CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/23/15 11:18:23 | Available memory: 6834.13 MB INPUT: Reading Input from file pt-test_highT.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 396.40 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 ] [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', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 50000 frames 1: [striped] 'aa-A-form.pdb', 65 atoms, 2 res, box: None, 1 mol INPUT TRAJECTORIES: 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 396.40 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 0.0083 seconds. BEGIN TRAJECTORY PROCESSING: REMD: OPENING 18 REMD TRAJECTORIES Warning: Active reference has only 65 atoms, parm '[traj]' has 3301. 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 1086 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: 366.5975 s TIME: Avg. throughput= 136.3894 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 test396_hist_rmsd-all_1000ns.dat norm] Hist: test396_hist_rmsd-all_1000ns.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 test396_hist_rmsd-all_1000ns.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 28 Coordinates out of bounds (-1) Warning: Frame 74 Coordinates out of bounds (-1) Warning: Frame 287 Coordinates out of bounds (-1) Warning: Frame 387 Coordinates out of bounds (-1) Warning: Frame 521 Coordinates out of bounds (-1) Warning: Frame 631 Coordinates out of bounds (-1) Warning: Frame 766 Coordinates out of bounds (-1) Warning: Frame 815 Coordinates out of bounds (-1) Warning: Frame 1750 Coordinates out of bounds (-1) Warning: Frame 1879 Coordinates out of bounds (-1) Warning: Frame 1880 Coordinates out of bounds (-1) Warning: Frame 2187 Coordinates out of bounds (-1) Warning: Frame 2493 Coordinates out of bounds (-1) Warning: Frame 2572 Coordinates out of bounds (-1) Warning: Frame 2637 Coordinates out of bounds (-1) Warning: Frame 2811 Coordinates out of bounds (-1) Warning: Frame 2870 Coordinates out of bounds (-1) Warning: Frame 2871 Coordinates out of bounds (-1) Warning: Frame 3158 Coordinates out of bounds (-1) Warning: Frame 3385 Coordinates out of bounds (-1) Warning: Frame 3439 Coordinates out of bounds (-1) Warning: Frame 3440 Coordinates out of bounds (-1) Warning: Frame 3512 Coordinates out of bounds (-1) Warning: Frame 3534 Coordinates out of bounds (-1) Warning: Frame 4427 Coordinates out of bounds (-1) Warning: Frame 4562 Coordinates out of bounds (-1) Warning: Frame 4567 Coordinates out of bounds (-1) Warning: Frame 4810 Coordinates out of bounds (-1) Warning: Frame 5025 Coordinates out of bounds (-1) Warning: Frame 5301 Coordinates out of bounds (-1) Warning: Frame 5360 Coordinates out of bounds (-1) Warning: Frame 5471 Coordinates out of bounds (-1) Warning: Frame 5474 Coordinates out of bounds (-1) Warning: Frame 5548 Coordinates out of bounds (-1) Warning: Frame 5582 Coordinates out of bounds (-1) Warning: Frame 5907 Coordinates out of bounds (-1) Warning: Frame 6374 Coordinates out of bounds (-1) Warning: Frame 6380 Coordinates out of bounds (-1) Warning: Frame 6796 Coordinates out of bounds (-1) Warning: Frame 6932 Coordinates out of bounds (-1) Warning: Frame 7029 Coordinates out of bounds (-1) Warning: Frame 7102 Coordinates out of bounds (-1) Warning: Frame 7330 Coordinates out of bounds (-1) Warning: Frame 7761 Coordinates out of bounds (-1) Warning: Frame 8220 Coordinates out of bounds (-1) Warning: Frame 8348 Coordinates out of bounds (-1) Warning: Frame 8591 Coordinates out of bounds (-1) Warning: Frame 8654 Coordinates out of bounds (-1) Warning: Frame 9310 Coordinates out of bounds (-1) Warning: Frame 9398 Coordinates out of bounds (-1) Warning: Frame 9790 Coordinates out of bounds (-1) Warning: Frame 9871 Coordinates out of bounds (-1) Warning: Frame 10100 Coordinates out of bounds (-1) Warning: Frame 10444 Coordinates out of bounds (-1) Warning: Frame 10478 Coordinates out of bounds (-1) Warning: Frame 13563 Coordinates out of bounds (-1) Warning: Frame 13833 Coordinates out of bounds (-1) Warning: Frame 13879 Coordinates out of bounds (-1) Warning: Frame 14810 Coordinates out of bounds (-1) Warning: Frame 14858 Coordinates out of bounds (-1) Warning: Frame 15876 Coordinates out of bounds (-1) Warning: Frame 16246 Coordinates out of bounds (-1) Warning: Frame 16247 Coordinates out of bounds (-1) Warning: Frame 16300 Coordinates out of bounds (-1) Warning: Frame 17130 Coordinates out of bounds (-1) Warning: Frame 17542 Coordinates out of bounds (-1) Warning: Frame 18629 Coordinates out of bounds (-1) Warning: Frame 19051 Coordinates out of bounds (-1) Warning: Frame 19059 Coordinates out of bounds (-1) Warning: Frame 19371 Coordinates out of bounds (-1) Warning: Frame 20335 Coordinates out of bounds (-1) Warning: Frame 20336 Coordinates out of bounds (-1) Warning: Frame 20368 Coordinates out of bounds (-1) Warning: Frame 20626 Coordinates out of bounds (-1) Warning: Frame 21446 Coordinates out of bounds (-1) Warning: Frame 22201 Coordinates out of bounds (-1) Warning: Frame 22254 Coordinates out of bounds (-1) Warning: Frame 22295 Coordinates out of bounds (-1) Warning: Frame 23346 Coordinates out of bounds (-1) Warning: Frame 24095 Coordinates out of bounds (-1) Warning: Frame 24496 Coordinates out of bounds (-1) Warning: Frame 25448 Coordinates out of bounds (-1) Warning: Frame 25581 Coordinates out of bounds (-1) Warning: Frame 25924 Coordinates out of bounds (-1) Warning: Frame 26613 Coordinates out of bounds (-1) Warning: Frame 27027 Coordinates out of bounds (-1) Warning: Frame 28216 Coordinates out of bounds (-1) Warning: Frame 28919 Coordinates out of bounds (-1) Warning: Frame 28922 Coordinates out of bounds (-1) Warning: Frame 28926 Coordinates out of bounds (-1) Warning: Frame 29172 Coordinates out of bounds (-1) Warning: Frame 29175 Coordinates out of bounds (-1) Warning: Frame 29854 Coordinates out of bounds (-1) Warning: Frame 31966 Coordinates out of bounds (-1) Warning: Frame 32118 Coordinates out of bounds (-1) Warning: Frame 33125 Coordinates out of bounds (-1) Warning: Frame 33851 Coordinates out of bounds (-1) Warning: Frame 33963 Coordinates out of bounds (-1) Warning: Frame 34173 Coordinates out of bounds (-1) Warning: Frame 34298 Coordinates out of bounds (-1) Warning: Frame 35131 Coordinates out of bounds (-1) Warning: Frame 35929 Coordinates out of bounds (-1) Warning: Frame 36129 Coordinates out of bounds (-1) Warning: Frame 36233 Coordinates out of bounds (-1) Warning: Frame 37254 Coordinates out of bounds (-1) Warning: Frame 37324 Coordinates out of bounds (-1) Warning: Frame 37362 Coordinates out of bounds (-1) Warning: Frame 37401 Coordinates out of bounds (-1) Warning: Frame 37402 Coordinates out of bounds (-1) Warning: Frame 37690 Coordinates out of bounds (-1) Warning: Frame 38805 Coordinates out of bounds (-1) Warning: Frame 38890 Coordinates out of bounds (-1) Warning: Frame 38900 Coordinates out of bounds (-1) Warning: Frame 38973 Coordinates out of bounds (-1) Warning: Frame 39027 Coordinates out of bounds (-1) Warning: Frame 40227 Coordinates out of bounds (-1) Warning: Frame 40489 Coordinates out of bounds (-1) Warning: Frame 41774 Coordinates out of bounds (-1) Warning: Frame 42798 Coordinates out of bounds (-1) Warning: Frame 42869 Coordinates out of bounds (-1) Warning: Frame 42973 Coordinates out of bounds (-1) Warning: Frame 43014 Coordinates out of bounds (-1) Warning: Frame 43054 Coordinates out of bounds (-1) Warning: Frame 43056 Coordinates out of bounds (-1) Warning: Frame 43113 Coordinates out of bounds (-1) Warning: Frame 43660 Coordinates out of bounds (-1) Warning: Frame 43957 Coordinates out of bounds (-1) Warning: Frame 43959 Coordinates out of bounds (-1) Warning: Frame 44125 Coordinates out of bounds (-1) Warning: Frame 44507 Coordinates out of bounds (-1) Warning: Frame 44509 Coordinates out of bounds (-1) Warning: Frame 44525 Coordinates out of bounds (-1) Warning: Frame 44857 Coordinates out of bounds (-1) Warning: Frame 45187 Coordinates out of bounds (-1) Warning: Frame 45189 Coordinates out of bounds (-1) Warning: Frame 45422 Coordinates out of bounds (-1) Warning: Frame 45424 Coordinates out of bounds (-1) Warning: Frame 46054 Coordinates out of bounds (-1) Warning: Frame 46366 Coordinates out of bounds (-1) Warning: Frame 46367 Coordinates out of bounds (-1) Warning: Frame 46656 Coordinates out of bounds (-1) Warning: Frame 46813 Coordinates out of bounds (-1) Warning: Frame 46814 Coordinates out of bounds (-1) Warning: Frame 47645 Coordinates out of bounds (-1) Warning: Frame 47646 Coordinates out of bounds (-1) Warning: Frame 47647 Coordinates out of bounds (-1) Warning: Frame 47653 Coordinates out of bounds (-1) Warning: Frame 47823 Coordinates out of bounds (-1) Warning: Frame 48689 Coordinates out of bounds (-1) Warning: Frame 48842 Coordinates out of bounds (-1) Warning: Frame 48980 Coordinates out of bounds (-1) Warning: Frame 49118 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 49848.000000 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: test396_hist_rmsd-all_1000ns.dat (Standard Data File): Hist_00002 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 368.6029 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.