CPPTRAJ: Trajectory Analysis. V15.00 OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/24/15 12:00:47 | Available memory: 90446.4 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,] Warning: RemdTraj: Replica ../../traj.1.08 frames (48446) does not match Warning: # frames in first replica (48447). Warning: RemdTraj: Setting total # of frames to 48446 Warning: RemdTraj: Replica ../../traj.1.10 frames (48447) does not match Warning: # frames in first replica (48446). Warning: RemdTraj: Replica ../../traj.1.11 frames (48447) does not match Warning: # frames in first replica (48446). Warning: RemdTraj: Replica ../../traj.1.12 frames (48447) does not match Warning: # frames in first replica (48446). Warning: RemdTraj: Replica ../../traj.1.14 frames (48447) does not match Warning: # frames in first replica (48446). Warning: RemdTraj: Replica ../../traj.1.15 frames (48447) does not match Warning: # frames in first replica (48446). Warning: RemdTraj: Replica ../../traj.1.16 frames (48447) does not match Warning: # frames in first replica (48446). [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', 4370 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 48446 frames INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 48446 of 48446) Looking for frames at 298.41 K Coordinate processing will occur on 48446 frames. TIME: Run Initialization took 0.0107 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES ..................................................... ACTION SETUP FOR PARM '[traj]' (3 actions): 0: [strip :WAT,Na+,Cl-] Stripping 4311 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 (48446 frames): 34 MB ----- traj.1.01 (1-48446, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 48446 frames and processed 48446 frames. TIME: Trajectory processing: 59.8850 s TIME: Avg. throughput= 808.9842 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: > 0.4478 MB Pair-wise matrix set up with sieve, 48446 frames, 485 sieved frames. 0% 11% 25% 33% 41% 57% 63% 71% 87% 92% Complete. Memory used by pair-wise matrix and other cluster data: 0.6789 MB Starting Hierarchical Agglomerative Clustering: Progress: '+' = 10 iterations. 485 initial clusters. 0 +++++++++++++++++++++++++ 250 ++++++++++++++++++++++ Target # of clusters (6) met (6), clustering complete. Completed after 478 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 48446 frames #Cluster 0 has average-distance-to-centroid 1.059852 #Cluster 1 has average-distance-to-centroid 1.227990 #Cluster 2 has average-distance-to-centroid 1.462517 #Cluster 3 has average-distance-to-centroid 1.481700 #Cluster 4 has average-distance-to-centroid 1.425173 #Cluster 5 has average-distance-to-centroid 1.375679 #DBI: 1.309721 #pSF: 14533.880467 #Algorithm: HierAgglo linkage average-linkage nclusters 6 epsilon 1.79769e+308 #Representative frames: 36401 32701 9801 4801 22801 12201 #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.: 0.0262 s (1.42%) TIME: Clustering : 1.1367 s (61.59%) TIME: Cluster Post. : 0.6826 s (36.99%) TIME: Total: 1.8456 s TIME: Analyses took 1.8457 seconds. DATASETS: 9 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 48446 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 48446 (33.82 MB) Box Coords, 59 atoms Cnum_00002 "Cnum_00002" (integer), size is 48446 Cnum_00002[Pop]:0 "Pop:0" (float), size is 48446 Cnum_00002[Pop]:1 "Pop:1" (float), size is 48446 Cnum_00002[Pop]:2 "Pop:2" (float), size is 48446 Cnum_00002[Pop]:3 "Pop:3" (float), size is 48446 Cnum_00002[Pop]:4 "Pop:4" (float), size is 48446 Cnum_00002[Pop]:5 "Pop:5" (float), size is 48446 DATAFILES: cluster_pop.agr (Grace File): Pop:0 Pop:1 Pop:2 Pop:3 Pop:4 Pop:5 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 63.7422 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.