CPPTRAJ: Trajectory Analysis. V16.00b ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 02/17/16 12:46:20 | Available memory: 15398.6 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 [trajin ../../../aa/tip3p/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa/tip3p/ff12sb/run1/traj.1.02,../../../aa/tip3p/ff12sb/run1/traj.1.03,../../../aa/tip3p/ff12sb/run1/traj.1.04,../../../aa/tip3p/ff12sb/run1/traj.1.05,../../../aa/tip3p/ff12sb/run1/traj.1.06,../../../aa/tip3p/ff12sb/run1/traj.1.07,../../../aa/tip3p/ff12sb/run1/traj.1.08,../../../aa/tip3p/ff12sb/run1/traj.1.09,../../../aa/tip3p/ff12sb/run1/traj.1.10,../../../aa/tip3p/ff12sb/run1/traj.1.11,../../../aa/tip3p/ff12sb/run1/traj.1.12,../../../aa/tip3p/ff12sb/run1/traj.1.13,../../../aa/tip3p/ff12sb/run1/traj.1.14,../../../aa/tip3p/ff12sb/run1/traj.1.15,../../../aa/tip3p/ff12sb/run1/traj.1.16,../../../aa/tip3p/ff12sb/run1/traj.1.17,../../../aa/tip3p/ff12sb/run1/traj.1.18 parm [tip3p-ff12sb]] Reading '../../../aa/tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.02' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.03' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.04' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.05' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.06' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.07' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.08' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.09' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.10' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.11' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.12' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.13' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.14' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.15' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.16' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.17' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run1/traj.1.18' as Amber NetCDF [trajin ../../../aa/tip3p/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa/tip3p/ff12sb/run2/traj.1.02,../../../aa/tip3p/ff12sb/run2/traj.1.03,../../../aa/tip3p/ff12sb/run2/traj.1.04,../../../aa/tip3p/ff12sb/run2/traj.1.05,../../../aa/tip3p/ff12sb/run2/traj.1.06,../../../aa/tip3p/ff12sb/run2/traj.1.07,../../../aa/tip3p/ff12sb/run2/traj.1.08,../../../aa/tip3p/ff12sb/run2/traj.1.09,../../../aa/tip3p/ff12sb/run2/traj.1.10,../../../aa/tip3p/ff12sb/run2/traj.1.11,../../../aa/tip3p/ff12sb/run2/traj.1.12,../../../aa/tip3p/ff12sb/run2/traj.1.13,../../../aa/tip3p/ff12sb/run2/traj.1.14,../../../aa/tip3p/ff12sb/run2/traj.1.15,../../../aa/tip3p/ff12sb/run2/traj.1.16,../../../aa/tip3p/ff12sb/run2/traj.1.17,../../../aa/tip3p/ff12sb/run2/traj.1.18 parm [tip3p-ff12sb]] Reading '../../../aa/tip3p/ff12sb/run2/traj.1.01' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.02' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.03' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.04' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.05' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.06' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.07' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.08' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.09' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.10' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.11' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.12' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.13' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.14' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.15' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.16' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.17' as Amber NetCDF Reading '../../../aa/tip3p/ff12sb/run2/traj.1.18' as Amber NetCDF [trajin ../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.02,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.03,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.04,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.05,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.06,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.07,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.08,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.09,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.10,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.11,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.12,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.13,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.14,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.15,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.16,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.17,../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.18 parm [tip3p-ff12sb]] Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.02' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.03' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.04' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.05' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.06' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.07' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.08' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.09' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.10' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.11' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.12' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.13' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.14' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.15' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.16' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.17' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.18' as Amber NetCDF Netcdf file has overall replica indices. [trajin ../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.02,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.03,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.04,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.05,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.06,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.07,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.08,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.09,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.10,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.11,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.12,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.13,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.14,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.15,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.16,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.17,../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.18 parm [tip3p-ff12sb]] Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.01' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.02' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.03' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.04' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.05' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.06' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.07' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.08' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.09' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.10' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.11' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.12' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.13' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.14' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.15' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.16' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.17' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.18' as Amber NetCDF Netcdf file has overall replica indices. [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 Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.02' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.03' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.04' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.05' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.06' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.07' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.08' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.09' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.10' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.11' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.12' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.13' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.14' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.15' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.16' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.17' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run1/traj.1.18' as Amber NetCDF Netcdf file has overall replica indices. [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 Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.02' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.03' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.04' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.05' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.06' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.07' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.08' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.09' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.10' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.11' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.12' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.13' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.14' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.15' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.16' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.17' as Amber NetCDF Netcdf file has overall replica indices. Reading '../../tip3p/ff12sb/run2/traj.1.18' as Amber NetCDF Netcdf file has overall replica indices. [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [rmsd :1-2&!@H= first mass] RMSD: (:1-2&!@H*), reference is first frame (:1-2&!@H*), with fitting, mass-weighted. [cluster :1,2&!@H= summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 7 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000,250000,300000] CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1,2&!@H=]) best-fit K-MEANS: Looking for 7 clusters. Sequentially modify each point. Cluster to cluster distance will be based on cluster centroids. Initial clustering will be randomly sieved (with value 200). Previously calcd pair distances CpptrajPairDist will be used if found. Summary of cluster results will be written to clust-summary.dat Summary comparing parts of trajectory data for clusters will be written to split.dat Frames will be split at: 50000 100000 150000 200000 250000 300000 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, 300000 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 Coordinate processing will occur on 300000 frames. TIME: Run Initialization took 0.0001 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[tip3p-ff12sb]' (3 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](41) Reference mask: [:1-2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 2: [createcrd _DEFAULTCRD_] Warning: COORDS data sets do not store temperatures. Warning: COORDS data sets do not store times. Estimated memory usage (300000 frames): 1.1e+04 MB ----- traj.1.01 (1-50000, 1) ----- 0% 10% REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 20% 30% REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 40% REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 50% 60% REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 70% 80% REMD: OPENING 18 REMD TRAJECTORIES ----- traj.1.01 (1-50000, 1) ----- 90% 100% Complete. Read 300000 frames and processed 300000 frames. TIME: Trajectory processing: 3580.5088 s TIME: Avg. throughput= 83.7870 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [cluster :1,2&!@H= summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 7 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000,250000,300000] Starting clustering. Mask [:1,2&!@H*] corresponds to 41 atoms. Loading pair-wise distances from CpptrajPairDist Warning: ClusterMatrix CpptrajPairDist contains sieved data. Loaded CpptrajPairDist: 300000 original rows, 1500 actual rows, 1124250 elements, sieve=-200 Memory used by pair-wise matrix and other cluster data: 5.7193 MB Round 0: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 0: 1493 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 67 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 45 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 130 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 59 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 28 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 25 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 6 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 5 points changed cluster assignment. Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 9: 3 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. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete. #Clustering: 7 clusters 300000 frames #Cluster 0 has average-distance-to-centroid 0.862291 #Cluster 1 has average-distance-to-centroid 1.287032 #Cluster 2 has average-distance-to-centroid 0.686518 #Cluster 3 has average-distance-to-centroid 1.055970 #Cluster 4 has average-distance-to-centroid 1.660668 #Cluster 5 has average-distance-to-centroid 1.549749 #Cluster 6 has average-distance-to-centroid 1.274096 #DBI: 1.341682 #pSF: 93678.061916 #Algorithm: Kmeans nclusters 7 maxit 100 #Representative frames: 124207 83980 152165 3159 172539 92241 114262 #Sieve value: 200 (random) #Sieved frames: 143 451 803 1203 1322 1923 1954 2066 2165 2237 2336 2439 2456 2827 3012 3159 3246 3363 3557 3623 3633 3792 3964 4191 4235 4261 4386 4391 4415 4464 4622 4719 4720 5050 5298 5365 5379 5419 5497 5520 5636 6134 6441 6642 6712 6809 6810 6916 6917 7790 8005 8962 8989 9043 9726 9895 9923 9955 10305 10334 10474 10493 10786 11852 11853 12043 12096 12367 12477 12569 12600 12679 12856 13079 13083 13112 13503 14035 14598 14843 14965 15259 15270 15293 15936 15957 16047 16330 16464 16714 16828 16877 17204 17223 17523 17901 18406 18650 18662 18856 19395 19400 19783 20485 20493 20666 21060 21155 21937 22063 22087 22108 22314 22611 22752 22819 22850 22884 23076 23140 23231 23317 23319 23785 24185 24221 24428 24594 24768 24906 25416 25607 25880 25933 26108 26127 26239 26282 26579 26692 26729 26787 26959 27023 27150 27527 27843 28059 28181 28194 28631 28860 29307 29461 29478 29729 29913 29932 30637 30952 31264 31574 31733 31855 32032 32040 32240 32755 32870 32955 32992 33146 33513 33543 33634 33702 33799 34122 34389 34526 34680 34739 35080 35114 35461 35515 35591 35673 35723 36033 36130 36177 36231 36349 36499 36957 36959 37118 37210 37308 37390 37535 38053 38518 38633 38684 39159 39317 39599 40102 40300 40546 40587 40619 40868 41219 41464 41585 41808 41916 42184 43610 43864 44178 44244 44308 44318 44324 45145 45390 45484 45513 45577 45870 46151 46215 46432 46564 46808 46825 46832 47117 47233 47443 47778 47922 48252 48385 48755 49378 49468 49536 49679 50496 51491 51790 51951 52036 52591 52721 52958 53132 53165 53299 53305 53313 53384 53836 53932 53934 53962 54068 54090 54383 54420 54675 54711 54942 54949 55538 55558 55879 56101 56383 56500 56546 56649 56777 56927 56937 57122 57345 57497 57629 57684 57915 58205 58546 58566 58800 58807 59121 59131 59313 59350 59401 59429 59485 59566 60124 60168 60231 60715 60915 60978 61131 61185 61284 61470 61486 61671 62051 62199 62487 62659 63254 63308 63363 63403 63516 63529 64017 64048 64100 64150 64457 64617 64720 64743 65314 65433 65604 65638 65972 66149 66164 66296 66310 66403 66655 66673 66775 66791 66873 66942 67156 67295 67410 67426 67592 67611 68091 68169 68473 68619 68778 69138 69993 70130 70146 70434 70590 70679 71422 71525 71630 71664 71751 71819 72636 72750 72806 72946 73050 73054 73070 73349 73413 73492 73729 73762 73834 74132 74291 74481 74606 74728 75526 75819 76041 76057 76265 76329 76416 76732 76767 76775 76991 76996 77157 77394 77407 77472 77916 78146 78239 78674 78692 78717 78864 78937 79034 79148 79312 79409 79418 79743 79750 79792 80087 80371 80780 80801 80805 81524 81649 81673 81795 81829 81862 82198 82341 82385 82488 83119 83390 83555 83780 83980 84136 84160 84182 84381 84419 84707 84710 84823 84849 85372 85491 85508 85521 85566 85637 86740 87110 87506 88074 88394 88405 88727 88833 89381 89687 89728 89773 89821 90329 90494 90824 90895 91054 91108 91514 91614 91730 92062 92153 92241 92464 92789 92990 92992 93048 93399 93646 93775 93840 93898 93958 94194 94486 94760 94875 95256 95355 95672 96011 96058 96459 96503 96663 96820 96907 96915 97295 97652 97667 97765 97793 98088 98142 98169 98771 98888 99039 99177 99257 99365 99602 99619 100454 101713 101788 102312 103098 103243 103646 103715 103752 103804 103991 104133 104332 104422 104572 104808 105314 105576 105680 105724 105930 106265 106609 106690 106884 107512 107591 107709 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223282 223314 223602 223663 224164 224359 224547 224560 224918 225013 225149 225160 225551 225950 225978 226126 226623 226706 226752 227195 227210 227264 227335 227382 227951 228957 229011 229397 229674 229716 229737 229939 230140 230645 230684 231011 231475 231978 232039 232300 232531 232661 232716 232968 233009 233041 233211 233229 233268 233601 233685 233731 233770 233782 233877 234215 234318 234468 234815 235101 235316 235332 235569 235645 235666 235910 235914 236342 236743 236809 236839 237304 238141 238193 238264 238523 238752 239197 239250 239743 240309 240890 240928 241145 241163 241243 241349 241738 241885 241890 241895 242004 242052 242171 242394 242423 242510 242618 242734 242838 243402 243972 243977 244773 245174 245218 245355 245391 245554 245568 247032 247224 247523 247578 247663 247847 247957 248471 248560 248600 248956 249350 249356 249503 250843 251543 251551 251690 252136 252179 252191 252256 252338 252425 252602 252675 252763 252889 253019 253301 253358 253425 253717 253831 253913 254506 255796 256440 256694 257016 257337 257385 257408 257415 257464 257901 258217 258772 259058 259161 259557 259627 259799 260234 260919 261133 261329 261521 261692 261802 263053 263166 263230 263242 263492 263674 263675 263899 263918 263970 264112 264569 264653 264735 265045 265067 265211 265313 265646 265654 265686 265736 265742 266045 266077 266106 266234 266351 266385 266558 266628 266903 267357 267622 267639 267666 267693 267735 267834 268131 268423 268542 268923 268950 269102 269207 269254 269302 269597 269610 270207 270324 270354 270464 270802 271009 271135 271141 271386 271992 272143 272205 272237 272300 272473 273148 273236 273880 274366 274473 274519 274854 275298 275325 275618 275706 275810 276128 276234 276462 276882 276964 277004 277034 277343 277431 277757 277838 278158 279264 279314 279378 279563 280186 280392 280588 280879 280962 281249 281437 281506 281768 282884 282983 283156 283232 283298 283311 283354 283505 283543 284115 284899 284972 285377 285448 285516 286155 286398 286511 286690 286796 287007 287123 287431 287441 287469 287510 287543 288086 288164 288262 288290 288420 288525 288648 288899 289164 289385 289645 290495 290500 290566 290596 290642 290997 291420 291422 291514 291693 292102 292425 292474 293054 293280 293468 293469 293499 293842 294035 294140 294430 294530 294815 295269 295420 295602 295872 295946 296057 296183 296581 296966 296989 297184 297568 297569 297693 297905 298034 298047 298172 298260 298544 298561 298568 298639 298704 298842 298844 298992 299058 299113 299212 299335 299396 299686 299785 299831 Warning: split frame 300000 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: 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. Writing 'rep.c5.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c6.pdb' as PDB Warning: No PDB space group specified. Cluster timing data: TIME: Cluster Init. : 0.0008 s (0.00%) TIME: Pairwise Calc.: 0.0870 s (0.02%) TIME: Clustering : 2.7596 s (0.58%) TIME: Cluster Post. : 471.7826 s (99.40%) TIME: Total: 474.6300 s TIME: Analyses took 474.6303 seconds. DATASETS: 3 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 300000 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 300000 (11339.95 MB) Box Coords, 3301 atoms Cnum_00002 "Cnum_00002" (integer), size is 300000 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 4058.6520 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. . 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.