CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 11:16:23 | Available memory: 12.635 GB INPUT: Reading input from 'pt-clust.in' [parm ../../../aa/tip3p/ff12sb/run1/build/full.topo.hmr [aa]] Reading '../../../aa/tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology [parm ../../../aa-neut/tip3p/ff12sb/run1/build/full.topo.hmr [neut]] Reading '../../../aa-neut/tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology [parm ../../../aa-2pO0/tip3p/ff12sb/run1/build/full.topo.hmr [2pO0]] Reading '../../../aa-2pO0/tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology [parm ../../../aa-5pO0/tip3p/ff12sb/run1/build/full.topo.hmr [5pO0]] Reading '../../../aa-5pO0/tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology [parm ../../../aa-3pchi/tip3p/ff12sb/run1/build/full.topo.hmr [3pchi]] Reading '../../../aa-3pchi/tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology [parm ../../../aa-pucker-north/tip3p/ff12sb/run1/build/full.topo.hmr [pucker-north]] Reading '../../../aa-pucker-north/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 [aa]] Reading '../../../aa/tip3p/ff12sb/run1/traj.1.01' 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 [aa]] Reading '../../../aa/tip3p/ff12sb/run2/traj.1.01' as Amber NetCDF [trajin ../../../aa-neut/tip3p/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa-neut/tip3p/ff12sb/run1/traj.1.02,../../../aa-neut/tip3p/ff12sb/run1/traj.1.03,../../../aa-neut/tip3p/ff12sb/run1/traj.1.04,../../../aa-neut/tip3p/ff12sb/run1/traj.1.05,../../../aa-neut/tip3p/ff12sb/run1/traj.1.06,../../../aa-neut/tip3p/ff12sb/run1/traj.1.07,../../../aa-neut/tip3p/ff12sb/run1/traj.1.08,../../../aa-neut/tip3p/ff12sb/run1/traj.1.09,../../../aa-neut/tip3p/ff12sb/run1/traj.1.10,../../../aa-neut/tip3p/ff12sb/run1/traj.1.11,../../../aa-neut/tip3p/ff12sb/run1/traj.1.12,../../../aa-neut/tip3p/ff12sb/run1/traj.1.13,../../../aa-neut/tip3p/ff12sb/run1/traj.1.14,../../../aa-neut/tip3p/ff12sb/run1/traj.1.15,../../../aa-neut/tip3p/ff12sb/run1/traj.1.16,../../../aa-neut/tip3p/ff12sb/run1/traj.1.17,../../../aa-neut/tip3p/ff12sb/run1/traj.1.18 parm [neut]] Reading '../../../aa-neut/tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF [trajin ../../../aa-neut/tip3p/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa-neut/tip3p/ff12sb/run2/traj.1.02,../../../aa-neut/tip3p/ff12sb/run2/traj.1.03,../../../aa-neut/tip3p/ff12sb/run2/traj.1.04,../../../aa-neut/tip3p/ff12sb/run2/traj.1.05,../../../aa-neut/tip3p/ff12sb/run2/traj.1.06,../../../aa-neut/tip3p/ff12sb/run2/traj.1.07,../../../aa-neut/tip3p/ff12sb/run2/traj.1.08,../../../aa-neut/tip3p/ff12sb/run2/traj.1.09,../../../aa-neut/tip3p/ff12sb/run2/traj.1.10,../../../aa-neut/tip3p/ff12sb/run2/traj.1.11,../../../aa-neut/tip3p/ff12sb/run2/traj.1.12,../../../aa-neut/tip3p/ff12sb/run2/traj.1.13,../../../aa-neut/tip3p/ff12sb/run2/traj.1.14,../../../aa-neut/tip3p/ff12sb/run2/traj.1.15,../../../aa-neut/tip3p/ff12sb/run2/traj.1.16,../../../aa-neut/tip3p/ff12sb/run2/traj.1.17,../../../aa-neut/tip3p/ff12sb/run2/traj.1.18 parm [neut]] Reading '../../../aa-neut/tip3p/ff12sb/run2/traj.1.01' as Amber NetCDF [trajin ../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.02,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.03,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.04,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.05,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.06,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.07,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.08,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.09,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.10,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.11,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.12,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.13,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.14,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.15,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.16,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.17,../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.18 parm [2pO0]] Reading '../../../aa-2pO0/tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF [trajin ../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.02,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.03,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.04,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.05,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.06,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.07,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.08,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.09,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.10,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.11,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.12,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.13,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.14,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.15,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.16,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.17,../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.18 parm [2pO0]] Reading '../../../aa-2pO0/tip3p/ff12sb/run2/traj.1.01' as Amber NetCDF [trajin ../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.02,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.03,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.04,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.05,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.06,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.07,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.08,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.09,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.10,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.11,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.12,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.13,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.14,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.15,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.16,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.17,../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.18 parm [5pO0]] Reading '../../../aa-5pO0/tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF [trajin ../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.02,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.03,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.04,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.05,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.06,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.07,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.08,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.09,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.10,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.11,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.12,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.13,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.14,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.15,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.16,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.17,../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.18 parm [5pO0]] Reading '../../../aa-5pO0/tip3p/ff12sb/run2/traj.1.01' 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 [3pchi]] Reading '../../../aa-3pchi/tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF [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 [3pchi]] Reading '../../../aa-3pchi/tip3p/ff12sb/run2/traj.1.01' as Amber NetCDF [trajin ../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.02,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.03,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.04,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.05,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.06,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.07,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.08,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.09,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.10,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.11,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.12,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.13,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.14,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.15,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.16,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.17,../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.18 parm [pucker-north]] Reading '../../../aa-pucker-north/tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF [trajin ../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.02,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.03,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.04,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.05,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.06,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.07,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.08,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.09,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.10,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.11,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.12,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.13,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.14,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.15,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.16,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.17,../../../aa-pucker-north/tip3p/ff12sb/run2/traj.1.18 parm [pucker-north]] Reading '../../../aa-pucker-north/tip3p/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 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&!@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 350000 400000 450000 500000 550000 600000 Cluster trajectories will be written to ctraj, format Amber NetCDF Cluster representatives will be written to separate trajectories, prefix (rep), format PDB Warning: One or more analyses requested creation of default COORDS DataSet. CREATECRD: Saving coordinates from Top full.topo.hmr to "_DEFAULTCRD_" ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (6 total): 0: [aa] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent 1: [neut] full.topo.hmr, 3321 atoms, 1088 res, box: Orthogonal, 1087 mol, 1085 solvent 2: [2pO0] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent 3: [5pO0] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent 4: [3pchi] full.topo.hmr, 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent 5: [pucker-north] full.topo.hmr, 3301 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 50000 of 50000) Looking for frames at 298.41 K 11: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K Coordinate processing will occur on 600000 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped topology: 65 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](41) Reference mask: [:1-2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] Warning: COORDS data sets do not store temperatures. Warning: COORDS data sets do not store times. Estimated memory usage (100000 frames): 80.400 MB ----- traj.1.01 (1-50000, 1) ----- 0% ----- traj.1.01 (1-50000, 1) ----- 10% ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3256 atoms. Stripped topology: 65 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-50000, 1) ----- 20% ----- traj.1.01 (1-50000, 1) ----- 30% ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped topology: 65 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-50000, 1) ----- 40% ----- traj.1.01 (1-50000, 1) ----- ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped topology: 65 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-50000, 1) ----- 50% ----- traj.1.01 (1-50000, 1) ----- 60% ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped topology: 65 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-50000, 1) ----- 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 3236 atoms. Stripped topology: 65 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass] Target mask: [:1-2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] ----- traj.1.01 (1-50000, 1) ----- 90% ----- traj.1.01 (1-50000, 1) ----- 100% Complete. Read 600000 frames and processed 600000 frames. TIME: Avg. throughput= 86.9572 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 50000,100000,150000,200000,250000,300000,350000,400000,450000,500000,550000,600000] Starting clustering. Mask [:1,2&!@H*] corresponds to 41 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (944050000) Estimated pair-wise matrix memory usage: > 17.994 MB Pair-wise matrix set up with sieve, 600000 frames, 3000 sieved frames. 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete. Saving pair-wise distances to CpptrajPairDist Memory used by pair-wise matrix and other cluster data: 20.994 MB Round 0: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 0: 2993 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 130 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 106 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 393 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 131 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 41 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 37 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 66 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 38 points changed cluster assignment. Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 9: 28 points changed cluster assignment. Round 10: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 10: 14 points changed cluster assignment. Round 11: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 11: 14 points changed cluster assignment. Round 12: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 12: 15 points changed cluster assignment. Round 13: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 13: 10 points changed cluster assignment. Round 14: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 14: 10 points changed cluster assignment. Round 15: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 15: 6 points changed cluster assignment. Round 16: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 16: 9 points changed cluster assignment. Round 17: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 17: 18 points changed cluster assignment. Round 18: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 18: 13 points changed cluster assignment. Round 19: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 19: 26 points changed cluster assignment. Round 20: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 20: 26 points changed cluster assignment. Round 21: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 21: 36 points changed cluster assignment. Round 22: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 22: 48 points changed cluster assignment. Round 23: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 23: 55 points changed cluster assignment. Round 24: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 24: 56 points changed cluster assignment. Round 25: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 25: 52 points changed cluster assignment. Round 26: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 26: 41 points changed cluster assignment. Round 27: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 27: 50 points changed cluster assignment. Round 28: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 28: 93 points changed cluster assignment. Round 29: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 29: 98 points changed cluster assignment. Round 30: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 30: 39 points changed cluster assignment. Round 31: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 31: 6 points changed cluster assignment. Round 32: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 32: 2 points changed cluster assignment. Round 33: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 33: 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: 7 clusters 600000 frames #Cluster 0 has average-distance-to-centroid 0.758636 #Cluster 1 has average-distance-to-centroid 1.123843 #Cluster 2 has average-distance-to-centroid 0.705984 #Cluster 3 has average-distance-to-centroid 1.169330 #Cluster 4 has average-distance-to-centroid 1.160812 #Cluster 5 has average-distance-to-centroid 0.850524 #Cluster 6 has average-distance-to-centroid 1.834291 #DBI: 1.333953 #pSF: 194177.002545 #Algorithm: Kmeans nclusters 7 maxit 100 #Representative frames: 186440 571399 236826 210362 159251 541357 287511 #Sieve value: 200 (random) #Sieved frames: 384 560 860 918 1036 1045 1126 1128 1294 1376 1421 1600 1980 2013 2073 2142 2226 2515 2563 2619 2662 2801 2918 3372 3491 4756 4827 4852 5190 5293 5297 5499 5857 5952 6107 6137 6254 6337 6444 6548 6694 6887 7012 7282 7473 7661 7873 7891 8084 8298 8324 8526 8739 8862 9442 9538 9605 9623 10240 10530 10553 10774 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365394 365399 365422 365712 365764 365777 366110 366283 366315 366567 366620 366757 366822 366875 366918 367099 367102 367530 367560 368427 368439 368448 368537 368812 368816 369307 369401 369737 369789 369891 370367 370435 370634 371170 371480 371738 371746 372090 372131 372253 372776 373162 373214 373231 373321 373507 373779 374283 374300 374793 374799 374950 374991 375002 375491 375563 375988 376278 376390 376421 376710 376736 376800 376828 377102 377215 377492 377571 377987 378209 378650 378986 378989 379306 379531 379962 380260 380465 380468 380577 380824 380964 381035 381145 381772 382537 382673 382839 382840 382889 383232 383316 383611 383739 384038 384646 384679 384762 384802 385633 385676 385744 385919 386376 386786 386852 386955 387192 387221 387247 387427 387602 387708 387771 387848 388315 388337 388780 388898 390285 390675 390949 391091 391131 391256 391580 391888 392074 392143 392559 392581 392628 392760 392890 393235 393299 393406 393461 393585 393641 393908 394098 394237 394613 394722 394815 395182 395220 395527 395665 395825 395972 396386 396542 396760 396836 397153 397211 397550 397609 397973 398045 398102 398326 398409 398700 399327 399794 399823 399966 400020 400119 400285 400422 400457 400642 400766 400793 400979 401138 401217 401342 401797 402326 402402 403127 403395 403804 404091 404221 404342 404478 405056 405634 405655 405814 406518 406519 406619 406869 407167 407249 407427 407532 407679 407718 407852 407873 407970 408075 408745 408772 408919 409103 409152 409294 409646 409691 409955 410326 410330 410563 410766 410812 410971 411347 411457 411635 412324 412627 412746 413064 413129 413212 413338 413458 413485 413741 414073 414101 414125 414246 414345 414413 414451 414666 414756 415493 415650 416106 416125 416347 416391 416712 417195 417592 418059 418263 418366 419102 419534 419592 419658 419737 419876 420000 420180 420743 420843 421142 421188 421593 421594 421915 422004 422468 422498 422583 422706 423122 423160 423219 423486 423676 424180 424438 424560 425169 425250 425955 426069 426075 426151 426822 426842 427055 427118 427127 427237 427414 427476 427954 428006 428013 428711 428745 428817 428932 429068 429197 429273 429485 429735 429835 429892 429942 430074 430196 430251 430328 430590 430671 431014 431164 431531 431707 431878 432037 432063 432067 432829 433062 433498 433875 434516 434726 435253 435897 436276 436728 436810 436892 436893 436972 437130 437580 437929 437950 437998 438088 438126 438256 438375 438522 438679 438753 438903 438944 439405 439406 439563 439961 440044 440070 440148 440249 440731 440762 441029 441167 441191 441309 441461 441501 441614 441710 441869 442244 442259 442692 442941 443369 443543 443731 443870 443893 444283 444395 444637 444913 445269 445307 445337 445444 445547 445579 445699 445762 445836 445901 446377 446829 447151 447317 447551 447769 447879 447923 448528 448933 449133 449150 449161 449313 450704 450936 451085 451112 451159 451251 451271 451425 452259 452394 452468 452726 452882 452901 453202 453557 453582 453905 454040 454150 454517 454525 454547 454610 455273 455355 455395 455608 455614 455628 455833 456063 456133 456255 456442 456519 456673 456816 456863 456918 457315 457366 457727 458174 458242 459594 459657 459884 459957 459976 459992 460007 460112 460341 460827 460868 461031 461316 461498 461648 462088 462192 462338 463176 463579 463807 464385 464487 464603 464866 465691 465761 465769 466019 466194 466422 466594 466598 466642 466714 467065 467457 467590 467791 468082 468295 468427 468470 468561 468662 469180 469416 469770 470003 470021 470344 470436 470462 470663 471279 471340 471568 471743 471808 471809 471870 471881 472382 472472 472524 472715 472747 472778 472803 473112 473130 473584 473896 473966 474079 474196 474435 474465 474507 474635 474703 475078 475097 475641 475780 475796 475870 476253 476445 476685 477236 477240 477418 477566 477877 477886 478241 478889 478923 479113 479406 479669 479754 479812 480133 480286 480369 480418 481887 482535 482625 482747 483124 483336 483424 484043 484628 484671 484707 484785 485316 485361 485423 485748 486590 486603 486658 487132 487159 487224 487326 487469 487482 487529 487571 487721 488241 488432 488522 488593 488611 488616 488723 489465 489510 489742 489921 490189 490207 490227 490253 490447 490703 490732 490737 490816 491165 491234 491525 491549 491562 491716 492031 492218 492343 492367 492464 492715 493168 493659 493842 494074 494099 494189 494235 494384 494395 494631 494914 494994 495036 495362 495508 495761 495776 496206 496231 496447 496719 497073 497256 497267 497927 497992 498320 498352 498507 498527 498984 499268 499473 499618 499837 499839 499933 500000 500112 500454 500733 500876 501554 502085 502590 502781 503035 503194 504066 504161 504755 505046 505295 505373 505384 505467 505485 505743 506094 506127 506566 506647 507106 507242 507347 507514 507636 508068 508238 508539 508627 508634 508896 509004 509118 509165 509340 509510 509816 510318 510368 510493 510549 510785 510806 510974 511060 511067 511820 512300 512363 512844 512845 512996 513285 513494 513672 513829 513866 513996 514334 514906 515060 515073 515199 515264 515307 515390 515714 515731 515771 516115 516255 516444 516969 516988 516992 517002 517157 517410 517766 517909 517928 518045 518317 518745 518757 518966 519527 519588 519790 519875 519921 520150 520506 520721 520816 521103 521160 521383 522186 522533 522565 522567 522592 522999 523018 523453 523706 523720 523727 523804 523902 524588 524685 525321 525721 526141 526283 526333 526483 526821 527249 527382 527591 527958 528362 528751 528916 528950 529063 529276 529543 529970 530008 530042 530084 530194 530327 530982 531172 531289 531326 531476 531563 531758 531793 531817 532129 532225 532239 532696 532893 533075 533154 533371 534344 534445 534731 534813 534962 535104 535131 535205 535216 535282 535682 535995 536017 536050 536169 536298 536465 536565 536816 536848 536888 536940 537178 537246 537549 537563 537636 537835 537951 537965 538102 538274 538438 538478 538520 538879 539474 539798 540007 540661 540803 540875 541032 541057 541080 541087 541357 541381 541596 541616 541663 542218 542349 542359 542731 542781 542821 542933 543092 543252 543321 543939 543995 544154 544613 544849 545145 545176 545183 545394 545426 545430 545439 545548 545730 546061 546152 546239 546261 546385 546493 546538 546622 546654 546722 547156 547231 547315 547435 548029 548282 548652 548668 550420 550448 550623 550922 551000 551091 551149 551420 551497 552003 552281 552671 552753 552870 552947 553052 553118 553128 553140 553255 553683 553818 554175 554644 555529 555536 555657 556009 556056 556124 556219 556255 556365 556372 556428 556500 557010 557291 557603 557952 558015 558169 558368 558974 558981 558993 559076 559453 559648 559886 559955 560029 560298 560425 560544 560825 561086 561090 561326 561417 561550 561577 561709 561824 562299 562691 562977 563111 563397 563623 563670 563995 564011 564352 564414 564487 564648 564893 565137 565325 565358 565775 565812 566472 566474 566509 566875 566948 567334 567462 567463 567529 567548 567679 567840 567886 567995 568152 568700 569280 569714 569763 570035 570092 570250 570531 570594 570703 570785 570810 570819 570910 571249 571334 571399 571572 571630 571681 571714 572720 572809 573197 573244 573448 573482 573806 574089 574265 574287 574531 574621 574710 574726 574817 574913 575168 575195 575247 575312 575624 575986 576210 577006 577136 577696 578094 578139 578284 578384 578394 578501 578768 579001 579080 579303 579446 579739 580193 580221 580675 580865 581648 581847 581988 582164 582458 582853 583427 583460 583587 584087 584399 584405 584982 585063 585247 585266 585619 586027 586199 586507 586760 586855 587088 587616 587818 587983 588227 588490 588887 589083 589325 590068 590146 590308 590427 590487 590768 590868 590910 591074 591101 591302 591310 591785 591952 592087 592498 592523 592672 592834 593062 593243 593415 593452 594058 594265 594376 594441 594820 594873 595125 595314 595727 595836 595881 595932 596016 596490 596559 596883 597062 597329 597862 597995 598676 598695 599125 599623 599625 599900 599960 599995 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: 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. : 0.3178 s ( 0.08%) TIME: Pairwise Calc.: 9.7731 s ( 2.46%) TIME: Clustering : 2.1680 s ( 0.55%) TIME: Cluster Post. : 384.8912 s ( 96.91%) TIME: Total: 397.1500 s TIME: Analyses took 397.1595 seconds. DATASETS (3 total): RMSD_00006 "RMSD_00006" (double, rms), size is 600000 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 600000 (482.400 MB) Box Coords, 65 atoms Cnum_00008 "Cnum_00008" (integer), size is 600000 RUN TIMING: TIME: Init : 0.0014 s ( 0.00%) TIME: Trajectory Process : 6899.9486 s ( 94.56%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 397.1595 s ( 5.44%) TIME: Data File Write : 0.0153 s ( 0.00%) TIME: Other : 0.0156 s ( 0.00%) TIME: Run Total 7297.1404 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 7302.2600 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.