CPPTRAJ: Trajectory Analysis. V15.00 OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/12/15 11:03:49 | Available memory: 83669.8 MB INPUT: Reading Input from file pt-cluster.in [parm ../../build/full.topo.hmr [traj]] Reading '../../build/full.topo.hmr' as Amber Topology [trajin ../../traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../traj.1.02,../../traj.1.03,../../traj.1.04,../../traj.1.05,../../traj.1.06,../../traj.1.07,../../traj.1.08,../../traj.1.09,../../traj.1.10,../../traj.1.11,../../traj.1.12,../../traj.1.13,../../traj.1.14,../../traj.1.15,../../traj.1.16,../../traj.1.17,../../traj.1.18,] [strip :WAT,Na+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [rmsd :1,2,C6,C5,C4,O4,N3,C2,O2 first mass] RMSD: (:1,2,C6,C5,C4,O4,N3,C2,O2), reference is first frame (:1,2,C6,C5,C4,O4,N3,C2,O2), with fitting, mass-weighted. [cluster summary summary.dat repout rep repfmt pdb sieve 100 clusterfmt netcdf averagelinkage rms mass :1-2 clusters 6 cpopvtime cluster_pop.agr normframe] Warning: No clustering algorithm specified; defaulting to 'hieragglo' CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1-2]), mass-weighted best-fit Hierarchical Agglomerative: 6 clusters, average-linkage. Initial clustering sieve value is 100 frames. Cluster pop vs time will be written to cluster_pop.agr (normalized by frame) Summary of cluster results will be written to summary.dat 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 [traj] to "_DEFAULTCRD_" ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3295 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames INPUT TRAJECTORIES: 0: 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 50000 frames. TIME: Run Initialization took 0.0099 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[traj]' (3 actions): 0: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 59 atoms, 2 res, box: Orthogonal, 1 mol 1: [rmsd :1,2,C6,C5,C4,O4,N3,C2,O2 first mass] Target mask: [:1,2,C6,C5,C4,O4,N3,C2,O2](59) Reference mask: [:1,2,C6,C5,C4,O4,N3,C2,O2](59) 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 (50000 frames): 35 MB ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 50000 frames and processed 50000 frames. TIME: Trajectory processing: 26.0344 s TIME: Avg. throughput= 1920.5372 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [cluster summary summary.dat repout rep repfmt pdb sieve 100 clusterfmt netcdf averagelinkage rms mass :1-2 clusters 6 cpopvtime cluster_pop.agr normframe] Starting clustering. Mask [:1-2] corresponds to 59 atoms. Calculating pair-wise distances. Estimated pair-wise matrix memory usage: > 0.4759 MB Pair-wise matrix set up with sieve, 50000 frames, 500 sieved frames. 0% 11% 24% 33% 43% 55% 62% 76% 84% 91% Complete. Memory used by pair-wise matrix and other cluster data: 0.7145 MB Starting Hierarchical Agglomerative Clustering: Progress: '+' = 10 iterations. 500 initial clusters. 0 +++++++++++++++++++++++++ 250 ++++++++++++++++++++++++ Target # of clusters (6) met (6), clustering complete. Completed after 493 iterations, 6 clusters. Restoring sieved frames. Parallelizing calculation with 24 threads 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete. #Clustering: 6 clusters 50000 frames #Cluster 0 has average-distance-to-centroid 1.102501 #Cluster 1 has average-distance-to-centroid 1.348052 #Cluster 2 has average-distance-to-centroid 1.423348 #Cluster 3 has average-distance-to-centroid 1.381847 #Cluster 4 has average-distance-to-centroid 1.525721 #Cluster 5 has average-distance-to-centroid 1.634429 #DBI: 1.411481 #pSF: 13847.688252 #Algorithm: HierAgglo linkage average-linkage nclusters 6 epsilon 1.79769e+308 #Representative frames: 46701 4701 31401 30801 34701 36901 #Sieve value: 100 Writing 'rep.c0.pdb' as PDB Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1. Warning: No PDB space group specified. Writing 'rep.c1.pdb' as PDB Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1. Warning: No PDB space group specified. Writing 'rep.c2.pdb' as PDB Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1. Warning: No PDB space group specified. Writing 'rep.c3.pdb' as PDB Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1. Warning: No PDB space group specified. Writing 'rep.c4.pdb' as PDB Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1. Warning: No PDB space group specified. Writing 'rep.c5.pdb' as PDB Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1. Warning: No PDB space group specified. Cluster timing data: TIME: Cluster Init. : 0.0000 s (0.00%) TIME: Pairwise Calc.: 0.0584 s (2.99%) TIME: Clustering : 1.2385 s (63.52%) TIME: Cluster Post. : 0.6529 s (33.49%) TIME: Total: 1.9498 s TIME: Analyses took 1.9499 seconds. DATASETS: 9 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 50000 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 50000 (34.90 MB) Box Coords, 59 atoms Cnum_00002 "Cnum_00002" (integer), size is 50000 Cnum_00002[Pop]:0 "Pop:0" (float), size is 50000 Cnum_00002[Pop]:1 "Pop:1" (float), size is 50000 Cnum_00002[Pop]:2 "Pop:2" (float), size is 50000 Cnum_00002[Pop]:3 "Pop:3" (float), size is 50000 Cnum_00002[Pop]:4 "Pop:4" (float), size is 50000 Cnum_00002[Pop]:5 "Pop:5" (float), size is 50000 DATAFILES: cluster_pop.agr (Grace File): Pop:0 Pop:1 Pop:2 Pop:3 Pop:4 Pop:5 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 29.1299 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.