CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/23/15 11:17:45 | Available memory: 7358.01 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 0.0006 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: 185.8361 s TIME: Avg. throughput= 269.0542 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 1078 Coordinates out of bounds (-1) Warning: Frame 1324 Coordinates out of bounds (-1) Warning: Frame 1891 Coordinates out of bounds (-1) Warning: Frame 3091 Coordinates out of bounds (-1) Warning: Frame 3152 Coordinates out of bounds (-1) Warning: Frame 3154 Coordinates out of bounds (-1) Warning: Frame 3763 Coordinates out of bounds (-1) Warning: Frame 3994 Coordinates out of bounds (-1) Warning: Frame 4641 Coordinates out of bounds (-1) Warning: Frame 4683 Coordinates out of bounds (-1) Warning: Frame 4852 Coordinates out of bounds (-1) Warning: Frame 5628 Coordinates out of bounds (-1) Warning: Frame 5645 Coordinates out of bounds (-1) Warning: Frame 5772 Coordinates out of bounds (-1) Warning: Frame 5981 Coordinates out of bounds (-1) Warning: Frame 5982 Coordinates out of bounds (-1) Warning: Frame 6105 Coordinates out of bounds (-1) Warning: Frame 6309 Coordinates out of bounds (-1) Warning: Frame 6862 Coordinates out of bounds (-1) Warning: Frame 7367 Coordinates out of bounds (-1) Warning: Frame 8217 Coordinates out of bounds (-1) Warning: Frame 8413 Coordinates out of bounds (-1) Warning: Frame 8864 Coordinates out of bounds (-1) Warning: Frame 9313 Coordinates out of bounds (-1) Warning: Frame 9316 Coordinates out of bounds (-1) Warning: Frame 9670 Coordinates out of bounds (-1) Warning: Frame 10071 Coordinates out of bounds (-1) Warning: Frame 10072 Coordinates out of bounds (-1) Warning: Frame 10461 Coordinates out of bounds (-1) Warning: Frame 10484 Coordinates out of bounds (-1) Warning: Frame 10706 Coordinates out of bounds (-1) Warning: Frame 11515 Coordinates out of bounds (-1) Warning: Frame 11556 Coordinates out of bounds (-1) Warning: Frame 13107 Coordinates out of bounds (-1) Warning: Frame 13566 Coordinates out of bounds (-1) Warning: Frame 13607 Coordinates out of bounds (-1) Warning: Frame 13636 Coordinates out of bounds (-1) Warning: Frame 13986 Coordinates out of bounds (-1) Warning: Frame 15710 Coordinates out of bounds (-1) Warning: Frame 15713 Coordinates out of bounds (-1) Warning: Frame 16309 Coordinates out of bounds (-1) Warning: Frame 17042 Coordinates out of bounds (-1) Warning: Frame 17811 Coordinates out of bounds (-1) Warning: Frame 17969 Coordinates out of bounds (-1) Warning: Frame 17976 Coordinates out of bounds (-1) Warning: Frame 17986 Coordinates out of bounds (-1) Warning: Frame 17990 Coordinates out of bounds (-1) Warning: Frame 18016 Coordinates out of bounds (-1) Warning: Frame 18017 Coordinates out of bounds (-1) Warning: Frame 18068 Coordinates out of bounds (-1) Warning: Frame 18155 Coordinates out of bounds (-1) Warning: Frame 18779 Coordinates out of bounds (-1) Warning: Frame 18928 Coordinates out of bounds (-1) Warning: Frame 19136 Coordinates out of bounds (-1) Warning: Frame 19414 Coordinates out of bounds (-1) Warning: Frame 19426 Coordinates out of bounds (-1) Warning: Frame 19583 Coordinates out of bounds (-1) Warning: Frame 19886 Coordinates out of bounds (-1) Warning: Frame 19893 Coordinates out of bounds (-1) Warning: Frame 19998 Coordinates out of bounds (-1) Warning: Frame 20044 Coordinates out of bounds (-1) Warning: Frame 20249 Coordinates out of bounds (-1) Warning: Frame 21755 Coordinates out of bounds (-1) Warning: Frame 21756 Coordinates out of bounds (-1) Warning: Frame 22476 Coordinates out of bounds (-1) Warning: Frame 22490 Coordinates out of bounds (-1) Warning: Frame 22518 Coordinates out of bounds (-1) Warning: Frame 22620 Coordinates out of bounds (-1) Warning: Frame 22737 Coordinates out of bounds (-1) Warning: Frame 22764 Coordinates out of bounds (-1) Warning: Frame 22974 Coordinates out of bounds (-1) Warning: Frame 23190 Coordinates out of bounds (-1) Warning: Frame 23195 Coordinates out of bounds (-1) Warning: Frame 23512 Coordinates out of bounds (-1) Warning: Frame 23528 Coordinates out of bounds (-1) Warning: Frame 24083 Coordinates out of bounds (-1) Warning: Frame 24375 Coordinates out of bounds (-1) Warning: Frame 24869 Coordinates out of bounds (-1) Warning: Frame 25685 Coordinates out of bounds (-1) Warning: Frame 26846 Coordinates out of bounds (-1) Warning: Frame 27004 Coordinates out of bounds (-1) Warning: Frame 27068 Coordinates out of bounds (-1) Warning: Frame 27205 Coordinates out of bounds (-1) Warning: Frame 27254 Coordinates out of bounds (-1) Warning: Frame 27828 Coordinates out of bounds (-1) Warning: Frame 28071 Coordinates out of bounds (-1) Warning: Frame 28501 Coordinates out of bounds (-1) Warning: Frame 28523 Coordinates out of bounds (-1) Warning: Frame 28527 Coordinates out of bounds (-1) Warning: Frame 29061 Coordinates out of bounds (-1) Warning: Frame 29433 Coordinates out of bounds (-1) Warning: Frame 29869 Coordinates out of bounds (-1) Warning: Frame 30838 Coordinates out of bounds (-1) Warning: Frame 31593 Coordinates out of bounds (-1) Warning: Frame 31649 Coordinates out of bounds (-1) Warning: Frame 31678 Coordinates out of bounds (-1) Warning: Frame 32937 Coordinates out of bounds (-1) Warning: Frame 33665 Coordinates out of bounds (-1) Warning: Frame 34133 Coordinates out of bounds (-1) Warning: Frame 34730 Coordinates out of bounds (-1) Warning: Frame 35740 Coordinates out of bounds (-1) Warning: Frame 36171 Coordinates out of bounds (-1) Warning: Frame 36317 Coordinates out of bounds (-1) Warning: Frame 36318 Coordinates out of bounds (-1) Warning: Frame 36704 Coordinates out of bounds (-1) Warning: Frame 36869 Coordinates out of bounds (-1) Warning: Frame 36870 Coordinates out of bounds (-1) Warning: Frame 36912 Coordinates out of bounds (-1) Warning: Frame 37934 Coordinates out of bounds (-1) Warning: Frame 37957 Coordinates out of bounds (-1) Warning: Frame 38260 Coordinates out of bounds (-1) Warning: Frame 38423 Coordinates out of bounds (-1) Warning: Frame 38731 Coordinates out of bounds (-1) Warning: Frame 38909 Coordinates out of bounds (-1) Warning: Frame 38910 Coordinates out of bounds (-1) Warning: Frame 39359 Coordinates out of bounds (-1) Warning: Frame 39578 Coordinates out of bounds (-1) Warning: Frame 40376 Coordinates out of bounds (-1) Warning: Frame 40704 Coordinates out of bounds (-1) Warning: Frame 41757 Coordinates out of bounds (-1) Warning: Frame 41986 Coordinates out of bounds (-1) Warning: Frame 43171 Coordinates out of bounds (-1) Warning: Frame 43468 Coordinates out of bounds (-1) Warning: Frame 43630 Coordinates out of bounds (-1) Warning: Frame 44119 Coordinates out of bounds (-1) Warning: Frame 45216 Coordinates out of bounds (-1) Warning: Frame 45823 Coordinates out of bounds (-1) Warning: Frame 45965 Coordinates out of bounds (-1) Warning: Frame 46107 Coordinates out of bounds (-1) Warning: Frame 46249 Coordinates out of bounds (-1) Warning: Frame 46474 Coordinates out of bounds (-1) Warning: Frame 46952 Coordinates out of bounds (-1) Warning: Frame 47865 Coordinates out of bounds (-1) Warning: Frame 48535 Coordinates out of bounds (-1) Warning: Frame 48879 Coordinates out of bounds (-1) Warning: Frame 48941 Coordinates out of bounds (-1) Warning: Frame 48969 Coordinates out of bounds (-1) Warning: Frame 49068 Coordinates out of bounds (-1) Warning: Frame 49519 Coordinates out of bounds (-1) Warning: Frame 49925 Coordinates out of bounds (-1) Warning: Frame 49926 Coordinates out of bounds (-1) Warning: Frame 49927 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 49858.000000 TIME: Analyses took 0.0150 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: 189.6489 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.