550008 550043 550500 550603 550846 551058 551152 551466 551718 551936 551963 552241 552576 552625 552674 552906 553004 553128 553517 553531 554046 554351 554386 554479 554510 554661 555011 555159 555203 555673 555820 556063 556335 557003 557316 557364 557476 557524 557573 557994 558067 558274 558351 558354 559081 559184 559684 559699 560300 561072 561170 561483 561521 561685 562230 562231 562351 562860 563093 563488 563538 563831 564021 564032 564191 564198 564423 564486 564604 564703 564730 564968 564976 565083 565100 565370 565588 565643 565871 566502 566646 566859 566962 567015 567338 567399 567675 567691 567864 568026 568092 568248 568517 568553 568899 569174 569265 569341 569616 569750 569802 571026 571276 571302 571403 571913 572079 572165 572224 572488 572800 572876 573035 573163 573365 573416 573502 573700 573731 573789 573992 574062 574551 574752 574896 575362 575415 575930 576074 576103 576394 577064 577173 577231 577609 578965 579354 579630 579663 579763 579955 581346 581365 581420 581883 581963 582021 582293 583379 583712 583928 584159 584164 584365 584716 584824 585423 585548 585612 585698 585890 586028 586112 586214 586685 586797 586815 587088 587232 587687 587814 587901 587943 588056 588085 588329 588458 589001 589045 589222 589403 589513 589765 589896 590628 591236 592290 592710 592821 592973 593148 593527 594289 594389 594488 594535 594716 594833 594874 595013 595223 595248 595349 595401 595474 595551 595819 595998 596036 596100 596469 596623 596652 596661 596814 596859 597014 597090 597314 597498 597772 597798 597875 598089 598232 598379 598717 598860 598901 599150 599490 Warning: split frame 599733 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. : 0.3464 s ( 0.07%) TIME: Pairwise Calc.: 6.2295 s ( 1.22%) TIME: Clustering : 0.8747 s ( 0.17%) TIME: Cluster Post. : 502.1838 s ( 98.54%) TIME: Total: 509.6343 s TIME: Analyses took 509.6385 seconds. DATASETS (3 total): RMSD_00006 "RMSD_00006" (double, rms), size is 599733 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 599733 (467.792 MB) Box Coords, 63 atoms Cnum_00008 "Cnum_00008" (integer), size is 599733 RUN TIMING: TIME: Init : 0.0018 s ( 0.00%) TIME: Trajectory Process : 12031.6562 s ( 95.86%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 509.6385 s ( 4.06%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 9.8180 s ( 0.00%) TIME: Run Total 12551.1146 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 12566.4887 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.