CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/21/15 16:12:21 | Available memory: 13400.8 MB INPUT: Reading Input from file pt-test-lowT.in [parm ../build/full.topo.hmr [traj]] Reading '../build/full.topo.hmr' as Amber Topology [parm ../../../../aa-A-form.pdb [striped]] Reading '../../../../aa-A-form.pdb' as PDB File aa-A-form.pdb: determining bond info from distances. Warning: aa-A-form.pdb: Determining default bond distances from element types. [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 ] [reference ../../../../aa-A-form.pdb parm [striped] [a-form]] Reading '../../../../aa-A-form.pdb' as PDB [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [rmsd rms_2_aform :1,2&!@H= ref [a-form] mass ] Reference mask: [:1,2&!@H*](41) RMSD: (:1,2&!@H*), reference is "aa-A-form.pdb" (:1,2&!@H*), with fitting, mass-weighted. [run ] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3286 atoms, 1083 res, box: Orthogonal, 1082 mol, 1070 solvent, 50000 frames 1: [striped] 'aa-A-form.pdb', 65 atoms, 2 res, box: None, 1 mol INPUT TRAJECTORIES: 0: REMD trajectories (12 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K Coordinate processing will occur on 50000 frames. REFERENCE FRAMES (1 total): 0: '../../../../aa-A-form.pdb', frame 1 Active reference frame for distance-based masks is 0 TIME: Run Initialization took 0.0001 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 12 REMD TRAJECTORIES Warning: Active reference has only 65 atoms, parm '[traj]' has 3286. Warning: Parm will only have reference coordinates for the first 65 atoms (distance-based masks only). ..................................................... ACTION SETUP FOR PARM '[traj]' (2 actions): 0: [autoimage origin] Anchor molecule is 1 1081 molecules are mobile. 1: [rmsd rms_2_aform :1,2&!@H= ref [a-form] 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. ----- 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: 248.3192 s TIME: Avg. throughput= 201.3537 frames / second. ACTION OUTPUT: DATASETS: 2 data sets: [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../../aa-A-form.pdb', refindex 0 (65 atoms) rms_2_aform "rms_2_aform" (double, rms), size is 50000 ---------- RUN END --------------------------------------------------- [hist rms_2_aform,0,5,0.1 out test298_hist_rmsd-all_500ns.dat norm] Hist: test298_hist_rmsd-all_500ns.dat: Set up for 1 dimensions using the following datasets: [ rms_2_aform ] norm: Sum over bins will be normalized to 1.0. ---------- RUN BEGIN ------------------------------------------------- Warning: No actions/output trajectories specified. ANALYSIS: Performing 1 analyses: 0: [hist rms_2_aform,0,5,0.1 out test298_hist_rmsd-all_500ns.dat norm] Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins. Hist: 50000 data points in each dimension. Hist: Allocating histogram, total bins = 50 Warning: Frame 577 Coordinates out of bounds (-1) Warning: Frame 1325 Coordinates out of bounds (-1) Warning: Frame 1565 Coordinates out of bounds (-1) Warning: Frame 1787 Coordinates out of bounds (-1) Warning: Frame 2121 Coordinates out of bounds (-1) Warning: Frame 2142 Coordinates out of bounds (-1) Warning: Frame 2182 Coordinates out of bounds (-1) Warning: Frame 2235 Coordinates out of bounds (-1) Warning: Frame 2424 Coordinates out of bounds (-1) Warning: Frame 2795 Coordinates out of bounds (-1) Warning: Frame 2896 Coordinates out of bounds (-1) Warning: Frame 5002 Coordinates out of bounds (-1) Warning: Frame 5807 Coordinates out of bounds (-1) Warning: Frame 7618 Coordinates out of bounds (-1) Warning: Frame 7711 Coordinates out of bounds (-1) Warning: Frame 7712 Coordinates out of bounds (-1) Warning: Frame 8406 Coordinates out of bounds (-1) Warning: Frame 8408 Coordinates out of bounds (-1) Warning: Frame 8484 Coordinates out of bounds (-1) Warning: Frame 9790 Coordinates out of bounds (-1) Warning: Frame 11492 Coordinates out of bounds (-1) Warning: Frame 11664 Coordinates out of bounds (-1) Warning: Frame 11774 Coordinates out of bounds (-1) Warning: Frame 11777 Coordinates out of bounds (-1) Warning: Frame 11781 Coordinates out of bounds (-1) Warning: Frame 11792 Coordinates out of bounds (-1) Warning: Frame 12167 Coordinates out of bounds (-1) Warning: Frame 13168 Coordinates out of bounds (-1) Warning: Frame 13711 Coordinates out of bounds (-1) Warning: Frame 13725 Coordinates out of bounds (-1) Warning: Frame 13829 Coordinates out of bounds (-1) Warning: Frame 15441 Coordinates out of bounds (-1) Warning: Frame 15610 Coordinates out of bounds (-1) Warning: Frame 16224 Coordinates out of bounds (-1) Warning: Frame 16326 Coordinates out of bounds (-1) Warning: Frame 16673 Coordinates out of bounds (-1) Warning: Frame 19602 Coordinates out of bounds (-1) Warning: Frame 20930 Coordinates out of bounds (-1) Warning: Frame 22325 Coordinates out of bounds (-1) Warning: Frame 23615 Coordinates out of bounds (-1) Warning: Frame 24210 Coordinates out of bounds (-1) Warning: Frame 24896 Coordinates out of bounds (-1) Warning: Frame 25593 Coordinates out of bounds (-1) Warning: Frame 25596 Coordinates out of bounds (-1) Warning: Frame 25668 Coordinates out of bounds (-1) Warning: Frame 26366 Coordinates out of bounds (-1) Warning: Frame 27744 Coordinates out of bounds (-1) Warning: Frame 27868 Coordinates out of bounds (-1) Warning: Frame 27869 Coordinates out of bounds (-1) Warning: Frame 27872 Coordinates out of bounds (-1) Warning: Frame 27990 Coordinates out of bounds (-1) Warning: Frame 27996 Coordinates out of bounds (-1) Warning: Frame 27997 Coordinates out of bounds (-1) Warning: Frame 29046 Coordinates out of bounds (-1) Warning: Frame 29072 Coordinates out of bounds (-1) Warning: Frame 30014 Coordinates out of bounds (-1) Warning: Frame 31836 Coordinates out of bounds (-1) Warning: Frame 32332 Coordinates out of bounds (-1) Warning: Frame 33367 Coordinates out of bounds (-1) Warning: Frame 33380 Coordinates out of bounds (-1) Warning: Frame 33834 Coordinates out of bounds (-1) Warning: Frame 34171 Coordinates out of bounds (-1) Warning: Frame 37422 Coordinates out of bounds (-1) Warning: Frame 37538 Coordinates out of bounds (-1) Warning: Frame 37821 Coordinates out of bounds (-1) Warning: Frame 38241 Coordinates out of bounds (-1) Warning: Frame 38415 Coordinates out of bounds (-1) Warning: Frame 38420 Coordinates out of bounds (-1) Warning: Frame 38464 Coordinates out of bounds (-1) Warning: Frame 38832 Coordinates out of bounds (-1) Warning: Frame 39004 Coordinates out of bounds (-1) Warning: Frame 39041 Coordinates out of bounds (-1) Warning: Frame 39107 Coordinates out of bounds (-1) Warning: Frame 39215 Coordinates out of bounds (-1) Warning: Frame 40103 Coordinates out of bounds (-1) Warning: Frame 40110 Coordinates out of bounds (-1) Warning: Frame 40112 Coordinates out of bounds (-1) Warning: Frame 40113 Coordinates out of bounds (-1) Warning: Frame 40139 Coordinates out of bounds (-1) Warning: Frame 41349 Coordinates out of bounds (-1) Warning: Frame 42309 Coordinates out of bounds (-1) Warning: Frame 42432 Coordinates out of bounds (-1) Warning: Frame 42502 Coordinates out of bounds (-1) Warning: Frame 42508 Coordinates out of bounds (-1) Warning: Frame 42540 Coordinates out of bounds (-1) Warning: Frame 42623 Coordinates out of bounds (-1) Warning: Frame 43399 Coordinates out of bounds (-1) Warning: Frame 43402 Coordinates out of bounds (-1) Warning: Frame 44185 Coordinates out of bounds (-1) Warning: Frame 44898 Coordinates out of bounds (-1) Warning: Frame 45063 Coordinates out of bounds (-1) Warning: Frame 45141 Coordinates out of bounds (-1) Warning: Frame 46860 Coordinates out of bounds (-1) Warning: Frame 47003 Coordinates out of bounds (-1) Warning: Frame 47244 Coordinates out of bounds (-1) Warning: Frame 47811 Coordinates out of bounds (-1) Warning: Frame 47860 Coordinates out of bounds (-1) Warning: Frame 48002 Coordinates out of bounds (-1) Warning: Frame 48744 Coordinates out of bounds (-1) Warning: Frame 48745 Coordinates out of bounds (-1) Warning: Frame 49419 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 49899.000000 TIME: Analyses took 0.0005 seconds. DATASETS: 3 data sets: [a-form]:1 "[a-form]:1" (reference), size is 1 '../../../../aa-A-form.pdb', refindex 0 (65 atoms) rms_2_aform "rms_2_aform" (double, rms), size is 50000 Hist_00002 "Hist_00002" (double), size is 50 DATAFILES: test298_hist_rmsd-all_500ns.dat (Standard Data File): Hist_00002 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 249.7020 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.