CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/02/16 16:01:36 | Available memory: 15.872 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 50000,100000,150000,200000,250000,300000,350000,400000,450000,500000,549996,599996] 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 500000 549996 599996 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 50000 of 50000) Looking for frames at 298.41 K 10: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 49996 of 49996) 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 599996 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 (1-50000, 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 (1-49996, 1) ----- 90% ----- traj.1.01 (1-50000, 1) ----- 100% Complete. Read 599996 frames and processed 599996 frames. TIME: Avg. throughput= 48.6084 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 50000,100000,150000,200000,250000,300000,350000,400000,450000,500000,549996,599996] Starting clustering. Mask [:1,2&!@H*] corresponds to 39 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (1255690000) Estimated pair-wise matrix memory usage: > 17.994 MB Pair-wise matrix set up with sieve, 599996 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: 86 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 52 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 29 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 6 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 2 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 4 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 3 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 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 599996 frames #Cluster 0 has average-distance-to-centroid 1.128254 #Cluster 1 has average-distance-to-centroid 1.170772 #Cluster 2 has average-distance-to-centroid 1.339003 #Cluster 3 has average-distance-to-centroid 1.597274 #Cluster 4 has average-distance-to-centroid 1.643050 #DBI: 1.273453 #pSF: 192063.942148 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 11792 532981 46930 319657 69865 #Sieve value: 200 (random) #Sieved frames: 201 269 379 434 668 943 1007 1028 1191 1511 2145 2407 2576 2679 2771 3685 3854 3889 4086 4259 4325 4480 5009 5294 5405 5485 5606 5746 5993 6018 6063 6103 6200 6220 6257 6853 6922 6978 7028 7225 7353 7933 8023 8815 8917 9850 10219 10490 10570 10760 10854 10974 11337 11344 11559 11716 11792 11950 12000 12022 12041 12438 12478 12795 12978 13096 13267 13437 13522 13573 13699 13714 13908 14108 14268 14308 14481 14613 14752 14851 15084 15131 15181 15260 15632 15851 16368 16494 16655 17774 17830 17913 18218 18335 18447 18500 18879 18883 19007 19147 19232 19640 19646 19714 19849 19857 20209 20322 20335 20521 20553 20719 21148 21237 21326 21371 21896 21965 22005 22083 22434 22711 22829 22941 22949 23157 23442 23783 24172 25024 25957 26068 26288 26316 26643 26977 27085 27090 27167 27803 27820 27966 28347 28438 28723 29217 30118 30604 30726 30912 31489 31853 31873 31901 31914 32287 32421 32573 32769 32867 32926 32947 33133 33301 33692 33863 34016 34159 34305 34306 34369 34452 34471 34554 35096 35550 36395 36555 36570 36756 37195 37500 37814 37909 37964 38094 38430 39000 39151 39504 39839 39951 40086 40592 40645 41088 41123 41744 42070 42201 42642 42897 42983 43153 43243 43376 43427 43451 43474 43711 43775 43919 44324 44461 44911 45104 45212 45374 45616 46035 46472 46494 46700 46778 46930 47192 47495 47650 47663 48066 48152 48653 48939 49065 49417 49500 49942 50099 50203 50336 50861 50892 50974 51014 51079 51172 51213 51281 51435 51483 51524 52370 52417 52679 52862 52999 53119 53157 53659 53661 54354 54394 54477 54518 54812 54898 55072 55093 55412 56170 56497 57004 57313 57543 57824 57908 58000 58349 58390 58543 58732 58837 59677 59689 59875 59998 60056 60184 60563 60637 60691 60861 60920 60932 61135 61173 61251 61386 61825 61881 62160 62208 62575 62704 63158 63380 63892 64056 64167 64173 64697 64844 65263 65543 65806 65903 65939 65965 65994 66258 66313 66423 66591 66635 66668 66752 66773 67133 67326 67361 67828 67849 67866 67916 67917 67951 68401 68456 68519 68565 68691 68858 69359 69653 69865 70133 70137 70142 70479 70532 70720 71629 72296 72432 72522 72643 72934 73466 73706 73900 74323 74784 74798 74977 75237 75253 75400 75478 75624 75721 75739 75782 75832 75870 76695 76940 76972 77086 77368 77392 77525 77536 78665 78672 79059 79251 79270 79414 80098 80137 80291 80617 81176 81374 81495 81556 82282 82310 82359 82497 82674 82862 83622 83886 84020 84021 84100 84168 84191 84308 84330 84640 85070 85118 85381 85878 86194 86722 86766 86904 86971 87000 87160 87208 87240 87648 87824 88033 88234 88331 88476 88560 88712 88776 89385 90018 90109 90223 90427 90641 91173 91219 91230 91240 91386 91529 91619 91674 91716 91730 91751 92328 93052 93226 93521 93567 93620 93675 93722 93841 94021 94181 94405 94452 94453 95079 95436 95454 95534 95612 95800 96081 96245 96250 96351 96459 96498 96735 96820 96839 96845 96873 96893 96896 97019 97116 97177 97191 97257 97398 97753 98159 98467 98523 98722 98845 99234 99427 99671 99821 100033 100229 100465 100485 100673 100723 101082 101270 101372 101936 101982 102053 102170 102262 102462 102599 103380 104217 104373 104548 104571 104693 104727 104828 104953 105072 105080 105108 105196 105219 105574 105952 106177 106296 106326 106383 106596 106765 106775 106932 106985 107169 107206 107326 107490 107669 107874 108399 108543 108745 108772 108810 109007 109028 109060 109256 109306 109428 109449 109599 109629 109733 109809 109922 109944 110066 110597 111102 111325 111373 111479 111894 111931 112088 112141 112346 112890 112947 113049 113103 113359 113402 113423 113669 113836 114334 114491 114514 114540 114659 114866 115190 115293 115325 115365 115403 115673 115726 116136 116169 116757 117422 117577 117770 118445 118925 119058 119123 119469 119509 119676 119820 120233 120325 120356 120359 120377 120683 120880 120964 121161 121243 121323 121748 121998 122264 122516 122562 122856 122861 123380 123417 123608 123750 123841 123925 124292 124345 124362 124723 124766 125040 125041 125214 125265 125505 125714 125837 126013 126018 126349 126541 126559 126601 126732 126955 126991 127042 127142 127187 127343 127370 127665 127699 127808 128020 128494 128595 128646 128868 128976 129582 130085 130147 130155 130259 130337 130393 130546 130619 131046 131053 131208 131308 131467 131483 131503 131563 131610 131755 132199 132215 132293 132535 132729 132878 132914 133126 133180 133511 133551 133650 133884 134303 134442 134982 135002 135245 135270 135801 135991 136180 136213 136369 136545 136590 136639 136686 136734 136945 136988 137401 137676 137704 137746 137832 137912 138020 138732 138807 139001 139322 139534 139760 140142 140455 140464 140948 141024 141115 141254 141425 141526 141636 141679 141987 142108 142605 142677 142689 142759 142997 143016 143033 143236 143243 143554 143761 144075 144125 144139 144687 144796 144832 145161 145171 145427 145709 145730 146439 146621 146732 147263 147489 147500 147603 147735 147810 147989 148390 148676 148907 149807 150064 150189 150253 150449 150693 150972 151802 151832 151930 152037 152109 152328 152554 152593 152887 152963 152971 153012 153089 153179 153252 153265 153386 153566 153571 153666 153887 153938 154364 154430 154920 155435 155727 155859 156044 156237 156353 156359 156694 156928 157118 157419 157430 157484 157677 157767 157883 157983 158631 158902 158937 159608 160405 160672 160715 161022 161399 161511 161619 161680 161833 161836 162347 162408 162494 162540 162704 162871 162904 163003 164138 164237 164508 164532 164707 164777 164852 165204 165235 165464 165986 166036 166551 166719 166833 167011 167230 167932 167956 168536 168985 170864 170872 170903 171088 171329 171455 171587 171806 171867 171945 172348 172875 172911 173017 173142 173234 173280 173697 173984 174208 174386 174568 174819 175136 175359 175474 175536 175732 175895 175900 175954 176083 176154 176179 176218 176266 176328 176615 176657 176689 177300 177305 177658 177913 178038 178103 178573 178797 178860 178967 179052 179066 179260 179359 179803 179811 179991 180750 180757 180898 181116 181224 181447 181605 181726 182045 182415 182869 183052 183492 183499 183677 184044 184212 184528 184571 184667 184716 184762 185104 185470 185956 186410 186524 187081 187376 187628 188089 188751 188877 189231 189392 189511 189568 189986 190302 190325 190551 191370 192138 192194 192368 192524 192601 192985 193162 193385 194146 194459 194504 194507 194535 194720 194868 194979 195142 195594 195913 196141 196397 196466 196500 196556 196832 196873 196891 196912 196979 197435 197601 197784 198223 198527 198531 198826 198989 199354 199868 200027 200223 200357 200612 200648 200801 200806 201038 201143 201211 201261 201376 201456 201480 201508 201561 201695 201835 202045 202232 202417 202430 202537 202582 202876 204265 204418 204422 205091 205620 205655 205733 205829 206119 206253 206264 206269 206325 206365 206883 206897 207256 207715 208085 208480 208543 208940 209015 209402 209520 209609 209725 209753 209822 209967 210083 210221 210390 210566 210759 210825 210832 210910 211522 211589 211599 211642 211707 211810 211858 211916 211926 212064 212322 212405 212662 212689 213066 213075 213637 213858 214303 215066 215430 215533 216105 216146 216201 216940 217252 217849 218347 218507 218664 219217 219413 219529 219573 219911 220038 220085 220126 220248 220471 220476 220800 220867 220954 221043 221324 221405 221608 221840 221939 222045 222272 222388 222525 222962 223086 223774 224131 224224 224281 224288 224309 224387 224481 224600 224765 224919 225039 225190 225354 225395 225686 226513 226929 227123 227596 227617 227636 227710 227898 227984 227996 228077 228131 228183 228266 228284 228674 229125 229330 229375 229892 229921 230532 230719 231055 231514 232179 232215 232423 232500 232781 233095 233289 233661 233682 234034 234413 234546 234605 235056 235128 235149 235202 235281 235318 235637 235710 236243 236964 237043 237782 238310 238449 238630 238692 238884 239207 239394 239492 239818 239858 240609 240784 240883 241087 241236 241613 241854 242052 242772 242985 243169 243575 243867 243912 244029 244109 244610 244624 244798 245266 245539 245549 245648 245691 245880 246135 246224 246352 246492 246567 246638 246667 246887 247016 247089 247190 247207 247218 247595 247675 248273 248551 248745 248790 248928 249163 249344 249413 249627 249628 250512 250601 250633 251157 251217 251241 251326 251756 251876 251898 252934 253193 253294 253317 253354 253359 253364 253861 253928 253950 254238 254273 254316 254336 254361 254430 255220 255279 255893 255963 255987 256038 256043 256088 256334 256370 256544 256610 257192 257280 257294 257329 257355 257703 257778 258015 258384 258540 258712 259285 259970 259975 260312 260653 260656 260812 260974 260983 260999 261292 261349 261365 261550 261905 262660 262978 263412 263647 263671 263741 263944 264418 264693 265013 265542 265572 265657 265891 265922 266022 266105 266147 266224 266285 266428 266497 266885 267139 267279 267329 267925 268088 268248 268521 268685 269270 269338 269530 269573 269854 270303 270494 270499 270949 271323 271349 271365 271499 271607 271830 272539 272697 272742 272934 273478 273704 273892 274117 274119 274323 274361 274417 274420 274535 274674 274801 274845 274991 275044 275230 275263 275820 276377 276509 276592 277131 277305 277365 277428 277692 277710 277784 277905 278575 278864 278983 278996 279036 279110 279112 279114 279122 279184 279381 279575 279847 279920 279937 280053 280106 280212 280238 280301 280422 280689 281006 281051 281195 281459 281684 281780 281821 281904 282057 282380 282884 283179 283767 283775 284355 284412 284441 284481 284568 284880 285623 285680 285733 286038 286092 286622 286942 287357 287804 287890 288032 288389 288590 288682 288958 289110 289518 289521 289541 289545 289619 289704 289955 290000 290023 290160 290352 290495 290509 290596 290802 290874 290945 291261 292319 292662 292788 292859 292917 293218 293448 294391 294441 294532 294681 294734 294933 295127 296045 296222 296487 296640 296690 297287 297330 297342 297524 297782 297851 297864 297913 297923 298036 298470 298633 298670 299105 299329 299620 299694 299696 299822 299892 299984 300237 300421 300523 300561 300593 300803 300818 300924 301089 301314 301398 301526 301530 301949 302026 302242 302376 302597 302604 303013 303025 303027 303206 303591 303612 304067 304627 305008 305053 305120 305308 305429 305883 305980 306097 306206 306521 306528 306530 306603 306840 306886 307052 307261 307654 307695 308053 308665 309027 309170 309998 310170 310207 310434 310574 310735 310901 311024 311035 311398 311445 311514 311657 311811 313226 313590 313621 313642 313721 313845 313906 314465 314551 314662 314675 314744 315446 315596 315613 315755 315762 315795 316016 316813 317038 317349 317372 317549 318012 318222 318339 318555 319169 319657 319671 319921 320516 320970 321507 321543 322085 322451 322465 322511 322717 322943 323021 323529 323588 323631 323786 324004 324100 324256 324341 324692 325020 325238 325299 325628 325706 325832 325958 326135 326193 326432 326639 326662 326665 326673 326905 326957 327073 327202 327323 327631 328066 328097 328315 328478 328935 329215 329419 329526 329755 330023 330110 330359 330670 331025 331205 331269 331388 331661 331735 331873 332436 332724 333237 333253 333291 333309 333329 334043 334180 334320 334461 334573 334998 335012 335133 335440 335603 335938 336262 336385 336541 336865 337113 337123 337218 337267 337500 337539 337674 338290 338455 338487 338612 338643 338868 338978 339109 339149 339339 340976 341287 341431 341696 341882 342050 342169 342464 342931 342996 343687 344137 344145 344164 344216 344240 344955 345049 345156 345335 345354 345769 345984 346087 346145 346310 346336 346748 346808 347266 347575 347991 348057 348082 348171 348812 349267 349341 349500 349955 350240 350463 350574 350610 350659 350853 350952 351028 351032 351143 351204 351381 351394 351515 351533 351734 351770 351782 351897 352537 352554 352659 353664 353895 353952 354430 354735 354789 354791 355013 355303 355554 355611 355850 355931 356082 356111 356223 356298 356312 357065 357197 357310 357426 357671 357780 358003 358196 358371 358436 358542 358850 358887 358913 358974 359152 359295 359562 359576 359795 360073 360151 360553 360587 360749 360927 360955 360991 361039 361419 361432 361522 361670 361953 362076 362200 362253 362711 362777 362888 362993 363150 363389 363543 363560 363666 363757 363858 363943 364152 364208 364231 364480 364528 364754 364896 364964 365171 365194 365245 365433 365522 365561 366238 366361 366536 366630 366679 366739 366899 366955 367026 367306 367323 367551 367626 367718 367795 367818 367956 368246 368372 368521 368682 368693 368835 369034 369173 369262 369929 370114 370412 370794 371024 371060 371379 371460 371551 371731 371755 371817 371942 371955 372196 372299 372476 372574 372620 373042 373140 373207 373271 373423 373593 374167 374355 374388 374739 374959 375113 375182 375195 375255 375271 375284 375343 375397 375634 375644 375820 376062 376242 376988 377036 377169 377340 377356 377685 377791 377805 378153 378392 378774 378852 378937 379743 380347 380411 380719 381039 381059 381147 381831 382038 382364 382386 382726 382881 383150 383314 383778 383964 384374 384807 384823 384892 385004 385131 385179 385182 385778 386560 387153 387897 388306 388424 388425 388524 388699 388707 388945 389236 389290 389295 389431 389753 389876 390227 390289 390313 390884 391176 391258 391282 391598 391749 391867 392307 392313 392357 392430 392658 392733 393043 393091 393098 393296 393351 393528 393533 393546 394644 394768 395249 395275 395291 395501 396062 396069 396115 396251 396258 396464 396476 396832 397127 397197 397679 397797 397957 397978 398914 399089 399658 400004 400250 400480 400718 400770 400784 400875 400955 401445 401557 401750 402105 402360 402376 402751 403049 404150 404267 405105 405412 405428 405458 405660 405772 405859 406026 406358 406908 407109 407529 407550 407639 408163 408316 408424 408640 408650 408869 409488 409718 409946 410223 410331 410724 410927 411336 411764 412033 412110 412338 412365 412636 412650 412659 412678 412710 412726 412974 413036 413263 413299 413454 413540 413636 413642 413850 413927 414031 414055 414962 414999 415077 415306 415647 415801 415833 416097 416360 416556 416629 416703 416801 416820 417425 418203 418469 418566 418619 418988 419452 419748 420030 420372 420509 420519 421062 421527 421735 422124 422510 422622 422982 423010 423071 423223 423408 423746 424039 424073 424080 424168 424244 424827 425306 425422 425581 425592 425722 425787 425958 426174 426355 426361 426393 426437 426468 426544 426725 427030 427428 427546 427691 427744 428026 428497 428799 428970 429192 429225 429244 429247 429365 429408 429458 429708 429998 430485 430521 430657 430731 430754 431011 431101 431387 431531 431722 432267 432318 432571 432649 433547 433988 434013 434492 434623 434894 434913 434921 434923 435036 435539 435655 435776 435821 436045 436523 436534 436667 436684 436771 436772 436805 436874 436953 437153 437478 437529 437960 438201 438304 438310 438345 438406 438418 438486 438562 438671 438705 438887 439606 439691 440012 440048 440350 440359 440733 441353 441457 441565 442700 442864 442954 443124 443316 443367 443731 443888 444092 444209 444317 444586 444681 444686 444761 445110 445152 445221 446089 446156 446279 446347 446593 446860 447227 447429 447581 448074 448225 448317 448500 448600 449108 449356 449576 449654 450222 450258 451252 451376 451539 451719 451870 452148 452184 452347 452634 452735 452869 452930 452969 453635 454272 454430 454659 454675 455012 455064 455207 455395 456201 456276 456384 456664 456797 456961 456986 457383 457422 457428 457505 457543 457556 457805 457866 458016 458255 458280 458352 458893 459175 459567 459921 459930 460188 460224 460583 460671 460682 461257 461278 461568 461830 461999 462127 462224 462264 462615 462976 463111 463143 463205 463893 464095 464155 464588 464691 464876 464946 465379 465487 465681 465805 465905 466152 466163 466355 466367 466409 466535 466689 466762 466930 466971 467236 467429 467613 468079 468115 468414 468435 468762 468867 469227 469441 469706 469898 470176 470194 470316 470536 470707 470850 470863 471062 471142 471270 471683 471871 471887 472185 472189 472213 472428 472828 472885 473006 473386 473407 473537 473762 473811 474164 474214 474918 474943 474983 475006 475146 475220 475517 476012 476200 476243 476434 476478 476512 476643 476719 476749 476920 477163 477372 477392 477438 477445 477518 477717 477925 477932 478123 478188 478232 478527 478642 478708 478838 478921 479281 479622 479650 479726 479804 479899 480049 480196 480358 481246 481473 481540 481707 482091 482203 482301 482356 482397 482759 482825 482847 482860 483020 483248 483432 483535 483783 484273 484354 484419 484747 485038 485405 485680 485689 486008 486036 486182 486429 486559 487235 487278 487772 487871 488324 488510 488546 489039 489343 489344 489688 489970 490253 490470 490562 490738 490828 491002 491208 491455 491530 491629 491716 491851 491872 492034 492606 492780 493366 493371 493655 493677 493932 493967 494415 494508 494546 495269 495278 495409 495458 495583 496027 496203 496238 496249 496367 496402 496422 496549 496670 496780 497461 498138 498487 498636 498653 498692 498771 498972 499003 499068 499096 499182 499197 499411 499420 499508 500358 500780 500965 501013 501265 501519 501605 502339 502431 502773 502824 502830 503093 503109 503256 503295 503612 503659 504221 504281 504322 504953 505089 505151 505252 505699 505883 505984 506031 506358 506432 506462 506537 507286 507301 507521 507688 507759 507827 507876 507949 508130 508144 508208 508475 508527 508977 509143 509159 509351 509386 509712 509804 510342 510750 510852 510943 511012 511181 511315 511658 511749 511914 512153 512170 512338 512509 512794 512912 512955 513054 513363 513643 513940 513949 513963 514849 514892 515140 515507 515545 515865 515909 516028 516865 517045 517419 517438 517588 517619 518142 518244 518321 518365 518554 519232 519243 519440 519441 519605 519617 520301 520885 521079 521677 521731 521852 522516 522641 523007 523306 523338 523762 523981 524154 524310 524445 524607 524635 524636 524693 524934 524964 525352 525383 525496 525651 525735 525989 526111 526150 526349 526473 527392 527656 528106 528165 528649 529253 529328 529806 529964 530180 530453 530553 530687 530873 530946 530972 531571 531979 532648 532688 532981 533178 533384 533545 533575 533842 533881 533903 534111 534734 535001 535210 535221 535289 536029 536178 536368 536388 536490 536542 536582 536672 536809 537110 537264 537323 538565 538817 539100 539119 539219 539289 539418 539716 540012 540014 540073 540125 540153 540298 540383 540699 540890 540894 541075 541182 541379 541555 541589 541754 541784 542043 542365 543144 543261 543622 544315 544363 544736 544920 545243 545728 545983 546002 546326 546608 546779 546810 546957 547075 547249 547520 547575 547740 547979 548026 548315 548409 548475 548522 549049 549356 549362 549485 549696 549700 550253 550792 550802 550835 550914 551006 551037 551653 551828 553046 553061 553275 553299 553381 553382 553452 553604 553882 554077 554197 554209 554650 554659 554666 555448 555540 555672 555997 556186 556979 557066 557213 557788 558110 558318 559196 559366 559391 559450 559654 559672 559701 559982 560268 560358 560967 561010 562377 562486 562651 562772 562870 562934 563620 563893 564321 564715 565362 565425 565535 565597 565932 565959 565971 566680 566696 566731 566850 567051 567281 567333 568031 568230 568254 568397 568625 568649 568705 569116 569232 569316 569384 569557 569711 570260 570354 570594 570599 570978 571092 571227 571418 571515 571716 571791 571981 572151 572388 572584 572946 573013 573302 573482 573844 574099 574109 574313 574884 574904 575023 575104 575363 575463 575653 575724 575915 575954 576112 576472 577320 577470 577528 578236 578357 578412 578998 579073 579186 579285 579517 579652 579897 580025 580154 580405 580762 581066 581394 581440 582064 582355 582597 582629 582773 582809 583214 583302 583393 583520 583630 583653 583849 583868 584066 584382 584385 584397 584538 584655 585018 585785 585910 586226 586445 586750 587243 587364 587707 587911 588353 588413 588633 588737 588886 589134 589160 589269 590003 590733 590851 591097 591180 591294 591896 591899 591995 592429 592769 592788 592849 593098 593346 593510 593793 593964 594002 594340 594436 594972 595695 596017 596516 596567 596682 596769 596781 596885 596923 597885 598088 598480 598728 598816 598933 598978 599322 599562 599618 599892 599982 Warning: split frame 599996 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. : 9.9262 s ( 2.02%) TIME: Pairwise Calc.: 6.8767 s ( 1.40%) TIME: Clustering : 0.6713 s ( 0.14%) TIME: Cluster Post. : 474.0248 s ( 96.44%) TIME: Total: 491.4991 s TIME: Analyses took 491.5000 seconds. DATASETS (3 total): RMSD_00006 "RMSD_00006" (double, rms), size is 599996 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 599996 (467.997 MB) Box Coords, 63 atoms Cnum_00008 "Cnum_00008" (integer), size is 599996 RUN TIMING: TIME: Init : 0.0009 s ( 0.00%) TIME: Trajectory Process : 12343.4542 s ( 96.17%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 491.5000 s ( 3.83%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 12834.9553 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 12852.7399 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.