CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/21/15 16:12:15 | Available memory: 13511.8 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 351.82 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 351.82 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: 252.2622 s TIME: Avg. throughput= 198.2065 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 test351_hist_rmsd-all_500ns.dat norm] Hist: test351_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 test351_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 1575 Coordinates out of bounds (-1) Warning: Frame 1705 Coordinates out of bounds (-1) Warning: Frame 1857 Coordinates out of bounds (-1) Warning: Frame 2213 Coordinates out of bounds (-1) Warning: Frame 2265 Coordinates out of bounds (-1) Warning: Frame 2472 Coordinates out of bounds (-1) Warning: Frame 2708 Coordinates out of bounds (-1) Warning: Frame 3410 Coordinates out of bounds (-1) Warning: Frame 3992 Coordinates out of bounds (-1) Warning: Frame 4730 Coordinates out of bounds (-1) Warning: Frame 4918 Coordinates out of bounds (-1) Warning: Frame 5028 Coordinates out of bounds (-1) Warning: Frame 5029 Coordinates out of bounds (-1) Warning: Frame 5534 Coordinates out of bounds (-1) Warning: Frame 6126 Coordinates out of bounds (-1) Warning: Frame 6305 Coordinates out of bounds (-1) Warning: Frame 6307 Coordinates out of bounds (-1) Warning: Frame 7277 Coordinates out of bounds (-1) Warning: Frame 7468 Coordinates out of bounds (-1) Warning: Frame 8389 Coordinates out of bounds (-1) Warning: Frame 8395 Coordinates out of bounds (-1) Warning: Frame 8428 Coordinates out of bounds (-1) Warning: Frame 8430 Coordinates out of bounds (-1) Warning: Frame 8431 Coordinates out of bounds (-1) Warning: Frame 8465 Coordinates out of bounds (-1) Warning: Frame 8526 Coordinates out of bounds (-1) Warning: Frame 8540 Coordinates out of bounds (-1) Warning: Frame 8807 Coordinates out of bounds (-1) Warning: Frame 8808 Coordinates out of bounds (-1) Warning: Frame 9374 Coordinates out of bounds (-1) Warning: Frame 9391 Coordinates out of bounds (-1) Warning: Frame 9798 Coordinates out of bounds (-1) Warning: Frame 9870 Coordinates out of bounds (-1) Warning: Frame 9971 Coordinates out of bounds (-1) Warning: Frame 9973 Coordinates out of bounds (-1) Warning: Frame 10075 Coordinates out of bounds (-1) Warning: Frame 10417 Coordinates out of bounds (-1) Warning: Frame 10421 Coordinates out of bounds (-1) Warning: Frame 10763 Coordinates out of bounds (-1) Warning: Frame 11189 Coordinates out of bounds (-1) Warning: Frame 11262 Coordinates out of bounds (-1) Warning: Frame 11267 Coordinates out of bounds (-1) Warning: Frame 11268 Coordinates out of bounds (-1) Warning: Frame 11563 Coordinates out of bounds (-1) Warning: Frame 12222 Coordinates out of bounds (-1) Warning: Frame 12266 Coordinates out of bounds (-1) Warning: Frame 12551 Coordinates out of bounds (-1) Warning: Frame 14267 Coordinates out of bounds (-1) Warning: Frame 14748 Coordinates out of bounds (-1) Warning: Frame 15031 Coordinates out of bounds (-1) Warning: Frame 15082 Coordinates out of bounds (-1) Warning: Frame 15175 Coordinates out of bounds (-1) Warning: Frame 15293 Coordinates out of bounds (-1) Warning: Frame 15380 Coordinates out of bounds (-1) Warning: Frame 16363 Coordinates out of bounds (-1) Warning: Frame 16440 Coordinates out of bounds (-1) Warning: Frame 17114 Coordinates out of bounds (-1) Warning: Frame 17119 Coordinates out of bounds (-1) Warning: Frame 17120 Coordinates out of bounds (-1) Warning: Frame 17131 Coordinates out of bounds (-1) Warning: Frame 17148 Coordinates out of bounds (-1) Warning: Frame 17380 Coordinates out of bounds (-1) Warning: Frame 18872 Coordinates out of bounds (-1) Warning: Frame 19136 Coordinates out of bounds (-1) Warning: Frame 19482 Coordinates out of bounds (-1) Warning: Frame 19611 Coordinates out of bounds (-1) Warning: Frame 19612 Coordinates out of bounds (-1) Warning: Frame 20532 Coordinates out of bounds (-1) Warning: Frame 20533 Coordinates out of bounds (-1) Warning: Frame 20788 Coordinates out of bounds (-1) Warning: Frame 21257 Coordinates out of bounds (-1) Warning: Frame 21586 Coordinates out of bounds (-1) Warning: Frame 21893 Coordinates out of bounds (-1) Warning: Frame 22137 Coordinates out of bounds (-1) Warning: Frame 22190 Coordinates out of bounds (-1) Warning: Frame 22344 Coordinates out of bounds (-1) Warning: Frame 22408 Coordinates out of bounds (-1) Warning: Frame 22842 Coordinates out of bounds (-1) Warning: Frame 23350 Coordinates out of bounds (-1) Warning: Frame 23551 Coordinates out of bounds (-1) Warning: Frame 23999 Coordinates out of bounds (-1) Warning: Frame 24924 Coordinates out of bounds (-1) Warning: Frame 25686 Coordinates out of bounds (-1) Warning: Frame 26180 Coordinates out of bounds (-1) Warning: Frame 26182 Coordinates out of bounds (-1) Warning: Frame 26188 Coordinates out of bounds (-1) Warning: Frame 26190 Coordinates out of bounds (-1) Warning: Frame 26810 Coordinates out of bounds (-1) Warning: Frame 27355 Coordinates out of bounds (-1) Warning: Frame 27750 Coordinates out of bounds (-1) Warning: Frame 27876 Coordinates out of bounds (-1) Warning: Frame 27881 Coordinates out of bounds (-1) Warning: Frame 27930 Coordinates out of bounds (-1) Warning: Frame 29007 Coordinates out of bounds (-1) Warning: Frame 29011 Coordinates out of bounds (-1) Warning: Frame 29022 Coordinates out of bounds (-1) Warning: Frame 29902 Coordinates out of bounds (-1) Warning: Frame 30078 Coordinates out of bounds (-1) Warning: Frame 30358 Coordinates out of bounds (-1) Warning: Frame 30395 Coordinates out of bounds (-1) Warning: Frame 30801 Coordinates out of bounds (-1) Warning: Frame 30821 Coordinates out of bounds (-1) Warning: Frame 30843 Coordinates out of bounds (-1) Warning: Frame 30868 Coordinates out of bounds (-1) Warning: Frame 31034 Coordinates out of bounds (-1) Warning: Frame 31932 Coordinates out of bounds (-1) Warning: Frame 31967 Coordinates out of bounds (-1) Warning: Frame 31968 Coordinates out of bounds (-1) Warning: Frame 32612 Coordinates out of bounds (-1) Warning: Frame 32613 Coordinates out of bounds (-1) Warning: Frame 32786 Coordinates out of bounds (-1) Warning: Frame 32979 Coordinates out of bounds (-1) Warning: Frame 32995 Coordinates out of bounds (-1) Warning: Frame 33034 Coordinates out of bounds (-1) Warning: Frame 33048 Coordinates out of bounds (-1) Warning: Frame 33055 Coordinates out of bounds (-1) Warning: Frame 33804 Coordinates out of bounds (-1) Warning: Frame 34110 Coordinates out of bounds (-1) Warning: Frame 34114 Coordinates out of bounds (-1) Warning: Frame 34214 Coordinates out of bounds (-1) Warning: Frame 34363 Coordinates out of bounds (-1) Warning: Frame 34456 Coordinates out of bounds (-1) Warning: Frame 34471 Coordinates out of bounds (-1) Warning: Frame 34489 Coordinates out of bounds (-1) Warning: Frame 34496 Coordinates out of bounds (-1) Warning: Frame 35562 Coordinates out of bounds (-1) Warning: Frame 35563 Coordinates out of bounds (-1) Warning: Frame 35564 Coordinates out of bounds (-1) Warning: Frame 35572 Coordinates out of bounds (-1) Warning: Frame 35792 Coordinates out of bounds (-1) Warning: Frame 35880 Coordinates out of bounds (-1) Warning: Frame 36004 Coordinates out of bounds (-1) Warning: Frame 36125 Coordinates out of bounds (-1) Warning: Frame 36147 Coordinates out of bounds (-1) Warning: Frame 36188 Coordinates out of bounds (-1) Warning: Frame 36248 Coordinates out of bounds (-1) Warning: Frame 36249 Coordinates out of bounds (-1) Warning: Frame 37191 Coordinates out of bounds (-1) Warning: Frame 37374 Coordinates out of bounds (-1) Warning: Frame 37473 Coordinates out of bounds (-1) Warning: Frame 37786 Coordinates out of bounds (-1) Warning: Frame 37814 Coordinates out of bounds (-1) Warning: Frame 38936 Coordinates out of bounds (-1) Warning: Frame 38945 Coordinates out of bounds (-1) Warning: Frame 38948 Coordinates out of bounds (-1) Warning: Frame 39640 Coordinates out of bounds (-1) Warning: Frame 39688 Coordinates out of bounds (-1) Warning: Frame 39846 Coordinates out of bounds (-1) Warning: Frame 39877 Coordinates out of bounds (-1) Warning: Frame 39909 Coordinates out of bounds (-1) Warning: Frame 39913 Coordinates out of bounds (-1) Warning: Frame 40098 Coordinates out of bounds (-1) Warning: Frame 40105 Coordinates out of bounds (-1) Warning: Frame 41673 Coordinates out of bounds (-1) Warning: Frame 43198 Coordinates out of bounds (-1) Warning: Frame 43648 Coordinates out of bounds (-1) Warning: Frame 43683 Coordinates out of bounds (-1) Warning: Frame 43702 Coordinates out of bounds (-1) Warning: Frame 43928 Coordinates out of bounds (-1) Warning: Frame 44129 Coordinates out of bounds (-1) Warning: Frame 44130 Coordinates out of bounds (-1) Warning: Frame 44210 Coordinates out of bounds (-1) Warning: Frame 45107 Coordinates out of bounds (-1) Warning: Frame 45711 Coordinates out of bounds (-1) Warning: Frame 45727 Coordinates out of bounds (-1) Warning: Frame 45730 Coordinates out of bounds (-1) Warning: Frame 45983 Coordinates out of bounds (-1) Warning: Frame 47148 Coordinates out of bounds (-1) Warning: Frame 47201 Coordinates out of bounds (-1) Warning: Frame 47243 Coordinates out of bounds (-1) Warning: Frame 47501 Coordinates out of bounds (-1) Warning: Frame 47758 Coordinates out of bounds (-1) Warning: Frame 47762 Coordinates out of bounds (-1) Warning: Frame 48025 Coordinates out of bounds (-1) Warning: Frame 49127 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 49825.000000 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: test351_hist_rmsd-all_500ns.dat (Standard Data File): Hist_00002 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 255.8414 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.