CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 06/22/16 11:15:48 | Available memory: 2.719 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 6 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 6 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= 86.9548 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 6 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 (958070000) 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: 2994 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 165 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 68 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 115 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 244 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 131 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 71 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 51 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 25 points changed cluster assignment. Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 9: 18 points changed cluster assignment. Round 10: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 10: 17 points changed cluster assignment. Round 11: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 11: 16 points changed cluster assignment. Round 12: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 12: 8 points changed cluster assignment. Round 13: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 13: 1 points changed cluster assignment. Round 14: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 14: 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: 6 clusters 600000 frames #Cluster 0 has average-distance-to-centroid 0.729882 #Cluster 1 has average-distance-to-centroid 1.265836 #Cluster 2 has average-distance-to-centroid 0.740289 #Cluster 3 has average-distance-to-centroid 1.105650 #Cluster 4 has average-distance-to-centroid 1.251227 #Cluster 5 has average-distance-to-centroid 1.864265 #DBI: 1.505539 #pSF: 193797.457915 #Algorithm: Kmeans nclusters 6 maxit 100 #Representative frames: 496260 578241 211721 405840 551917 89260 #Sieve value: 200 (random) #Sieved frames: 223 236 321 754 767 891 983 1129 1497 1521 1770 1786 1832 2068 2227 2590 2726 2976 3310 3360 4252 4265 4347 4724 4880 4966 4977 5103 5206 5258 5332 5474 5587 5880 6041 6145 6188 6334 6448 6475 6802 6821 6839 7893 8302 8446 8530 8949 9057 9329 9367 9544 9568 9677 9690 9995 10197 10346 10453 10553 10674 10808 10815 10849 10864 11343 11372 11602 11644 12268 12692 12909 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598791 598831 599285 599371 599591 599807 599885 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 '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. Cluster timing data: TIME: Cluster Init. : 0.3453 s ( 0.09%) TIME: Pairwise Calc.: 7.1867 s ( 1.79%) TIME: Clustering : 0.9009 s ( 0.22%) TIME: Cluster Post. : 392.6626 s ( 97.90%) TIME: Total: 401.0955 s TIME: Analyses took 401.1079 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 : 6900.1342 s ( 94.51%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 401.1079 s ( 5.49%) TIME: Data File Write : 0.0000 s ( 0.00%) TIME: Other : 0.0001 s ( 0.00%) TIME: Run Total 7301.2437 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 7306.4266 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.