CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 10/23/15 11:11:50 | Available memory: 10987.4 MB INPUT: Reading Input from file pt-rmsd.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.1.18 ] Reading '../traj.1.18' as Amber NetCDF [trajin ../traj.2.18] Reading '../traj.2.18' as Amber NetCDF [trajin ../traj.2.18] Reading '../traj.2.18' as Amber NetCDF [reference ../../../../aa-A-form.pdb parm [striped] [a-form]] Reading '../../../../aa-A-form.pdb' as PDB [strip :WAT,Na+,K+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,K+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [rmsd rms_2_aform :1,2&!@H= ref [a-form]] Reference mask: [:1,2&!@H*](41) RMSD: (:1,2&!@H*), reference is "aa-A-form.pdb" (:1,2&!@H*), with fitting. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'full.topo.hmr', 3301 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent, 84078 frames 1: [striped] 'aa-A-form.pdb', 65 atoms, 2 res, box: None, 1 mol INPUT TRAJECTORIES: 0: 'traj.1.18' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 50000 of 50000) 1: 'traj.2.18' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 17039 of 17039) 2: 'traj.2.18' is a NetCDF AMBER trajectory with replica temperatures, Parm [traj] (Orthogonal box) (reading 17039 of 17039) Coordinate processing will occur on 84078 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 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: 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]' (3 actions): 0: [strip :WAT,Na+,K+,Cl-] Stripping 3236 atoms. Stripped parm: 'full.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd rms_2_aform :1,2&!@H= ref [a-form]] 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.1.18 (1-50000, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.18 (1-17039, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. ----- traj.2.18 (1-17039, 1) ----- 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 84078 frames and processed 84078 frames. TIME: Trajectory processing: 10.1581 s TIME: Avg. throughput= 8276.9139 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 84078 ---------- RUN END --------------------------------------------------- [hist rms_2_aform,0,5,0.1 out hist_rmsd_18.dat norm] Hist: hist_rmsd_18.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 hist_rmsd_18.dat norm] Dim rms_2_aform: 0.000000->5.000000, step 0.100000, 50 bins. Hist: 84078 data points in each dimension. Hist: Allocating histogram, total bins = 50 Warning: Frame 2406 Coordinates out of bounds (-1) Warning: Frame 5327 Coordinates out of bounds (-1) Warning: Frame 5344 Coordinates out of bounds (-1) Warning: Frame 5695 Coordinates out of bounds (-1) Warning: Frame 5711 Coordinates out of bounds (-1) Warning: Frame 5772 Coordinates out of bounds (-1) Warning: Frame 5904 Coordinates out of bounds (-1) Warning: Frame 5910 Coordinates out of bounds (-1) Warning: Frame 5913 Coordinates out of bounds (-1) Warning: Frame 5920 Coordinates out of bounds (-1) Warning: Frame 8664 Coordinates out of bounds (-1) Warning: Frame 9607 Coordinates out of bounds (-1) Warning: Frame 9612 Coordinates out of bounds (-1) Warning: Frame 9614 Coordinates out of bounds (-1) Warning: Frame 10731 Coordinates out of bounds (-1) Warning: Frame 11233 Coordinates out of bounds (-1) Warning: Frame 12614 Coordinates out of bounds (-1) Warning: Frame 13107 Coordinates out of bounds (-1) Warning: Frame 13108 Coordinates out of bounds (-1) Warning: Frame 13138 Coordinates out of bounds (-1) Warning: Frame 15280 Coordinates out of bounds (-1) Warning: Frame 15292 Coordinates out of bounds (-1) Warning: Frame 15298 Coordinates out of bounds (-1) Warning: Frame 17073 Coordinates out of bounds (-1) Warning: Frame 17801 Coordinates out of bounds (-1) Warning: Frame 17805 Coordinates out of bounds (-1) Warning: Frame 17941 Coordinates out of bounds (-1) Warning: Frame 17944 Coordinates out of bounds (-1) Warning: Frame 18386 Coordinates out of bounds (-1) Warning: Frame 18387 Coordinates out of bounds (-1) Warning: Frame 18388 Coordinates out of bounds (-1) Warning: Frame 24869 Coordinates out of bounds (-1) Warning: Frame 24885 Coordinates out of bounds (-1) Warning: Frame 26913 Coordinates out of bounds (-1) Warning: Frame 29688 Coordinates out of bounds (-1) Warning: Frame 29691 Coordinates out of bounds (-1) Warning: Frame 29692 Coordinates out of bounds (-1) Warning: Frame 29861 Coordinates out of bounds (-1) Warning: Frame 29865 Coordinates out of bounds (-1) Warning: Frame 29869 Coordinates out of bounds (-1) Warning: Frame 29872 Coordinates out of bounds (-1) Warning: Frame 29883 Coordinates out of bounds (-1) Warning: Frame 29902 Coordinates out of bounds (-1) Warning: Frame 32937 Coordinates out of bounds (-1) Warning: Frame 33203 Coordinates out of bounds (-1) Warning: Frame 34058 Coordinates out of bounds (-1) Warning: Frame 37240 Coordinates out of bounds (-1) Warning: Frame 37246 Coordinates out of bounds (-1) Warning: Frame 38187 Coordinates out of bounds (-1) Warning: Frame 38188 Coordinates out of bounds (-1) Warning: Frame 38215 Coordinates out of bounds (-1) Warning: Frame 38216 Coordinates out of bounds (-1) Warning: Frame 39376 Coordinates out of bounds (-1) Warning: Frame 39443 Coordinates out of bounds (-1) Warning: Frame 39448 Coordinates out of bounds (-1) Warning: Frame 39450 Coordinates out of bounds (-1) Warning: Frame 39453 Coordinates out of bounds (-1) Warning: Frame 40376 Coordinates out of bounds (-1) Warning: Frame 41985 Coordinates out of bounds (-1) Warning: Frame 41986 Coordinates out of bounds (-1) Warning: Frame 41987 Coordinates out of bounds (-1) Warning: Frame 41988 Coordinates out of bounds (-1) Warning: Frame 42167 Coordinates out of bounds (-1) Warning: Frame 43171 Coordinates out of bounds (-1) Warning: Frame 43237 Coordinates out of bounds (-1) Warning: Frame 43240 Coordinates out of bounds (-1) Warning: Frame 43288 Coordinates out of bounds (-1) Warning: Frame 43328 Coordinates out of bounds (-1) Warning: Frame 43335 Coordinates out of bounds (-1) Warning: Frame 43341 Coordinates out of bounds (-1) Warning: Frame 43344 Coordinates out of bounds (-1) Warning: Frame 43601 Coordinates out of bounds (-1) Warning: Frame 45226 Coordinates out of bounds (-1) Warning: Frame 48509 Coordinates out of bounds (-1) Warning: Frame 49800 Coordinates out of bounds (-1) Warning: Frame 49802 Coordinates out of bounds (-1) Warning: 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Coordinates out of bounds (-1) Warning: Frame 56562 Coordinates out of bounds (-1) Warning: Frame 56564 Coordinates out of bounds (-1) Warning: Frame 56567 Coordinates out of bounds (-1) Warning: Frame 56574 Coordinates out of bounds (-1) Warning: Frame 57589 Coordinates out of bounds (-1) Warning: Frame 57928 Coordinates out of bounds (-1) Warning: Frame 58621 Coordinates out of bounds (-1) Warning: Frame 58625 Coordinates out of bounds (-1) Warning: Frame 58654 Coordinates out of bounds (-1) Warning: Frame 58657 Coordinates out of bounds (-1) Warning: Frame 59200 Coordinates out of bounds (-1) Warning: Frame 59204 Coordinates out of bounds (-1) Warning: Frame 59211 Coordinates out of bounds (-1) Warning: Frame 59224 Coordinates out of bounds (-1) Warning: Frame 59225 Coordinates out of bounds (-1) Warning: Frame 59227 Coordinates out of bounds (-1) Warning: Frame 59233 Coordinates out of bounds (-1) Warning: Frame 59235 Coordinates out of bounds (-1) Warning: Frame 59275 Coordinates out of bounds (-1) Warning: Frame 59279 Coordinates out of bounds (-1) Warning: Frame 59280 Coordinates out of bounds (-1) Warning: Frame 59289 Coordinates out of bounds (-1) Warning: Frame 59294 Coordinates out of bounds (-1) Warning: Frame 60324 Coordinates out of bounds (-1) Warning: Frame 61361 Coordinates out of bounds (-1) Warning: Frame 61362 Coordinates out of bounds (-1) Warning: Frame 61404 Coordinates out of bounds (-1) Warning: Frame 61410 Coordinates out of bounds (-1) Warning: Frame 63768 Coordinates out of bounds (-1) Warning: Frame 63769 Coordinates out of bounds (-1) Warning: Frame 64987 Coordinates out of bounds (-1) Warning: Frame 64995 Coordinates out of bounds (-1) Warning: Frame 65481 Coordinates out of bounds (-1) Warning: Frame 67477 Coordinates out of bounds (-1) Warning: Frame 67504 Coordinates out of bounds (-1) Warning: Frame 67509 Coordinates out of bounds (-1) Warning: Frame 67537 Coordinates out of bounds (-1) Warning: Frame 68681 Coordinates out of bounds (-1) Warning: Frame 68725 Coordinates out of bounds (-1) Warning: Frame 68733 Coordinates out of bounds (-1) Warning: Frame 68738 Coordinates out of bounds (-1) Warning: Frame 70767 Coordinates out of bounds (-1) Warning: Frame 70797 Coordinates out of bounds (-1) Warning: Frame 70799 Coordinates out of bounds (-1) Warning: Frame 70805 Coordinates out of bounds (-1) Warning: Frame 70808 Coordinates out of bounds (-1) Warning: Frame 71763 Coordinates out of bounds (-1) Warning: Frame 71766 Coordinates out of bounds (-1) Warning: Frame 71767 Coordinates out of bounds (-1) Warning: Frame 71777 Coordinates out of bounds (-1) Warning: Frame 73555 Coordinates out of bounds (-1) Warning: Frame 73601 Coordinates out of bounds (-1) Warning: Frame 73603 Coordinates out of bounds (-1) Warning: Frame 73606 Coordinates out of bounds (-1) Warning: Frame 73613 Coordinates out of bounds (-1) Warning: Frame 74628 Coordinates out of bounds (-1) Warning: Frame 74967 Coordinates out of bounds (-1) Warning: Frame 75660 Coordinates out of bounds (-1) Warning: Frame 75664 Coordinates out of bounds (-1) Warning: Frame 75693 Coordinates out of bounds (-1) Warning: Frame 75696 Coordinates out of bounds (-1) Warning: Frame 76239 Coordinates out of bounds (-1) Warning: Frame 76243 Coordinates out of bounds (-1) Warning: Frame 76250 Coordinates out of bounds (-1) Warning: Frame 76263 Coordinates out of bounds (-1) Warning: Frame 76264 Coordinates out of bounds (-1) Warning: Frame 76266 Coordinates out of bounds (-1) Warning: Frame 76272 Coordinates out of bounds (-1) Warning: Frame 76274 Coordinates out of bounds (-1) Warning: Frame 76314 Coordinates out of bounds (-1) Warning: Frame 76318 Coordinates out of bounds (-1) Warning: Frame 76319 Coordinates out of bounds (-1) Warning: Frame 76328 Coordinates out of bounds (-1) Warning: Frame 76333 Coordinates out of bounds (-1) Warning: Frame 77363 Coordinates out of bounds (-1) Warning: Frame 78400 Coordinates out of bounds (-1) Warning: Frame 78401 Coordinates out of bounds (-1) Warning: Frame 78443 Coordinates out of bounds (-1) Warning: Frame 78449 Coordinates out of bounds (-1) Warning: Frame 80807 Coordinates out of bounds (-1) Warning: Frame 80808 Coordinates out of bounds (-1) Warning: Frame 82026 Coordinates out of bounds (-1) Warning: Frame 82034 Coordinates out of bounds (-1) Warning: Frame 82520 Coordinates out of bounds (-1) Histogram: Normalizing sum of bin populations to 1.0 Sum over all bins is 83898.000000 TIME: Analyses took 0.0008 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 84078 Hist_00002 "Hist_00002" (double), size is 50 DATAFILES: hist_rmsd_18.dat (Standard Data File): Hist_00002 ---------- RUN END --------------------------------------------------- TIME: Total execution time: 11.7481 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.