CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 11:14:52 | Available memory: 14.568 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 5 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 5 clusters. Sequentially modify each point. Cluster to cluster distance will be based on cluster centroids. Initial clustering will be randomly sieved (with value 200). Previously calcd pair distances CpptrajPairDist will be used if found. Summary of cluster results will be written to clust-summary.dat Summary comparing parts of trajectory data for clusters will be written to split.dat Frames will be split at: 50000 100000 150000 200000 250000 300000 350000 400000 450000 500000 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= 86.7126 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [cluster :1,2&!@H= summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 5 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000,150000,200000,250000,300000,350000,400000,450000,500000,550000,600000] Starting clustering. Mask [:1,2&!@H*] corresponds to 41 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (944530000) 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: 2995 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 66 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 15 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 12 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 16 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 18 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 19 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 16 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 40 points changed cluster assignment. Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 9: 70 points changed cluster assignment. Round 10: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 10: 74 points changed cluster assignment. Round 11: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 11: 140 points changed cluster assignment. Round 12: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 12: 179 points changed cluster assignment. Round 13: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 13: 270 points changed cluster assignment. Round 14: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 14: 165 points changed cluster assignment. Round 15: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 15: 70 points changed cluster assignment. Round 16: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 16: 23 points changed cluster assignment. Round 17: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 17: 5 points changed cluster assignment. Round 18: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 18: No change. Skipping the rest of the iterations. Restoring sieved frames. Parallelizing calculation with 8 threads 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete. #Clustering: 5 clusters 600000 frames #Cluster 0 has average-distance-to-centroid 0.875407 #Cluster 1 has average-distance-to-centroid 1.268886 #Cluster 2 has average-distance-to-centroid 0.733644 #Cluster 3 has average-distance-to-centroid 1.298085 #Cluster 4 has average-distance-to-centroid 1.836589 #DBI: 1.280834 #pSF: 222528.511130 #Algorithm: Kmeans nclusters 5 maxit 100 #Representative frames: 376136 392000 213445 120548 38492 #Sieve value: 200 (random) #Sieved frames: 18 273 372 728 869 1493 2337 2513 2635 2939 3003 3062 3096 3246 3569 3854 3926 4106 4135 4247 4443 4459 4557 4589 4739 4879 4968 5099 5267 5314 5361 5754 5991 6140 7189 7252 7394 7416 8122 8189 8462 8644 9047 9053 9247 9290 9445 9522 9691 9738 9907 9912 9953 10148 10204 10246 10775 10927 11049 11403 11556 11606 11665 11891 12179 12539 12563 12646 12833 13054 13090 13097 13110 13131 13409 13499 13798 13903 14199 14306 14461 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570493 570648 570675 571412 571475 571511 571578 571692 571824 572023 572293 572418 572448 572625 572975 573152 573252 573411 573502 573580 573635 574302 574675 575169 575195 575282 575625 575842 575993 576070 576639 577437 577740 577750 577930 578174 578337 578344 578573 578718 578792 578906 578953 579051 579085 579320 579352 579360 579411 579735 579764 579926 580144 580783 580902 581229 581476 581651 581864 581964 582142 582205 582714 582716 582780 583525 583707 584332 584808 584815 585226 585320 585468 586386 586960 587027 587519 587802 587874 587888 588495 589038 589122 589203 589272 589342 589361 589752 590139 590335 590337 590689 590729 591005 591491 591610 591675 591715 591716 591840 592047 592080 592208 592705 593051 593344 593782 593823 593935 594037 594285 594318 595003 595059 595511 595522 596098 596112 596157 596231 596246 596406 596568 596582 596833 596927 597106 597137 597325 597496 597548 597731 597774 598279 598430 598464 598887 599345 599377 599474 599574 599648 599755 599835 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 'rep.c0.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c1.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c2.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c3.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c4.pdb' as PDB Warning: No PDB space group specified. Cluster timing data: TIME: Cluster Init. : 0.3234 s ( 0.08%) TIME: Pairwise Calc.: 1.4552 s ( 0.38%) TIME: Clustering : 0.9928 s ( 0.26%) TIME: Cluster Post. : 383.5625 s ( 99.28%) TIME: Total: 386.3339 s TIME: Analyses took 386.3339 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 : 0.0015 s ( 0.00%) TIME: Trajectory Process : 6919.4085 s ( 94.71%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 386.3339 s ( 5.29%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 7305.7440 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 7324.0053 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.