CPPTRAJ: Trajectory Analysis. V15.00 OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 19:12:51 | Available memory: 123613 MB INPUT: Reading Input from file pt-clust.in [parm ../../tip3p/ff12sb/run1/build/full.topo.hmr [tip3p-ff12sb]] Reading '../../tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology [parm ../../tip3p/dacP-ff12sb/run1/build/full.topo.hmr [tip3p-dacP-ff12sb]] Reading '../../tip3p/dacP-ff12sb/run1/build/full.topo.hmr' as Amber Topology [parm ../../tip3p/chen-garcia/run1/build/full.topo.hmr [tip3p-chen-garcia]] Reading '../../tip3p/chen-garcia/run1/build/full.topo.hmr' as Amber Topology [parm ../../tip3p/charmm36/run1/build/full.topo.hmr [tip3p-charmm36]] Reading '../../tip3p/charmm36/run1/build/full.topo.hmr' as Amber Topology CHAMBER topology: 1: CHARMM 361 * \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File /// [parm ../../opc/ff12sb/run1/build/full.topo.hmr [opc-ff12sb]] Reading '../../opc/ff12sb/run1/build/full.topo.hmr' as Amber Topology [parm ../../opc/dacP-ff12sb/run1/build/full.topo.hmr [opc-dacP-ff12sb]] Reading '../../opc/dacP-ff12sb/run1/build/full.topo.hmr' as Amber Topology [trajin ../../tip3p/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/ff12sb/run1/traj.1.02,../../tip3p/ff12sb/run1/traj.1.03,../../tip3p/ff12sb/run1/traj.1.04,../../tip3p/ff12sb/run1/traj.1.05,../../tip3p/ff12sb/run1/traj.1.06,../../tip3p/ff12sb/run1/traj.1.07,../../tip3p/ff12sb/run1/traj.1.08,../../tip3p/ff12sb/run1/traj.1.09,../../tip3p/ff12sb/run1/traj.1.10,../../tip3p/ff12sb/run1/traj.1.11,../../tip3p/ff12sb/run1/traj.1.12,../../tip3p/ff12sb/run1/traj.1.13,../../tip3p/ff12sb/run1/traj.1.14,../../tip3p/ff12sb/run1/traj.1.15,../../tip3p/ff12sb/run1/traj.1.16,../../tip3p/ff12sb/run1/traj.1.17,../../tip3p/ff12sb/run1/traj.1.18 parm [tip3p-ff12sb]] [trajin ../../tip3p/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/ff12sb/run2/traj.1.02,../../tip3p/ff12sb/run2/traj.1.03,../../tip3p/ff12sb/run2/traj.1.04,../../tip3p/ff12sb/run2/traj.1.05,../../tip3p/ff12sb/run2/traj.1.06,../../tip3p/ff12sb/run2/traj.1.07,../../tip3p/ff12sb/run2/traj.1.08,../../tip3p/ff12sb/run2/traj.1.09,../../tip3p/ff12sb/run2/traj.1.10,../../tip3p/ff12sb/run2/traj.1.11,../../tip3p/ff12sb/run2/traj.1.12,../../tip3p/ff12sb/run2/traj.1.13,../../tip3p/ff12sb/run2/traj.1.14,../../tip3p/ff12sb/run2/traj.1.15,../../tip3p/ff12sb/run2/traj.1.16,../../tip3p/ff12sb/run2/traj.1.17,../../tip3p/ff12sb/run2/traj.1.18 parm [tip3p-ff12sb]] [trajin ../../tip3p/dacP-ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/dacP-ff12sb/run1/traj.1.02,../../tip3p/dacP-ff12sb/run1/traj.1.03,../../tip3p/dacP-ff12sb/run1/traj.1.04,../../tip3p/dacP-ff12sb/run1/traj.1.05,../../tip3p/dacP-ff12sb/run1/traj.1.06,../../tip3p/dacP-ff12sb/run1/traj.1.07,../../tip3p/dacP-ff12sb/run1/traj.1.08,../../tip3p/dacP-ff12sb/run1/traj.1.09,../../tip3p/dacP-ff12sb/run1/traj.1.10,../../tip3p/dacP-ff12sb/run1/traj.1.11,../../tip3p/dacP-ff12sb/run1/traj.1.12,../../tip3p/dacP-ff12sb/run1/traj.1.13,../../tip3p/dacP-ff12sb/run1/traj.1.14,../../tip3p/dacP-ff12sb/run1/traj.1.15,../../tip3p/dacP-ff12sb/run1/traj.1.16,../../tip3p/dacP-ff12sb/run1/traj.1.17,../../tip3p/dacP-ff12sb/run1/traj.1.18 parm [tip3p-dacP-ff12sb]] [trajin ../../tip3p/dacP-ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/dacP-ff12sb/run2/traj.1.02,../../tip3p/dacP-ff12sb/run2/traj.1.03,../../tip3p/dacP-ff12sb/run2/traj.1.04,../../tip3p/dacP-ff12sb/run2/traj.1.05,../../tip3p/dacP-ff12sb/run2/traj.1.06,../../tip3p/dacP-ff12sb/run2/traj.1.07,../../tip3p/dacP-ff12sb/run2/traj.1.08,../../tip3p/dacP-ff12sb/run2/traj.1.09,../../tip3p/dacP-ff12sb/run2/traj.1.10,../../tip3p/dacP-ff12sb/run2/traj.1.11,../../tip3p/dacP-ff12sb/run2/traj.1.12,../../tip3p/dacP-ff12sb/run2/traj.1.13,../../tip3p/dacP-ff12sb/run2/traj.1.14,../../tip3p/dacP-ff12sb/run2/traj.1.15,../../tip3p/dacP-ff12sb/run2/traj.1.16,../../tip3p/dacP-ff12sb/run2/traj.1.17,../../tip3p/dacP-ff12sb/run2/traj.1.18 parm [tip3p-dacP-ff12sb] ] [trajin ../../tip3p/chen-garcia/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/chen-garcia/run1/traj.1.02,../../tip3p/chen-garcia/run1/traj.1.03,../../tip3p/chen-garcia/run1/traj.1.04,../../tip3p/chen-garcia/run1/traj.1.05,../../tip3p/chen-garcia/run1/traj.1.06,../../tip3p/chen-garcia/run1/traj.1.07,../../tip3p/chen-garcia/run1/traj.1.08,../../tip3p/chen-garcia/run1/traj.1.09,../../tip3p/chen-garcia/run1/traj.1.10,../../tip3p/chen-garcia/run1/traj.1.11,../../tip3p/chen-garcia/run1/traj.1.12,../../tip3p/chen-garcia/run1/traj.1.13,../../tip3p/chen-garcia/run1/traj.1.14,../../tip3p/chen-garcia/run1/traj.1.15,../../tip3p/chen-garcia/run1/traj.1.16,../../tip3p/chen-garcia/run1/traj.1.17,../../tip3p/chen-garcia/run1/traj.1.18 parm [tip3p-chen-garcia]] [trajin ../../tip3p/chen-garcia/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/chen-garcia/run2/traj.1.02,../../tip3p/chen-garcia/run2/traj.1.03,../../tip3p/chen-garcia/run2/traj.1.04,../../tip3p/chen-garcia/run2/traj.1.05,../../tip3p/chen-garcia/run2/traj.1.06,../../tip3p/chen-garcia/run2/traj.1.07,../../tip3p/chen-garcia/run2/traj.1.08,../../tip3p/chen-garcia/run2/traj.1.09,../../tip3p/chen-garcia/run2/traj.1.10,../../tip3p/chen-garcia/run2/traj.1.11,../../tip3p/chen-garcia/run2/traj.1.12,../../tip3p/chen-garcia/run2/traj.1.13,../../tip3p/chen-garcia/run2/traj.1.14,../../tip3p/chen-garcia/run2/traj.1.15,../../tip3p/chen-garcia/run2/traj.1.16,../../tip3p/chen-garcia/run2/traj.1.17,../../tip3p/chen-garcia/run2/traj.1.18 parm [tip3p-chen-garcia]] [trajin ../../tip3p/charmm36/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/charmm36/run1/traj.1.02,../../tip3p/charmm36/run1/traj.1.03,../../tip3p/charmm36/run1/traj.1.04,../../tip3p/charmm36/run1/traj.1.05,../../tip3p/charmm36/run1/traj.1.06,../../tip3p/charmm36/run1/traj.1.07,../../tip3p/charmm36/run1/traj.1.08,../../tip3p/charmm36/run1/traj.1.09,../../tip3p/charmm36/run1/traj.1.10,../../tip3p/charmm36/run1/traj.1.11,../../tip3p/charmm36/run1/traj.1.12,../../tip3p/charmm36/run1/traj.1.13,../../tip3p/charmm36/run1/traj.1.14,../../tip3p/charmm36/run1/traj.1.15,../../tip3p/charmm36/run1/traj.1.16,../../tip3p/charmm36/run1/traj.1.17,../../tip3p/charmm36/run1/traj.1.18 parm [tip3p-charmm36]] [trajin ../../tip3p/charmm36/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/charmm36/run2/traj.1.02,../../tip3p/charmm36/run2/traj.1.03,../../tip3p/charmm36/run2/traj.1.04,../../tip3p/charmm36/run2/traj.1.05,../../tip3p/charmm36/run2/traj.1.06,../../tip3p/charmm36/run2/traj.1.07,../../tip3p/charmm36/run2/traj.1.08,../../tip3p/charmm36/run2/traj.1.09,../../tip3p/charmm36/run2/traj.1.10,../../tip3p/charmm36/run2/traj.1.11,../../tip3p/charmm36/run2/traj.1.12,../../tip3p/charmm36/run2/traj.1.13,../../tip3p/charmm36/run2/traj.1.14,../../tip3p/charmm36/run2/traj.1.15,../../tip3p/charmm36/run2/traj.1.16,../../tip3p/charmm36/run2/traj.1.17,../../tip3p/charmm36/run2/traj.1.18 parm [tip3p-charmm36]] [trajin ../../opc/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../opc/ff12sb/run1/traj.1.02,../../opc/ff12sb/run1/traj.1.03,../../opc/ff12sb/run1/traj.1.04,../../opc/ff12sb/run1/traj.1.05,../../opc/ff12sb/run1/traj.1.06,../../opc/ff12sb/run1/traj.1.07,../../opc/ff12sb/run1/traj.1.08,../../opc/ff12sb/run1/traj.1.09,../../opc/ff12sb/run1/traj.1.10,../../opc/ff12sb/run1/traj.1.11,../../opc/ff12sb/run1/traj.1.12,../../opc/ff12sb/run1/traj.1.13,../../opc/ff12sb/run1/traj.1.14,../../opc/ff12sb/run1/traj.1.15,../../opc/ff12sb/run1/traj.1.16,../../opc/ff12sb/run1/traj.1.17,../../opc/ff12sb/run1/traj.1.18 parm [opc-ff12sb]] [trajin ../../opc/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../opc/ff12sb/run2/traj.1.02,../../opc/ff12sb/run2/traj.1.03,../../opc/ff12sb/run2/traj.1.04,../../opc/ff12sb/run2/traj.1.05,../../opc/ff12sb/run2/traj.1.06,../../opc/ff12sb/run2/traj.1.07,../../opc/ff12sb/run2/traj.1.08,../../opc/ff12sb/run2/traj.1.09,../../opc/ff12sb/run2/traj.1.10,../../opc/ff12sb/run2/traj.1.11,../../opc/ff12sb/run2/traj.1.12,../../opc/ff12sb/run2/traj.1.13,../../opc/ff12sb/run2/traj.1.14,../../opc/ff12sb/run2/traj.1.15,../../opc/ff12sb/run2/traj.1.16,../../opc/ff12sb/run2/traj.1.17,../../opc/ff12sb/run2/traj.1.18 parm [opc-ff12sb]] [trajin ../../opc/dacP-ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../opc/dacP-ff12sb/run1/traj.1.02,../../opc/dacP-ff12sb/run1/traj.1.03,../../opc/dacP-ff12sb/run1/traj.1.04,../../opc/dacP-ff12sb/run1/traj.1.05,../../opc/dacP-ff12sb/run1/traj.1.06,../../opc/dacP-ff12sb/run1/traj.1.07,../../opc/dacP-ff12sb/run1/traj.1.08,../../opc/dacP-ff12sb/run1/traj.1.09,../../opc/dacP-ff12sb/run1/traj.1.10,../../opc/dacP-ff12sb/run1/traj.1.11,../../opc/dacP-ff12sb/run1/traj.1.12,../../opc/dacP-ff12sb/run1/traj.1.13,../../opc/dacP-ff12sb/run1/traj.1.14,../../opc/dacP-ff12sb/run1/traj.1.15,../../opc/dacP-ff12sb/run1/traj.1.16,../../opc/dacP-ff12sb/run1/traj.1.17,../../opc/dacP-ff12sb/run1/traj.1.18 parm [opc-dacP-ff12sb]] [trajin ../../opc/dacP-ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../opc/dacP-ff12sb/run2/traj.1.02,../../opc/dacP-ff12sb/run2/traj.1.03,../../opc/dacP-ff12sb/run2/traj.1.04,../../opc/dacP-ff12sb/run2/traj.1.05,../../opc/dacP-ff12sb/run2/traj.1.06,../../opc/dacP-ff12sb/run2/traj.1.07,../../opc/dacP-ff12sb/run2/traj.1.08,../../opc/dacP-ff12sb/run2/traj.1.09,../../opc/dacP-ff12sb/run2/traj.1.10,../../opc/dacP-ff12sb/run2/traj.1.11,../../opc/dacP-ff12sb/run2/traj.1.12,../../opc/dacP-ff12sb/run2/traj.1.13,../../opc/dacP-ff12sb/run2/traj.1.14,../../opc/dacP-ff12sb/run2/traj.1.15,../../opc/dacP-ff12sb/run2/traj.1.16,../../opc/dacP-ff12sb/run2/traj.1.17,../../opc/dacP-ff12sb/run2/traj.1.18 parm [opc-dacP-ff12sb]] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [strip :WAT,Na+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [rmsd :1-2&!@H= first mass out test.dat] RMSD: (:1-2&!@H*), reference is first frame (:1-2&!@H*), with fitting, mass-weighted. [cluster rms :1,2@@H2,N6,C1',P summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 7 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000,250000,300000,350000,400000,450000,500000,550000,600000] CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1,2@@H2,N6,C1',P]) best-fit K-MEANS: Looking for 7 clusters. Sequentially modify each point. Cluster to cluster distance will be based on cluster centroids. Initial clustering will be randomly sieved (with value 200). Previously calcd pair distances CpptrajPairDist will be used if found. Summary of cluster results will be written to clust-summary.dat Summary comparing parts of trajectory data for clusters will be written to split.dat Frames will be split at: 50000 100000 150000 200000 250000 300000 350000 400000 450000 500000 550000 600000 Cluster trajectories will be written to ctraj, format Amber NetCDF Cluster representatives will be written to separate trajectories, prefix (rep), format PDB Warning: One or more analyses requested creation of default COORDS DataSet. CREATECRD: Saving coordinates from Top [tip3p-ff12sb] to "_DEFAULTCRD_" ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [tip3p-ff12sb] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 100000 frames 1: [tip3p-dacP-ff12sb] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 100000 frames 2: [tip3p-chen-garcia] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 100000 frames 3: [tip3p-charmm36] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 100000 frames 4: [opc-ff12sb] 'full.topo.hmr', 4368 atoms, 1086 res, box: Orthogonal, 1085 mol, 1073 solvent, 100000 frames 5: [opc-dacP-ff12sb] 'full.topo.hmr', 4368 atoms, 1086 res, box: Orthogonal, 1085 mol, 1073 solvent, 100000 frames INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 1: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 2: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 3: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 4: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 5: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 6: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 7: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 8: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 9: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 10: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 11: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K Coordinate processing will occur on 600000 frames. TIME: Run Initialization took 0.0122 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[tip3p-ff12sb]' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](41) Reference mask: [:1-2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] Warning: COORDS data sets do not store temperatures. Warning: COORDS data sets do not store times. Estimated memory usage (100000 frames): 77 MB ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[tip3p-dacP-ff12sb]' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[tip3p-chen-garcia]' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[tip3p-charmm36]' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[opc-ff12sb]' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1084 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 4303 atoms. Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[opc-dacP-ff12sb]' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1084 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 4303 atoms. Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 600000 frames and processed 600000 frames. TIME: Trajectory processing: 716.4903 s TIME: Avg. throughput= 837.4154 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [cluster rms :1,2@@H2,N6,C1',P summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 7 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000,250000,300000,350000,400000,450000,500000,550000,600000] Starting clustering. Mask [:1,2@@H2,N6,C1',P] corresponds to 65 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (670530000) Estimated pair-wise matrix memory usage: > 17.1605 MB Pair-wise matrix set up with sieve, 600000 frames, 3000 sieved frames. 0% 11% 20% 30% 40% 50% 60% 71% 80% 91% Complete. Saving pair-wise distances to CpptrajPairDist Memory used by pair-wise matrix and other cluster data: 20.0216 MB Round 0: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 0: 2993 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 164 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 186 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 316 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 264 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 152 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 71 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 43 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 37 points changed cluster assignment. Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 9: 27 points changed cluster assignment. Round 10: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 10: 25 points changed cluster assignment. Round 11: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 11: 12 points changed cluster assignment. Round 12: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 12: 10 points changed cluster assignment. Round 13: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 13: 4 points changed cluster assignment. Round 14: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 14: 3 points changed cluster assignment. Round 15: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 15: 5 points changed cluster assignment. Round 16: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 16: 1 points changed cluster assignment. Round 17: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 17: No change. Skipping the rest of the iterations. Restoring sieved frames. Parallelizing calculation with 24 threads 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete. #Clustering: 7 clusters 600000 frames #Cluster 0 has average-distance-to-centroid 1.083523 #Cluster 1 has average-distance-to-centroid 1.608673 #Cluster 2 has average-distance-to-centroid 1.306604 #Cluster 3 has average-distance-to-centroid 0.947384 #Cluster 4 has average-distance-to-centroid 1.819644 #Cluster 5 has average-distance-to-centroid 1.500622 #Cluster 6 has average-distance-to-centroid 2.014783 #DBI: 1.509432 #pSF: 141735.417440 #Algorithm: Kmeans nclusters 7 maxit 100 #Representative frames: 140411 594594 522091 201687 230751 346235 485933 #Sieve value: 200 (random) #Sieved frames: 50 112 427 444 465 962 1759 1813 1976 2216 2482 2794 3182 3289 3388 3402 3416 3576 3713 4086 4364 4417 4514 4811 4835 5054 5151 5371 5439 5568 5603 5698 5745 5905 6083 6222 6392 6456 6927 7440 7587 7625 7680 7712 8281 8327 8374 8594 8611 8891 9115 9218 9226 9504 9898 10008 10059 10130 10262 10624 10684 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508099 508428 508774 508779 509454 509536 509764 510119 510262 510342 511484 511777 512446 512471 512610 512614 512763 513062 513110 513438 513769 513997 514135 514229 514963 514982 515017 515250 515347 515830 515895 516112 516136 516148 516497 516514 516690 516882 516970 517220 517410 517461 517535 517552 517591 517638 518545 518547 518744 518800 518864 519260 519852 520031 520065 520489 520611 520693 520721 521416 521507 521732 521924 522091 522166 522313 522556 522662 522857 523117 523648 523814 523949 524016 524641 524751 526330 526393 526692 526783 526817 526888 526899 527022 527029 527092 527178 527207 527219 528149 528261 528265 528337 528394 528565 528600 528821 529114 529315 529714 529986 530086 530273 530401 530590 530646 530943 531037 531241 531440 531547 531804 532357 532787 532796 533000 533751 533813 534074 534276 534981 535196 535206 535211 535235 535637 535853 535980 537183 537683 537747 537946 537965 538073 538081 538164 538567 538737 538910 539022 539076 539287 539321 539601 540060 540443 540466 540614 540755 540974 541367 541591 541793 542039 542147 542284 542426 542583 542822 543004 543031 543145 543263 543538 543720 544023 544075 544183 544248 544466 544568 544666 545047 545116 545364 545378 545648 545982 546182 546259 546372 546492 546670 546676 546806 546900 547011 547223 547336 547414 547614 548253 548261 548751 548814 549207 549330 549812 549814 549855 550109 550214 550232 550335 550666 550824 550854 551019 551108 551404 551455 551531 551701 551736 551754 552070 552168 552183 552242 552244 552872 552975 553130 553295 553301 553376 553429 553895 554016 554335 554483 554500 554628 554676 554873 554970 555542 556154 556305 556356 556366 556389 556412 556524 556566 556610 556778 557116 557296 557724 557865 558095 558109 558349 558696 558774 559027 559321 559499 559610 559985 560025 560045 560117 560280 560424 560535 560579 560599 560610 560653 561195 561329 561808 562882 563622 563682 563742 564567 565244 565603 565690 565949 566161 566242 566314 566846 567784 567945 568155 568210 568278 568279 568280 568309 568463 568532 568716 569445 569896 569906 570129 570304 570327 570880 571290 571296 571422 571483 571735 571752 571759 572039 572042 572139 572187 572362 572377 572698 573382 573458 574225 574244 574365 574560 575163 575444 575627 575710 575832 576110 576275 576505 576882 576898 577024 577221 577253 577478 577484 577989 577991 578007 578060 578077 578473 578549 578586 578946 579081 579149 579697 579751 579773 579888 580036 580203 580407 580794 581291 581424 581539 581578 581759 581798 581814 581817 581867 582204 582520 582603 582608 582611 582710 583255 583363 583416 583593 583918 583996 584260 585185 585236 585264 585369 585687 585708 585860 585947 586131 586369 586474 586511 586556 586609 586850 586938 587395 587715 587752 587959 588264 588488 588516 588703 588816 589133 589204 589717 590312 590339 590416 590422 590732 591233 591448 591478 591617 591868 592049 592093 592368 592703 593327 593573 593884 593940 594261 594465 594491 594594 594677 595228 595304 595872 595963 596038 596056 596347 596941 597276 598000 598501 598623 598701 598733 599247 599330 599744 599884 Warning: split frame 600000 is out of bounds; ignoring. Writing 'ctraj.c0' as Amber NetCDF Writing 'ctraj.c1' as Amber NetCDF Writing 'ctraj.c2' as Amber NetCDF Writing 'ctraj.c3' as Amber NetCDF Writing 'ctraj.c4' as Amber NetCDF Writing 'ctraj.c5' as Amber NetCDF Writing 'ctraj.c6' as Amber NetCDF Writing 'rep.c0.pdb' as PDB Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1. Warning: No PDB space group specified. Writing 'rep.c1.pdb' as PDB Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1. Warning: No PDB space group specified. Writing 'rep.c2.pdb' as PDB Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1. Warning: No PDB space group specified. Writing 'rep.c3.pdb' as PDB Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1. Warning: No PDB space group specified. Writing 'rep.c4.pdb' as PDB Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1. Warning: No PDB space group specified. Writing 'rep.c5.pdb' as PDB Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1. Warning: No PDB space group specified. Writing 'rep.c6.pdb' as PDB Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1. Warning: No PDB space group specified. Cluster timing data: TIME: Cluster Init. : 0.0044 s (0.00%) TIME: Pairwise Calc.: 0.4531 s (0.00%) TIME: Clustering : 0.9446 s (0.01%) TIME: Cluster Post. : 9426.1191 s (99.99%) TIME: Total: 9427.5261 s TIME: Analyses took 9427.5368 seconds. DATASETS: 3 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 600000 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 600000 (460.05 MB) Box Coords, 65 atoms Cnum_00002 "Cnum_00002" (integer), size is 600000 DATAFILES: test.dat (Standard Data File): RMSD_00000 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 10161.5930 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.